Broken pipe with samtools view upon conversion from minimap2 SAM -> BAM #124
Description
This error occurs when using map() together with minimap2 and saving as a .bam.
import "minimap2" version "1.0"
...
minimap_mapped = map(input, fafile=REFDB, mode_all=True, mapper="minimap2")
write(minimap_mapped, ofile="output/" + sample + ".minimap2_mapped.bam")
This is possibly another instance of #121 which is also the same problem mentioned in #92 (comment) so perhaps the fix from #121 should be (re)used for samtools invocations as well?
Currently running this process without memory limits to check if this is the cause of the failure.
[Tue 15-10-2019 21:21:28] Line 16: Interpreting [interpretIO]: minimap_mapped = map(Lookup 'input' as NGLReadSet; fafile=Lookup 'REFDB' as NGLString; mode_all=True; mapper="minimap2")
[Tue 15-10-2019 21:21:28] Line 16: Interpreting [assignment]: map(Lookup 'input' as NGLReadSet; fafile=Lookup 'REFDB' as NGLString; mode_all=True; mapper="minimap2")
[Tue 15-10-2019 21:21:28] Line 16: Looking for file 'data/db.fna.gz' (search path is [])
[Tue 15-10-2019 21:21:28] Line 16: Looking for file (data/db.fna.gz) in data/db.fna.gz
[Tue 15-10-2019 21:21:28] Line 16: Index for data/db.fna.gz already exists.
[Tue 15-10-2019 21:21:28] Line 16: Created & opened temporary file /local/151163.6.all.q/map7710-3.sam
[Tue 15-10-2019 21:21:28] Line 16: Starting mapping to data/db.fna.gz (minimap2)
[Tue 15-10-2019 21:21:28] Line 16: Calling: /home/u/.local/share/ngless/bin/ngless-1.0.1-minimap2-t 4 -a -a data/db.fna.gz -
[Tue 15-10-2019 21:21:28] Line 16: Created & opened temporary file /local/151163.6.all.q/minimap2.fastq7710-4.sam
[Tue 15-10-2019 21:49:43] Line 16: minimap2 info: [M::mm_idx_gen::107.903*2.22] collected minimizers
[M::mm_idx_gen::132.153*2.54] sorted minimizers
[WARNING]�[1;31m For a multi-part index, no @SQ lines will be outputted. Please use --split-prefix.�[0m
[M::main::132.153*2.54] loaded/built the index for 243405 target sequence(s)
[M::mm_mapopt_update::132.341*2.53] mid_occ = 4707
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 243405
[M::mm_idx_stat::132.417*2.53] distinct minimizers: 3810226 (29.92% are singletons); average occurrences: 197.075; average spacing: 5.349
[M::worker_pipeline::187.777*2.75] mapped 5029626 sequences
[M::worker_pipeline::225.696*3.00] mapped 5034089 sequences
[M::worker_pipeline::264.024*3.18] mapped 5033270 sequences
[M::worker_pipeline::301.172*3.30] mapped 5034339 sequences
[M::worker_pipeline::338.720*3.41] mapped 5035375 sequences
[M::worker_pipeline::377.322*3.49] mapped 5029166 sequences
[M::worker_pipeline::414.757*3.56] mapped 5035639 sequences
[M::worker_pipeline::452.527*3.61] mapped 5029915 sequences
[M::worker_pipeline::490.151*3.66] mapped 5036599 sequences
[M::worker_pipeline::528.478*3.70] mapped 5035897 sequences
[M::worker_pipeline::565.704*3.74] mapped 5024910 sequences
[M::worker_pipeline::603.621*3.77] mapped 5033565 sequences
[M::worker_pipeline::642.266*3.80] mapped 5032410 sequences
[M::worker_pipeline::679.802*3.82] mapped 5059099 sequences
[M::worker_pipeline::717.283*3.84] mapped 5093125 sequences
[M::worker_pipeline::754.579*3.86] mapped 5076182 sequences
[M::worker_pipeline::792.123*3.88] mapped 5081635 sequences
[M::worker_pipeline::829.318*3.89] mapped 5078224 sequences
[M::worker_pipeline::867.134*3.91] mapped 5077554 sequences
[M::worker_pipeline::904.434*3.92] mapped 5075590 sequences
[M::worker_pipeline::941.508*3.93] mapped 5071193 sequences
[M::worker_pipeline::978.489*3.95] mapped 5084361 sequences
[M::worker_pipeline::1016.157*3.96] mapped 5085565 sequences
[M::worker_pipeline::1052.996*3.97] mapped 5076897 sequences
[M::worker_pipeline::1089.985*3.98] mapped 5086056 sequences
[M::worker_pipeline::1126.592*3.98] mapped 5077032 sequences
[M::worker_pipeline::1163.942*3.99] mapped 5081415 sequences
[M::worker_pipeline::1200.465*4.00] mapped 5095551 sequences
[M::worker_pipeline::1237.552*4.01] mapped 5080041 sequences
[M::worker_pipeline::1274.166*4.01] mapped 5085140 sequences
[M::worker_pipeline::1311.070*4.02] mapped 5071866 sequences
[M::worker_pipeline::1347.943*4.02] mapped 5078243 sequences
[M::worker_pipeline::1384.660*4.03] mapped 5076065 sequences
[M::worker_pipeline::1418.190*4.04] mapped 5081771 sequences
[M::worker_pipeline::1452.987*4.04] mapped 5081115 sequences
[M::worker_pipeline::1490.116*4.05] mapped 5072325 sequences
[M::worker_pipeline::1526.066*4.05] mapped 5073026 sequences
[M::worker_pipeline::1562.427*4.05] mapped 5093953 sequences
[M::worker_pipeline::1599.618*4.06] mapped 5092291 sequences
[M::worker_pipeline::1635.527*4.05] mapped 5031065 sequences
[M::mm_idx_gen::1682.980*3.99] collected minimizers
[M::mm_idx_gen::1693.134*3.99] sorted minimizers
[M::main::1693.134*3.99] loaded/built the index for 132374 target sequence(s)
[M::mm_mapopt_update::1693.134*3.99] mid_occ = 4707
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 132374
[M::mm_idx_stat::1693.217*3.99] distinct minimizers: 3237951 (30.88% are singletons); average occurrences: 86.738; average spacing: 5.352
[M::main] Version: 2.16-r922
[M::main] CMD: /home/u/.local/share/ngless/bin/ngless-1.0.1-minimap2 -t 4 -a -a data/db.fna.gz -
[M::main] Real time: 1694.554 sec; CPU: 6759.325 sec; Peak RSS: 24.945 GB
[Tue 15-10-2019 21:49:43] Line 16: Finished mapping to data/db.fna.gz
[Tue 15-10-2019 21:49:46] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-5.sam
[Tue 15-10-2019 21:49:50] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-6.sam
[Tue 15-10-2019 21:49:54] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-7.sam
[Tue 15-10-2019 21:49:57] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-8.sam
[Tue 15-10-2019 21:50:00] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-9.sam
[Tue 15-10-2019 21:50:04] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-10.sam
[Tue 15-10-2019 21:50:08] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-11.sam
[Tue 15-10-2019 21:50:11] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-12.sam
[Tue 15-10-2019 21:50:15] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-13.sam
[Tue 15-10-2019 21:50:18] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-14.sam
[Tue 15-10-2019 21:50:21] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-15.sam
[Tue 15-10-2019 21:50:25] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-16.sam
[Tue 15-10-2019 21:50:28] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-17.sam
[Tue 15-10-2019 21:50:32] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-18.sam
[Tue 15-10-2019 21:50:35] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-19.sam
[Tue 15-10-2019 21:50:39] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-20.sam
[Tue 15-10-2019 21:50:42] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-21.sam
[Tue 15-10-2019 21:50:45] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-22.sam
[Tue 15-10-2019 21:50:48] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-23.sam
[Tue 15-10-2019 21:50:56] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-24.sam
[Tue 15-10-2019 21:50:59] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-25.sam
[Tue 15-10-2019 21:51:02] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-26.sam
[Tue 15-10-2019 21:51:05] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-27.sam
[Tue 15-10-2019 21:51:09] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-28.sam
[Tue 15-10-2019 21:51:12] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-29.sam
[Tue 15-10-2019 21:51:15] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-30.sam
[Tue 15-10-2019 21:51:19] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-31.sam
[Tue 15-10-2019 21:51:23] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-32.sam
[Tue 15-10-2019 21:51:26] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-33.sam
[Tue 15-10-2019 21:51:30] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-34.sam
[Tue 15-10-2019 21:51:35] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-35.sam
[Tue 15-10-2019 21:51:38] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-36.sam
[Tue 15-10-2019 21:51:41] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-37.sam
[Tue 15-10-2019 21:51:45] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-38.sam
[Tue 15-10-2019 21:51:48] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-39.sam
[Tue 15-10-2019 21:51:51] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-40.sam
[Tue 15-10-2019 21:51:54] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-41.sam
[Tue 15-10-2019 21:51:57] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-42.sam
[Tue 15-10-2019 21:52:01] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-43.sam
[Tue 15-10-2019 21:52:04] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-44.sam
[Tue 15-10-2019 21:52:08] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-45.sam
[Tue 15-10-2019 21:52:12] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-46.sam
[Tue 15-10-2019 21:52:15] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-47.sam
[Tue 15-10-2019 21:52:19] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-48.sam
[Tue 15-10-2019 21:52:23] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-49.sam
[Tue 15-10-2019 21:52:27] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-50.sam
[Tue 15-10-2019 21:52:30] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-51.sam
[Tue 15-10-2019 21:52:34] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-52.sam
[Tue 15-10-2019 21:52:37] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-53.sam
[Tue 15-10-2019 21:52:41] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-54.sam
[Tue 15-10-2019 21:52:44] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-55.sam
[Tue 15-10-2019 21:52:48] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-56.sam
[Tue 15-10-2019 21:52:51] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-57.sam
[Tue 15-10-2019 21:52:54] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-58.sam
[Tue 15-10-2019 21:52:57] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-59.sam
[Tue 15-10-2019 21:53:00] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-60.sam
[Tue 15-10-2019 21:53:03] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-61.sam
[Tue 15-10-2019 21:53:07] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-62.sam
[Tue 15-10-2019 21:53:11] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-63.sam
[Tue 15-10-2019 21:53:15] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-64.sam
[Tue 15-10-2019 21:53:19] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-65.sam
[Tue 15-10-2019 21:53:22] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-66.sam
[Tue 15-10-2019 21:53:26] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-67.sam
[Tue 15-10-2019 21:53:29] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-68.sam
[Tue 15-10-2019 21:53:32] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-69.sam
[Tue 15-10-2019 21:53:36] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-70.sam
[Tue 15-10-2019 21:53:39] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-71.sam
[Tue 15-10-2019 21:53:42] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-72.sam
[Tue 15-10-2019 21:53:45] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-73.sam
[Tue 15-10-2019 21:53:48] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-74.sam
[Tue 15-10-2019 21:53:52] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-75.sam
[Tue 15-10-2019 21:53:55] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-76.sam
[Tue 15-10-2019 21:53:58] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-77.sam
[Tue 15-10-2019 21:54:01] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-78.sam
[Tue 15-10-2019 21:54:06] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-79.sam
[Tue 15-10-2019 21:54:09] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-80.sam
[Tue 15-10-2019 21:54:12] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-81.sam
[Tue 15-10-2019 21:54:15] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-82.sam
[Tue 15-10-2019 21:54:18] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-83.sam
[Tue 15-10-2019 21:54:23] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-84.sam
[Tue 15-10-2019 21:54:27] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-85.sam
[Tue 15-10-2019 21:54:30] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-86.sam
[Tue 15-10-2019 21:54:34] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-87.sam
[Tue 15-10-2019 21:54:37] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-88.sam
[Tue 15-10-2019 21:54:40] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-89.sam
[Tue 15-10-2019 21:54:43] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-90.sam
[Tue 15-10-2019 21:54:46] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-91.sam
[Tue 15-10-2019 21:54:49] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-92.sam
[Tue 15-10-2019 21:54:52] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-93.sam
[Tue 15-10-2019 21:54:55] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-94.sam
[Tue 15-10-2019 21:55:00] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-95.sam
[Tue 15-10-2019 21:55:03] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-96.sam
[Tue 15-10-2019 21:55:06] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-97.sam
[Tue 15-10-2019 21:55:10] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-98.sam
[Tue 15-10-2019 21:55:13] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-99.sam
[Tue 15-10-2019 21:55:16] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-100.sam
[Tue 15-10-2019 21:55:19] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-101.sam
[Tue 15-10-2019 21:55:22] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-102.sam
[Tue 15-10-2019 21:55:25] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-103.sam
[Tue 15-10-2019 21:55:28] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-104.sam
[Tue 15-10-2019 21:55:31] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-105.sam
[Tue 15-10-2019 21:55:34] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-106.sam
[Tue 15-10-2019 21:55:37] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-107.sam
[Tue 15-10-2019 21:55:40] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-108.sam
[Tue 15-10-2019 21:55:43] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-109.sam
[Tue 15-10-2019 21:55:46] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-110.sam
[Tue 15-10-2019 21:55:50] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-111.sam
[Tue 15-10-2019 21:55:54] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-112.sam
[Tue 15-10-2019 21:55:58] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-113.sam
[Tue 15-10-2019 21:56:01] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-114.sam
[Tue 15-10-2019 21:56:05] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-115.sam
[Tue 15-10-2019 21:56:08] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-116.sam
[Tue 15-10-2019 21:56:11] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-117.sam
[Tue 15-10-2019 21:56:15] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-118.sam
[Tue 15-10-2019 21:56:19] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-119.sam
[Tue 15-10-2019 21:56:22] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-120.sam
[Tue 15-10-2019 21:56:25] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-121.sam
[Tue 15-10-2019 21:56:28] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-122.sam
[Tue 15-10-2019 21:56:32] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-123.sam
[Tue 15-10-2019 21:56:35] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-124.sam
[Tue 15-10-2019 21:56:38] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-125.sam
[Tue 15-10-2019 21:56:42] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-126.sam
[Tue 15-10-2019 21:56:45] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-127.sam
[Tue 15-10-2019 21:56:48] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-128.sam
[Tue 15-10-2019 21:56:51] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-129.sam
[Tue 15-10-2019 21:56:54] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-130.sam
[Tue 15-10-2019 21:56:57] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-131.sam
[Tue 15-10-2019 21:57:01] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-132.sam
[Tue 15-10-2019 21:57:04] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-133.sam
[Tue 15-10-2019 21:57:07] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-134.sam
[Tue 15-10-2019 21:57:11] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-135.sam
[Tue 15-10-2019 21:57:14] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-136.sam
[Tue 15-10-2019 21:57:17] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-137.sam
[Tue 15-10-2019 21:57:20] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-138.sam
[Tue 15-10-2019 21:57:23] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-139.sam
[Tue 15-10-2019 21:57:27] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-140.sam
[Tue 15-10-2019 21:57:30] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-141.sam
[Tue 15-10-2019 21:57:33] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-142.sam
[Tue 15-10-2019 21:57:36] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-143.sam
[Tue 15-10-2019 21:57:39] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-144.sam
[Tue 15-10-2019 21:57:42] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-145.sam
[Tue 15-10-2019 21:57:46] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-146.sam
[Tue 15-10-2019 21:57:49] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-147.sam
[Tue 15-10-2019 21:57:52] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-148.sam
[Tue 15-10-2019 21:57:54] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-149.sam
[Tue 15-10-2019 21:57:58] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-150.sam
[Tue 15-10-2019 21:58:01] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-151.sam
[Tue 15-10-2019 21:58:04] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-152.sam
[Tue 15-10-2019 21:58:08] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-153.sam
[Tue 15-10-2019 21:58:11] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-154.sam
[Tue 15-10-2019 21:58:14] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-155.sam
[Tue 15-10-2019 21:58:17] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-156.sam
[Tue 15-10-2019 21:58:20] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-157.sam
[Tue 15-10-2019 21:58:27] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-158.sam
[Tue 15-10-2019 21:58:30] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-159.sam
[Tue 15-10-2019 21:58:33] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-160.sam
[Tue 15-10-2019 21:58:37] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-161.sam
[Tue 15-10-2019 21:58:40] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-162.sam
[Tue 15-10-2019 21:58:43] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-163.sam
[Tue 15-10-2019 21:58:46] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-164.sam
[Tue 15-10-2019 21:58:49] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-165.sam
[Tue 15-10-2019 21:58:52] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-166.sam
[Tue 15-10-2019 21:58:55] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-167.sam
[Tue 15-10-2019 21:58:58] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-168.sam
[Tue 15-10-2019 21:59:02] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-169.sam
[Tue 15-10-2019 21:59:05] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-170.sam
[Tue 15-10-2019 21:59:08] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-171.sam
[Tue 15-10-2019 21:59:11] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-172.sam
[Tue 15-10-2019 21:59:14] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-173.sam
[Tue 15-10-2019 21:59:17] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-174.sam
[Tue 15-10-2019 21:59:21] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-175.sam
[Tue 15-10-2019 21:59:24] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-176.sam
[Tue 15-10-2019 21:59:28] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-177.sam
[Tue 15-10-2019 21:59:32] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-178.sam
[Tue 15-10-2019 21:59:35] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-179.sam
[Tue 15-10-2019 21:59:41] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-180.sam
[Tue 15-10-2019 21:59:44] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-181.sam
[Tue 15-10-2019 21:59:47] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-182.sam
[Tue 15-10-2019 21:59:50] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-183.sam
[Tue 15-10-2019 21:59:53] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-184.sam
[Tue 15-10-2019 21:59:57] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-185.sam
[Tue 15-10-2019 22:00:01] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-186.sam
[Tue 15-10-2019 22:00:04] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-187.sam
[Tue 15-10-2019 22:00:07] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-188.sam
[Tue 15-10-2019 22:00:10] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-189.sam
[Tue 15-10-2019 22:00:14] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-190.sam
[Tue 15-10-2019 22:00:17] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-191.sam
[Tue 15-10-2019 22:00:20] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-192.sam
[Tue 15-10-2019 22:00:24] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-193.sam
[Tue 15-10-2019 22:00:27] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-194.sam
[Tue 15-10-2019 22:00:30] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-195.sam
[Tue 15-10-2019 22:00:33] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-196.sam
[Tue 15-10-2019 22:00:36] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-197.sam
[Tue 15-10-2019 22:00:40] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-198.sam
[Tue 15-10-2019 22:00:43] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-199.sam
[Tue 15-10-2019 22:00:48] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-200.sam
[Tue 15-10-2019 22:00:51] Line 16: Created & opened temporary file /local/151163.6.all.q/partialminimap27710-201.sam
[Tue 15-10-2019 22:17:41] Line 16: Mapped readset stats (data/db.fna.gz):
[Tue 15-10-2019 22:17:41] Line 16: Total reads: 101270590
[Tue 15-10-2019 22:17:41] Line 16: Total reads aligned: 1052653 [1.04%]
[Tue 15-10-2019 22:17:41] Line 16: Total reads Unique map: 259077 [0.26%]
[Tue 15-10-2019 22:17:41] Line 16: Total reads Non-Unique map: 793576 [0.78%]
[Tue 15-10-2019 22:17:41] Line 17: Running garbage collection.
[Tue 15-10-2019 22:17:41] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-201.sam
[Tue 15-10-2019 22:17:41] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-200.sam
[Tue 15-10-2019 22:17:41] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-199.sam
[Tue 15-10-2019 22:17:41] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-198.sam
[Tue 15-10-2019 22:17:41] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-197.sam
[Tue 15-10-2019 22:17:41] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-196.sam
[Tue 15-10-2019 22:17:41] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-195.sam
[Tue 15-10-2019 22:17:41] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-194.sam
[Tue 15-10-2019 22:17:41] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-193.sam
[Tue 15-10-2019 22:17:41] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-192.sam
[Tue 15-10-2019 22:17:41] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-191.sam
[Tue 15-10-2019 22:17:41] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-190.sam
[Tue 15-10-2019 22:17:41] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-189.sam
[Tue 15-10-2019 22:17:41] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-188.sam
[Tue 15-10-2019 22:17:42] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-187.sam
[Tue 15-10-2019 22:17:42] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-186.sam
[Tue 15-10-2019 22:17:42] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-185.sam
[Tue 15-10-2019 22:17:42] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-184.sam
[Tue 15-10-2019 22:17:42] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-183.sam
[Tue 15-10-2019 22:17:42] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-182.sam
[Tue 15-10-2019 22:17:42] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-181.sam
[Tue 15-10-2019 22:17:42] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-180.sam
[Tue 15-10-2019 22:17:42] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-179.sam
[Tue 15-10-2019 22:17:42] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-178.sam
[Tue 15-10-2019 22:17:42] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-177.sam
[Tue 15-10-2019 22:17:42] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-176.sam
[Tue 15-10-2019 22:17:42] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-175.sam
[Tue 15-10-2019 22:17:42] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-174.sam
[Tue 15-10-2019 22:17:42] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-173.sam
[Tue 15-10-2019 22:17:42] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-172.sam
[Tue 15-10-2019 22:17:42] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-171.sam
[Tue 15-10-2019 22:17:42] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-170.sam
[Tue 15-10-2019 22:17:42] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-169.sam
[Tue 15-10-2019 22:17:42] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-168.sam
[Tue 15-10-2019 22:17:43] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-167.sam
[Tue 15-10-2019 22:17:43] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-166.sam
[Tue 15-10-2019 22:17:43] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-165.sam
[Tue 15-10-2019 22:17:43] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-164.sam
[Tue 15-10-2019 22:17:43] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-163.sam
[Tue 15-10-2019 22:17:43] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-162.sam
[Tue 15-10-2019 22:17:43] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-161.sam
[Tue 15-10-2019 22:17:43] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-160.sam
[Tue 15-10-2019 22:17:43] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-159.sam
[Tue 15-10-2019 22:17:43] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-158.sam
[Tue 15-10-2019 22:17:43] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-157.sam
[Tue 15-10-2019 22:17:43] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-156.sam
[Tue 15-10-2019 22:17:43] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-155.sam
[Tue 15-10-2019 22:17:43] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-154.sam
[Tue 15-10-2019 22:17:43] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-153.sam
[Tue 15-10-2019 22:17:43] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-152.sam
[Tue 15-10-2019 22:17:43] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-151.sam
[Tue 15-10-2019 22:17:43] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-150.sam
[Tue 15-10-2019 22:17:43] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-149.sam
[Tue 15-10-2019 22:17:43] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-148.sam
[Tue 15-10-2019 22:17:44] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-147.sam
[Tue 15-10-2019 22:17:44] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-146.sam
[Tue 15-10-2019 22:17:44] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-145.sam
[Tue 15-10-2019 22:17:44] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-144.sam
[Tue 15-10-2019 22:17:44] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-143.sam
[Tue 15-10-2019 22:17:44] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-142.sam
[Tue 15-10-2019 22:17:44] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-141.sam
[Tue 15-10-2019 22:17:44] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-140.sam
[Tue 15-10-2019 22:17:44] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-139.sam
[Tue 15-10-2019 22:17:44] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-138.sam
[Tue 15-10-2019 22:17:44] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-137.sam
[Tue 15-10-2019 22:17:44] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-136.sam
[Tue 15-10-2019 22:17:44] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-135.sam
[Tue 15-10-2019 22:17:44] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-134.sam
[Tue 15-10-2019 22:17:44] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-133.sam
[Tue 15-10-2019 22:17:44] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-132.sam
[Tue 15-10-2019 22:17:44] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-131.sam
[Tue 15-10-2019 22:17:44] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-130.sam
[Tue 15-10-2019 22:17:44] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-129.sam
[Tue 15-10-2019 22:17:45] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-128.sam
[Tue 15-10-2019 22:17:45] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-127.sam
[Tue 15-10-2019 22:17:45] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-126.sam
[Tue 15-10-2019 22:17:45] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-125.sam
[Tue 15-10-2019 22:17:45] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-124.sam
[Tue 15-10-2019 22:17:45] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-123.sam
[Tue 15-10-2019 22:17:45] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-122.sam
[Tue 15-10-2019 22:17:45] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-121.sam
[Tue 15-10-2019 22:17:45] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-120.sam
[Tue 15-10-2019 22:17:45] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-119.sam
[Tue 15-10-2019 22:17:45] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-118.sam
[Tue 15-10-2019 22:17:45] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-117.sam
[Tue 15-10-2019 22:17:45] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-116.sam
[Tue 15-10-2019 22:17:45] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-115.sam
[Tue 15-10-2019 22:17:45] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-114.sam
[Tue 15-10-2019 22:17:45] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-113.sam
[Tue 15-10-2019 22:17:45] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-112.sam
[Tue 15-10-2019 22:17:46] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-111.sam
[Tue 15-10-2019 22:17:46] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-110.sam
[Tue 15-10-2019 22:17:46] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-109.sam
[Tue 15-10-2019 22:17:46] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-108.sam
[Tue 15-10-2019 22:17:46] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-107.sam
[Tue 15-10-2019 22:17:46] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-106.sam
[Tue 15-10-2019 22:17:46] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-105.sam
[Tue 15-10-2019 22:17:46] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-104.sam
[Tue 15-10-2019 22:17:46] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-103.sam
[Tue 15-10-2019 22:17:46] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-102.sam
[Tue 15-10-2019 22:17:46] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-101.sam
[Tue 15-10-2019 22:17:46] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-100.sam
[Tue 15-10-2019 22:17:46] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-99.sam
[Tue 15-10-2019 22:17:46] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-98.sam
[Tue 15-10-2019 22:17:46] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-97.sam
[Tue 15-10-2019 22:17:46] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-96.sam
[Tue 15-10-2019 22:17:46] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-95.sam
[Tue 15-10-2019 22:17:46] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-94.sam
[Tue 15-10-2019 22:17:47] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-93.sam
[Tue 15-10-2019 22:17:47] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-92.sam
[Tue 15-10-2019 22:17:47] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-91.sam
[Tue 15-10-2019 22:17:47] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-90.sam
[Tue 15-10-2019 22:17:47] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-89.sam
[Tue 15-10-2019 22:17:47] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-88.sam
[Tue 15-10-2019 22:17:47] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-87.sam
[Tue 15-10-2019 22:17:47] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-86.sam
[Tue 15-10-2019 22:17:47] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-85.sam
[Tue 15-10-2019 22:17:47] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-84.sam
[Tue 15-10-2019 22:17:47] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-83.sam
[Tue 15-10-2019 22:17:47] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-82.sam
[Tue 15-10-2019 22:17:47] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-81.sam
[Tue 15-10-2019 22:17:47] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-80.sam
[Tue 15-10-2019 22:17:47] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-79.sam
[Tue 15-10-2019 22:17:47] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-78.sam
[Tue 15-10-2019 22:17:48] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-77.sam
[Tue 15-10-2019 22:17:48] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-76.sam
[Tue 15-10-2019 22:17:48] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-75.sam
[Tue 15-10-2019 22:17:48] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-74.sam
[Tue 15-10-2019 22:17:48] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-73.sam
[Tue 15-10-2019 22:17:48] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-72.sam
[Tue 15-10-2019 22:17:48] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-71.sam
[Tue 15-10-2019 22:17:48] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-70.sam
[Tue 15-10-2019 22:17:48] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-69.sam
[Tue 15-10-2019 22:17:48] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-68.sam
[Tue 15-10-2019 22:17:48] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-67.sam
[Tue 15-10-2019 22:17:48] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-66.sam
[Tue 15-10-2019 22:17:48] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-65.sam
[Tue 15-10-2019 22:17:48] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-64.sam
[Tue 15-10-2019 22:17:48] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-63.sam
[Tue 15-10-2019 22:17:49] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-62.sam
[Tue 15-10-2019 22:17:49] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-61.sam
[Tue 15-10-2019 22:17:49] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-60.sam
[Tue 15-10-2019 22:17:49] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-59.sam
[Tue 15-10-2019 22:17:49] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-58.sam
[Tue 15-10-2019 22:17:49] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-57.sam
[Tue 15-10-2019 22:17:49] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-56.sam
[Tue 15-10-2019 22:17:49] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-55.sam
[Tue 15-10-2019 22:17:49] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-54.sam
[Tue 15-10-2019 22:17:49] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-53.sam
[Tue 15-10-2019 22:17:49] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-52.sam
[Tue 15-10-2019 22:17:49] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-51.sam
[Tue 15-10-2019 22:17:49] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-50.sam
[Tue 15-10-2019 22:17:49] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-49.sam
[Tue 15-10-2019 22:17:49] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-48.sam
[Tue 15-10-2019 22:17:50] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-47.sam
[Tue 15-10-2019 22:17:50] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-46.sam
[Tue 15-10-2019 22:17:50] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-45.sam
[Tue 15-10-2019 22:17:50] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-44.sam
[Tue 15-10-2019 22:17:50] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-43.sam
[Tue 15-10-2019 22:17:50] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-42.sam
[Tue 15-10-2019 22:17:50] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-41.sam
[Tue 15-10-2019 22:17:50] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-40.sam
[Tue 15-10-2019 22:17:50] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-39.sam
[Tue 15-10-2019 22:17:50] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-38.sam
[Tue 15-10-2019 22:17:50] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-37.sam
[Tue 15-10-2019 22:17:50] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-36.sam
[Tue 15-10-2019 22:17:50] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-35.sam
[Tue 15-10-2019 22:17:50] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-34.sam
[Tue 15-10-2019 22:17:51] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-33.sam
[Tue 15-10-2019 22:17:51] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-32.sam
[Tue 15-10-2019 22:17:51] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-31.sam
[Tue 15-10-2019 22:17:51] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-30.sam
[Tue 15-10-2019 22:17:51] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-29.sam
[Tue 15-10-2019 22:17:51] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-28.sam
[Tue 15-10-2019 22:17:51] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-27.sam
[Tue 15-10-2019 22:17:51] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-26.sam
[Tue 15-10-2019 22:17:51] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-25.sam
[Tue 15-10-2019 22:17:51] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-24.sam
[Tue 15-10-2019 22:17:51] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-23.sam
[Tue 15-10-2019 22:17:51] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-22.sam
[Tue 15-10-2019 22:17:51] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-21.sam
[Tue 15-10-2019 22:17:51] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-20.sam
[Tue 15-10-2019 22:17:51] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-19.sam
[Tue 15-10-2019 22:17:52] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-18.sam
[Tue 15-10-2019 22:17:52] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-17.sam
[Tue 15-10-2019 22:17:52] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-16.sam
[Tue 15-10-2019 22:17:52] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-15.sam
[Tue 15-10-2019 22:17:52] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-14.sam
[Tue 15-10-2019 22:17:52] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-13.sam
[Tue 15-10-2019 22:17:52] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-12.sam
[Tue 15-10-2019 22:17:52] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-11.sam
[Tue 15-10-2019 22:17:52] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-10.sam
[Tue 15-10-2019 22:17:52] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-9.sam
[Tue 15-10-2019 22:17:52] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-8.sam
[Tue 15-10-2019 22:17:52] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-7.sam
[Tue 15-10-2019 22:17:52] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-6.sam
[Tue 15-10-2019 22:17:52] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-5.sam
[Tue 15-10-2019 22:17:52] Line 17: Removing temporary file: /local/151163.6.all.q/minimap2.fastq7710-4.sam
[Tue 15-10-2019 22:18:03] Line 17: Interpreting [interpretIO]: __check_ofile(BinaryOp("output/" -BOpAdd- BinaryOp(Lookup 'sample' as NGLString -BOpAdd- ".minimap2_mapped.bam")); original_lno=17)
[Tue 15-10-2019 22:18:03] Line 17: Interpreting [executing module function: '__check_ofile']: NGOString "output/sample.minimap2_mapped.bam"
[Tue 15-10-2019 22:18:03] Line 17: Running garbage collection.
[Tue 15-10-2019 22:18:03] Line 17: Interpreting [interpretIO]: write(Lookup 'minimap_mapped' as NGLMappedReadSet; __can_move=True; __hash="fe235049467b8419f7283e034c7cabf9"; ofile=BinaryOp("output/" -BOpAdd- BinaryOp(Lookup 'sample' as NGLString -BOpAdd- ".minimap2_mapped.bam")))
[Tue 15-10-2019 22:18:03] Line 17: Interpreting [write]: NGOMappedReadSet {nglgroupName = "data/sample", nglSamFile = File /local/151163.6.all.q/map7710-3.sam, nglReference = Nothing}
[Tue 15-10-2019 22:18:03] Line 17: Created & opened temporary file /local/151163.6.all.q/converted_map7710-37710-202.bam
[Tue 15-10-2019 22:18:03] Line 17: SAM->BAM Conversion start ('/local/151163.6.all.q/map7710-3.sam' -> '/local/151163.6.all.q/converted_map7710-37710-202.bam')
Exiting after internal error. If you can reproduce this issue, please run your script with the --trace flag and report a bug at https://github.com/ngless-toolkit/ngless/issues
fd:24: hPutBuf: resource vanished (Broken pipe)