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Broken pipe with samtools view upon conversion from minimap2 SAM -> BAM #124

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unode opened this issue Oct 15, 2019 · 1 comment
Open

Broken pipe with samtools view upon conversion from minimap2 SAM -> BAM #124

unode opened this issue Oct 15, 2019 · 1 comment

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@unode
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unode commented Oct 15, 2019 •
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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
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[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
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[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
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[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
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[Tue 15-10-2019 22:17:42] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-168.sam
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[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
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[Tue 15-10-2019 22:17:44] Line 17: Removing temporary file: /local/151163.6.all.q/partialminimap27710-140.sam
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[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)
@luispedro
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Yes, #121 is messing up the error messages here. My guess is that the SAM file has no header and thus samtools view fails.

The underlying problem is that minimap2 will not output a header file if the reference is too big unless you use the --split-index argument. I ran into it too (and should have fixed it, but actually lh3/minimap2#430 got in the way, which is another reason to keep treating minimap2 as beta software)

@unode unode changed the title Broken pipe with samtools view Broken pipe with samtools view upon conversion from minimap2 SAM -> BAM Oct 16, 2019
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@luispedro @unode