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Isoseq cluster2 doesn't produce output and doesn't produce error message #736

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chvandijk opened this issue Jan 9, 2025 · 0 comments
Open

Isoseq cluster2 doesn't produce output and doesn't produce error message #736

chvandijk opened this issue Jan 9, 2025 · 0 comments

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@chvandijk
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chvandijk commented Jan 9, 2025 •
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Operating system
Linux (HPC)

Package name
isoseq cluster2 - 4.0.0 (commit v4.0.0)

Describe the bug
I run the following code:

isoseq cluster2 ${in} ${out} --log-level DEBUG --log-file ${log} -j 128

Whereby ${in} is the bam file produced by isoseq refine and ${out} is a path to an output.bam file.
The submitted job keeps running without producing an error but there are no files created. The job is given 128 threads and 50G of memory. The input bam file is 17M reads. Based on the benchmark posted in this previous post , you would expect the job to done in under an hour, however, it can run for more than two days and still produce nothing and the log file remains the same after 5 minutes of run time.

Using samtools to view the first line of the input file, I get no error messages suggesting no truncated file and this is the first line:
m84056R1_241224_232213_s4/249435319/ccs/2311_3611 4 * 0 255 * * 0 0 ATCAACAATCGGCTGGTTTACCATGACTTCTTCAGAGACCCTCTCAACTGGTCAAAAACTGAGGAGGCCTTTCCTGGGGGGCCGCTGGGAGCCTTGAGAGCCATGTGCAAGAGGACAGATCCTGTTCCTGTCACCATTGCTCTCGATTCACTCAGCTGGCTGCTACTTCGCCTTCCCTGCACCACACTCTGCCAGGTCCTGCATGCTGTGAGCCATCAGGACTCTTGTCCTGGTGACAGCTCCTCAGTGGGGAAAGTGAGTGTGCTGGGCTTGCTACATGAAGAGCTTCATGGACCAGGCCCTGTGGGAGCTCTCAGCAGCCTTGCTCAGACTGAGGTGACCCTGGGCGGTACCATGGGCCAGGCCTCGGCCCACATCCTGTGTCGGAGGCCCCGACAGCGCCCAACTGACCAGACTCAGTGGTTCTCCATCCTTCCGGACTTCAGCCTGGATCTCCAAGAGGGGCCCTCTGTAGAGTCCCAGCCCTACTCCGATCCTCATATACCCCCGGTATCTAAGAATGCCAAGGCCAGAACAAGGAAATGTAGTTTAGTATCTGGTCACGGGAGAGAAAATAAAAGCTGCAGAGGTTGGGGGTGGGGTCAGGGATTCTAGGGATGGGGCAGAGTGGCAGCATCCTTTGTACCTACAGGTGGATCCCACAACTCATTTGACCTTTAACCTTCACCTGTCCAAGAAAGAGAGAGAAGCCAGAGATAGCCTGATCCTGCCCTTCCAGTTCAGTTCTGAAAAGTAAGGTTGGGACCTGGGTACGTGGATCCCTGAGTAGATCCCAGCATCTGGGCCATGGAGAGGTTGGGGCAACAGGTTATTGATTAACCTGACTTTATAGGGACTGAAGTCCACCTCCAGAGACAAGTCCAAGTTCTTGATCCACCCATTCCCCCTATAATGGCAGAGGACCTTTATGTCTCTTTTCTCTCCCTTATACCCTTGGGTCACAGCTCCAGTTGTCCCCAGAGCACCCTGGGCCTGGGCTGAGCCAGACCAGACCCTTGGGAGGTGGCCCTATCCCTAGGCAGTGGTGCTAGGAGGACAGAAGGCTATATGGGCGTGGCAGAGGCTGGTTAACAAGGGCTTAGTACACGCTTGCTGTTCTGTGCCCAGTATGTGGGCGGATGACGCAAGACTACAAGATCCTTGCCCTCAAGCTGCTAGGAACTTACGGTTTTATTAGGAGAGCAGTACAAGGGTATCTATCCCAGTACCAAATGGTGCTTCAGCTCTAACATGGAGGTCAGAGAAAGGGACTTGGACCAATAAAATGACATGGAGGCCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII2IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII2IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIDIIDIIIII2IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII2IIIIDIIIIIIIIIIIIIIIIIIIIIIDIIIIIIIIIIIIIIIIIIIIIDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIDIIIIDIIIIIIIIIIIIIIDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIDIIIIIIIIIIIIIIIIIIIDIIIIIIIIIIDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIDIIIIIIIIIIIIIIIIIIIDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIDIIIIDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIDIIIIIIIIIIIIIIIIIIIIIIII ML:B:C,201,86,1,27,51,100,237,213,17,141,110,229,91,181,56,63,54,219 MM:Z:C+m?,30,7,2,9,11,79,63,13,0,13,5,1,3,3,6,53,4,16; RG:Z:ba97205d/0--12 bc:B:S,12,0 bl:Z:ACAGTC bq:i:100 bt:Z:GACTG bx:B:i,6,5 cx:i:12 di:i:2 dl:i:6 dr:i:5 ds:B:C,130,164,108,101,102,116,145,135,162,97,99,148,14,0,14,0,165,108,97,98,101,108,161,54,162,109,97,0,162,113,101,205,8,238,162,113,115,205,8,222,164,113,117,97,108,176,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,163,115,101,113,176,67,67,71,84,84,65,65,71,67,67,84,84,71,65,84,84,165,114,105,103,104,116,145,135,162,97,99,148,14,0,14,0,165,108,97,98,101,108,161,53,162,109,97,0,162,113,101,205,14,136,162,113,115,205,14,120,164,113,117,97,108,176,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,163,115,101,113,176,67,84,71,67,71,65,65,84,84,71,71,65,67,84,67,84 ec:f:13.3772 ls:B:C,137,162,98,99,165,49,50,45,45,48,162,98,113,100,163,99,115,97,255,164,108,101,97,100,132,164,99,53,109,99,145,2,164,113,53,109,99,145,29,162,113,108,185,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,162,115,113,185,65,65,71,67,65,71,84,71,71,84,65,84,67,65,65,67,71,67,65,71,65,71,84,65,67,166,110,101,115,116,101,100,137,162,98,99,164,48,45,45,48,162,98,113,91,163,99,115,97,255,164,108,101,97,100,130,162,113,108,166,73,73,73,73,73,73,162,115,113,166,65,67,65,71,84,67,166,110,101,115,116,101,100,192,164,112,53,109,99,2,163,112,115,97,0,163,115,115,97,0,165,116,114,97,105,108,130,162,113,108,165,73,73,73,73,73,162,115,113,165,71,65,67,84,71,164,112,53,109,99,2,163,112,115,97,0,163,115,115,97,0,165,116,114,97,105,108,132,164,99,53,109,99,149,6,2,0,0,0,164,113,53,109,99,149,69,71,75,93,93,162,113,108,217,52,68,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,73,162,115,113,217,52,67,67,67,65,65,67,67,67,84,71,67,71,65,67,84,84,67,65,84,84,71,67,71,84,71,84,65,71,84,65,71,65,84,67,71,71,65,65,71,65,71,67,71,84,67,71,84,71,84,65,71,65 np:i:13 ql:Z:IIIIII qt:Z:IIIII rq:f:0.999498 sn:B:f,11.5737,17.2233,4.40108,7.53184 we:i:8638399 ws:i:499710 zm:i:249435319 qs:i:2311 qe:i:3611

Error message
There is no error message. This is the produced log file:

| 20250108 10:42:22.472 | INFO | Effective commandline : cluster2 S13_133.bam S13_133_transcripts.bam --log-level DEBUG --log-file S13_133_transcripts.log -j 128
| 20250108 10:42:22.472 | INFO | Version : 4.0.0 (commit v4.0.0)
| 20250108 10:42:22.473 | INFO | Options
| 20250108 10:42:22.473 | INFO | - CPU threads : 80
| 20250108 10:42:22.473 | INFO | - Sorting threads : 80
| 20250108 10:42:22.473 | INFO | - Kmer size : 17
| 20250108 10:42:22.473 | INFO | - Merge rounds : 2
| 20250108 10:42:22.473 | INFO | - 5' overhang : 100
| 20250108 10:42:22.473 | INFO | - 3' overhang : 30
| 20250108 10:42:22.473 | INFO | - 5' errors : 5
| 20250108 10:42:22.473 | INFO | - 3' errors : 10
| 20250108 10:42:22.473 | INFO | - 5' non-match window : 10
| 20250108 10:42:22.473 | INFO | - 3' non-match window : 10
| 20250108 10:42:22.473 | INFO | - Max gaps : 5
| 20250108 10:42:22.473 | INFO | - Gap window : 20
| 20250108 10:42:22.473 | INFO | - Max consensus cov : 50
| 20250108 10:42:22.473 | INFO | - Deduplicate : True
| 20250108 10:42:22.473 | INFO | - Break clusters : True
| 20250108 10:42:22.473 | INFO | - Break consensus : True
| 20250108 10:42:22.473 | INFO | - Output singletons : False
| 20250108 10:42:22.473 | INFO | - POA intermediate : False
| 20250108 10:42:22.473 | INFO | - POA final : True
| 20250108 10:42:22.473 | INFO | - Use QVs for POA : False
| 20250108 10:42:22.473 | INFO | Temp file name : /scratch/30429983/tmp.1119153.bam
| 20250108 10:42:22.480 | INFO | Get offsets
| 20250108 10:42:22.744 | VERBOSE | Offsets: 100000
| 20250108 10:42:22.985 | VERBOSE | Offsets: 200000
| 20250108 10:42:23.227 | VERBOSE | Offsets: 300000
| 20250108 10:42:23.467 | VERBOSE | Offsets: 400000
| 20250108 10:42:23.709 | VERBOSE | Offsets: 500000
| 20250108 10:42:23.955 | VERBOSE | Offsets: 600000
| 20250108 10:42:24.200 | VERBOSE | Offsets: 700000
| 20250108 10:42:24.447 | VERBOSE | Offsets: 800000
| 20250108 10:42:24.690 | VERBOSE | Offsets: 900000
| 20250108 10:42:24.931 | VERBOSE | Offsets: 1000000
| 20250108 10:42:25.180 | VERBOSE | Offsets: 1100000
| 20250108 10:42:25.430 | VERBOSE | Offsets: 1200000
| 20250108 10:42:25.666 | VERBOSE | Offsets: 1300000
| 20250108 10:42:25.903 | VERBOSE | Offsets: 1400000
| 20250108 10:42:26.141 | VERBOSE | Offsets: 1500000
| 20250108 10:42:26.383 | VERBOSE | Offsets: 1600000
| 20250108 10:42:26.623 | VERBOSE | Offsets: 1700000
| 20250108 10:42:26.862 | VERBOSE | Offsets: 1800000
| 20250108 10:42:27.101 | VERBOSE | Offsets: 1900000
| 20250108 10:42:27.332 | VERBOSE | Offsets: 2000000
| 20250108 10:42:27.579 | VERBOSE | Offsets: 2100000
| 20250108 10:42:27.830 | VERBOSE | Offsets: 2200000
| 20250108 10:42:28.078 | VERBOSE | Offsets: 2300000
| 20250108 10:42:28.337 | VERBOSE | Offsets: 2400000
| 20250108 10:42:28.590 | VERBOSE | Offsets: 2500000
| 20250108 10:42:28.843 | VERBOSE | Offsets: 2600000
| 20250108 10:42:29.088 | VERBOSE | Offsets: 2700000
| 20250108 10:42:29.338 | VERBOSE | Offsets: 2800000
| 20250108 10:42:29.589 | VERBOSE | Offsets: 2900000
| 20250108 10:42:29.842 | VERBOSE | Offsets: 3000000
| 20250108 10:42:30.093 | VERBOSE | Offsets: 3100000
| 20250108 10:42:30.335 | VERBOSE | Offsets: 3200000
| 20250108 10:42:30.574 | VERBOSE | Offsets: 3300000
| 20250108 10:42:30.812 | VERBOSE | Offsets: 3400000
| 20250108 10:42:31.048 | VERBOSE | Offsets: 3500000
| 20250108 10:42:31.286 | VERBOSE | Offsets: 3600000
| 20250108 10:42:31.528 | VERBOSE | Offsets: 3700000
| 20250108 10:42:31.766 | VERBOSE | Offsets: 3800000
| 20250108 10:42:32.009 | VERBOSE | Offsets: 3900000
| 20250108 10:42:32.258 | VERBOSE | Offsets: 4000000
| 20250108 10:42:32.493 | VERBOSE | Offsets: 4100000
| 20250108 10:42:32.750 | VERBOSE | Offsets: 4200000
| 20250108 10:42:33.000 | VERBOSE | Offsets: 4300000
| 20250108 10:42:33.242 | VERBOSE | Offsets: 4400000
| 20250108 10:42:33.484 | VERBOSE | Offsets: 4500000
| 20250108 10:42:33.723 | VERBOSE | Offsets: 4600000
| 20250108 10:42:33.962 | VERBOSE | Offsets: 4700000
| 20250108 10:42:34.201 | VERBOSE | Offsets: 4800000
| 20250108 10:42:34.445 | VERBOSE | Offsets: 4900000
| 20250108 10:42:34.691 | VERBOSE | Offsets: 5000000
| 20250108 10:42:34.937 | VERBOSE | Offsets: 5100000
| 20250108 10:42:35.173 | VERBOSE | Offsets: 5200000
| 20250108 10:42:35.410 | VERBOSE | Offsets: 5300000
| 20250108 10:42:35.647 | VERBOSE | Offsets: 5400000
| 20250108 10:42:35.882 | VERBOSE | Offsets: 5500000
| 20250108 10:42:36.124 | VERBOSE | Offsets: 5600000
| 20250108 10:42:36.360 | VERBOSE | Offsets: 5700000
| 20250108 10:42:36.601 | VERBOSE | Offsets: 5800000
| 20250108 10:42:36.853 | VERBOSE | Offsets: 5900000
| 20250108 10:42:37.093 | VERBOSE | Offsets: 6000000
| 20250108 10:42:37.333 | VERBOSE | Offsets: 6100000
| 20250108 10:42:37.573 | VERBOSE | Offsets: 6200000
| 20250108 10:42:37.810 | VERBOSE | Offsets: 6300000
| 20250108 10:42:38.058 | VERBOSE | Offsets: 6400000
| 20250108 10:42:38.309 | VERBOSE | Offsets: 6500000
| 20250108 10:42:38.556 | VERBOSE | Offsets: 6600000
| 20250108 10:42:38.799 | VERBOSE | Offsets: 6700000
| 20250108 10:42:39.046 | VERBOSE | Offsets: 6800000
| 20250108 10:42:39.300 | VERBOSE | Offsets: 6900000
| 20250108 10:42:39.551 | VERBOSE | Offsets: 7000000
| 20250108 10:42:39.798 | VERBOSE | Offsets: 7100000
| 20250108 10:42:40.040 | VERBOSE | Offsets: 7200000
| 20250108 10:42:40.279 | VERBOSE | Offsets: 7300000
| 20250108 10:42:40.524 | VERBOSE | Offsets: 7400000
| 20250108 10:42:40.767 | VERBOSE | Offsets: 7500000
| 20250108 10:42:41.002 | VERBOSE | Offsets: 7600000
| 20250108 10:42:41.241 | VERBOSE | Offsets: 7700000
| 20250108 10:42:41.483 | VERBOSE | Offsets: 7800000
| 20250108 10:42:41.725 | VERBOSE | Offsets: 7900000
| 20250108 10:42:41.971 | VERBOSE | Offsets: 8000000
| 20250108 10:42:42.205 | VERBOSE | Offsets: 8100000
| 20250108 10:42:42.439 | VERBOSE | Offsets: 8200000
| 20250108 10:42:42.672 | VERBOSE | Offsets: 8300000
| 20250108 10:42:42.946 | VERBOSE | Offsets: 8400000
| 20250108 10:42:43.186 | VERBOSE | Offsets: 8500000
| 20250108 10:42:43.431 | VERBOSE | Offsets: 8600000
| 20250108 10:42:43.673 | VERBOSE | Offsets: 8700000
| 20250108 10:42:43.923 | VERBOSE | Offsets: 8800000
| 20250108 10:42:44.164 | VERBOSE | Offsets: 8900000
| 20250108 10:42:44.404 | VERBOSE | Offsets: 9000000
| 20250108 10:42:44.645 | VERBOSE | Offsets: 9100000
| 20250108 10:42:44.886 | VERBOSE | Offsets: 9200000
| 20250108 10:42:45.126 | VERBOSE | Offsets: 9300000
| 20250108 10:42:45.363 | VERBOSE | Offsets: 9400000
| 20250108 10:42:45.600 | VERBOSE | Offsets: 9500000
| 20250108 10:42:45.839 | VERBOSE | Offsets: 9600000
| 20250108 10:42:46.082 | VERBOSE | Offsets: 9700000
| 20250108 10:42:46.320 | VERBOSE | Offsets: 9800000
| 20250108 10:42:46.556 | VERBOSE | Offsets: 9900000
| 20250108 10:42:46.794 | VERBOSE | Offsets: 10000000
| 20250108 10:42:47.030 | VERBOSE | Offsets: 10100000
| 20250108 10:42:47.263 | VERBOSE | Offsets: 10200000
| 20250108 10:42:47.497 | VERBOSE | Offsets: 10300000
| 20250108 10:42:47.728 | VERBOSE | Offsets: 10400000
| 20250108 10:42:47.957 | VERBOSE | Offsets: 10500000
| 20250108 10:42:48.191 | VERBOSE | Offsets: 10600000
| 20250108 10:42:48.432 | VERBOSE | Offsets: 10700000
| 20250108 10:42:48.673 | VERBOSE | Offsets: 10800000
| 20250108 10:42:48.917 | VERBOSE | Offsets: 10900000
| 20250108 10:42:49.162 | VERBOSE | Offsets: 11000000
| 20250108 10:42:49.403 | VERBOSE | Offsets: 11100000
| 20250108 10:42:49.643 | VERBOSE | Offsets: 11200000
| 20250108 10:42:49.883 | VERBOSE | Offsets: 11300000
| 20250108 10:42:50.125 | VERBOSE | Offsets: 11400000
| 20250108 10:42:50.366 | VERBOSE | Offsets: 11500000
| 20250108 10:42:50.611 | VERBOSE | Offsets: 11600000
| 20250108 10:42:50.853 | VERBOSE | Offsets: 11700000
| 20250108 10:42:51.089 | VERBOSE | Offsets: 11800000
| 20250108 10:42:51.326 | VERBOSE | Offsets: 11900000
| 20250108 10:42:51.567 | VERBOSE | Offsets: 12000000
| 20250108 10:42:51.805 | VERBOSE | Offsets: 12100000
| 20250108 10:42:52.047 | VERBOSE | Offsets: 12200000
| 20250108 10:42:52.281 | VERBOSE | Offsets: 12300000
| 20250108 10:42:52.515 | VERBOSE | Offsets: 12400000
| 20250108 10:42:52.748 | VERBOSE | Offsets: 12500000
| 20250108 10:42:52.978 | VERBOSE | Offsets: 12600000
| 20250108 10:42:53.211 | VERBOSE | Offsets: 12700000
| 20250108 10:42:53.451 | VERBOSE | Offsets: 12800000
| 20250108 10:42:53.692 | VERBOSE | Offsets: 12900000
| 20250108 10:42:53.934 | VERBOSE | Offsets: 13000000
| 20250108 10:42:54.174 | VERBOSE | Offsets: 13100000
| 20250108 10:42:54.419 | VERBOSE | Offsets: 13200000
| 20250108 10:42:54.659 | VERBOSE | Offsets: 13300000
| 20250108 10:42:54.898 | VERBOSE | Offsets: 13400000
| 20250108 10:42:55.136 | VERBOSE | Offsets: 13500000
| 20250108 10:42:55.374 | VERBOSE | Offsets: 13600000
| 20250108 10:42:55.615 | VERBOSE | Offsets: 13700000
| 20250108 10:42:55.852 | VERBOSE | Offsets: 13800000
| 20250108 10:42:56.093 | VERBOSE | Offsets: 13900000
| 20250108 10:42:56.329 | VERBOSE | Offsets: 14000000
| 20250108 10:42:56.569 | VERBOSE | Offsets: 14100000
| 20250108 10:42:56.810 | VERBOSE | Offsets: 14200000
| 20250108 10:42:57.045 | VERBOSE | Offsets: 14300000
| 20250108 10:42:57.279 | VERBOSE | Offsets: 14400000
| 20250108 10:42:57.519 | VERBOSE | Offsets: 14500000
| 20250108 10:42:57.755 | VERBOSE | Offsets: 14600000
| 20250108 10:42:57.985 | VERBOSE | Offsets: 14700000
| 20250108 10:42:58.216 | VERBOSE | Offsets: 14800000
| 20250108 10:42:58.456 | VERBOSE | Offsets: 14900000
| 20250108 10:42:58.696 | VERBOSE | Offsets: 15000000
| 20250108 10:42:58.938 | VERBOSE | Offsets: 15100000
| 20250108 10:42:59.178 | VERBOSE | Offsets: 15200000
| 20250108 10:42:59.418 | VERBOSE | Offsets: 15300000
| 20250108 10:42:59.658 | VERBOSE | Offsets: 15400000
| 20250108 10:42:59.900 | VERBOSE | Offsets: 15500000
| 20250108 10:43:00.144 | VERBOSE | Offsets: 15600000
| 20250108 10:43:00.386 | VERBOSE | Offsets: 15700000
| 20250108 10:43:00.627 | VERBOSE | Offsets: 15800000
| 20250108 10:43:00.868 | VERBOSE | Offsets: 15900000
| 20250108 10:43:01.110 | VERBOSE | Offsets: 16000000
| 20250108 10:43:01.349 | VERBOSE | Offsets: 16100000
| 20250108 10:43:01.594 | VERBOSE | Offsets: 16200000
| 20250108 10:43:01.836 | VERBOSE | Offsets: 16300000
| 20250108 10:43:02.071 | VERBOSE | Offsets: 16400000
| 20250108 10:43:02.303 | VERBOSE | Offsets: 16500000
| 20250108 10:43:02.538 | VERBOSE | Offsets: 16600000
| 20250108 10:43:02.780 | VERBOSE | Offsets: 16700000
| 20250108 10:43:03.104 | VERBOSE | Offsets: 16800000
| 20250108 10:43:03.344 | VERBOSE | Offsets: 16900000
| 20250108 10:43:03.592 | VERBOSE | Offsets: 17000000
| 20250108 10:43:03.835 | VERBOSE | Offsets: 17100000
| 20250108 10:43:04.084 | VERBOSE | Offsets: 17200000
| 20250108 10:43:04.334 | VERBOSE | Offsets: 17300000
| 20250108 10:43:04.578 | VERBOSE | Offsets: 17400000
| 20250108 10:43:04.819 | VERBOSE | Offsets: 17500000
| 20250108 10:43:05.064 | VERBOSE | Offsets: 17600000
| 20250108 10:43:05.313 | VERBOSE | Offsets: 17700000
| 20250108 10:43:05.564 | VERBOSE | Offsets: 17800000
| 20250108 10:43:05.814 | VERBOSE | Offsets: 17900000
| 20250108 10:43:06.062 | VERBOSE | Offsets: 18000000
| 20250108 10:43:06.311 | VERBOSE | Offsets: 18100000
| 20250108 10:43:06.555 | VERBOSE | Offsets: 18200000
| 20250108 10:43:06.793 | VERBOSE | Offsets: 18300000
| 20250108 10:43:07.028 | VERBOSE | Offsets: 18400000
| 20250108 10:43:07.267 | VERBOSE | Offsets: 18500000
| 20250108 10:43:07.514 | VERBOSE | Offsets: 18600000
| 20250108 10:43:07.751 | VERBOSE | Offsets: 18700000
| 20250108 10:43:07.986 | VERBOSE | Offsets: 18800000
| 20250108 10:43:08.228 | VERBOSE | Offsets: 18900000
| 20250108 10:43:08.455 | VERBOSE | Offsets: 19000000
| 20250108 10:43:08.501 | INFO | Get offsets : 46s 27ms
| 20250108 10:43:08.501 | INFO | Consolidate offsets
| 20250108 10:43:08.787 | INFO | Consolidate offsets : 286ms 578us
| 20250108 10:43:08.787 | INFO | Sorting
| 20250108 10:43:09.742 | INFO | Sorting : 954ms 941us
| 20250108 10:43:09.785 | INFO | Write sorted
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Expected behavior
To produce an output transcripts BAM file.

Conda environment:"
Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
_r-mutex 1.0.0 anacondar_1
agat 1.4.0 pl5321hdfd78af_0 bioconda
anndata 0.10.7 pypi_0 pypi
argcomplete 3.4.0 pyhd8ed1ab_0 conda-forge
argh 0.29.4 py310h06a4308_0
array-api-compat 1.6 pypi_0 pypi
bedtools 2.31.1 hf5e1c6e_1 bioconda
binutils_impl_linux-64 2.40 h5293946_0
biopython 1.84 py310hc51659f_0 conda-forge
boltons 23.0.0 py310h06a4308_0
brotli-python 1.0.9 py310h6a678d5_8
bwidget 1.9.16 h9eba36c_0
bx-python 0.12.0 py310ha025fb0_0 bioconda
bzip2 1.0.8 h5eee18b_6
c-ares 1.19.1 h5eee18b_0
ca-certificates 2024.11.26 h06a4308_0
cairo 1.16.0 hb05425b_5
certifi 2024.8.30 py310h06a4308_0
cffi 1.17.1 py310h1fdaa30_0
charset-normalizer 3.3.2 pyhd3eb1b0_0
conda 23.9.0 py310h06a4308_0
conda-content-trust 0.2.0 pyhd8ed1ab_0 conda-forge
conda-libmamba-solver 23.7.0 pyhd8ed1ab_0 conda-forge
conda-package-handling 2.4.0 py310h06a4308_0
conda-package-streaming 0.11.0 py310h06a4308_0
contourpy 1.2.1 pypi_0 pypi
cryptography 41.0.3 py310h130f0dd_0
curl 7.88.1 h37d81fd_2
cycler 0.12.1 pypi_0 pypi
cython 3.0.10 py310hc6cd4ac_0 conda-forge
dbus 1.13.18 hb2f20db_0
dill 0.3.8 pyhd8ed1ab_0 conda-forge
exceptiongroup 1.2.1 pypi_0 pypi
expat 2.6.4 h6a678d5_0
fastqc 0.12.1 hdfd78af_0 bioconda
fmt 9.1.0 hdb19cb5_1
font-ttf-dejavu-sans-mono 2.37 hd3eb1b0_0
font-ttf-inconsolata 2.001 hcb22688_0
font-ttf-source-code-pro 2.030 hd3eb1b0_0
font-ttf-ubuntu 0.83 h8b1ccd4_0
fontconfig 2.14.2 h14ed4e7_0 conda-forge
fonts-anaconda 1 h8fa9717_0
fonts-conda-ecosystem 1 hd3eb1b0_0
fonttools 4.51.0 pypi_0 pypi
freetype 2.12.1 h4a9f257_0
fribidi 1.0.10 h7b6447c_0
gcc_impl_linux-64 13.2.0 h9eb54c0_13 conda-forge
gettext 0.22.5 h59595ed_2 conda-forge
gettext-tools 0.22.5 h59595ed_2 conda-forge
gffutils 0.12 pyh7cba7a3_1 bioconda
gfortran_impl_linux-64 13.2.0 h9efe08d_13 conda-forge
glib 2.78.1 hfc55251_0 conda-forge
glib-tools 2.78.1 hfc55251_0 conda-forge
graphite2 1.3.14 h295c915_1
gsl 2.7.1 h6e86dc7_1
gxx_impl_linux-64 13.2.0 h2a599c4_13 conda-forge
h5py 3.11.0 pypi_0 pypi
harfbuzz 6.0.0 h8e241bc_0 conda-forge
htslib 1.17 h6bc39ce_1 bioconda
icu 70.1 h27087fc_0 conda-forge
idna 3.7 py310h06a4308_0
importlib-metadata 8.5.0 py310h06a4308_0
isoseq 4.0.0 h9ee0642_0 bioconda
joblib 1.4.2 pypi_0 pypi
jsonpatch 1.33 py310h06a4308_1
jsonpointer 2.1 pyhd3eb1b0_0
kernel-headers_linux-64 2.6.32 he073ed8_17 conda-forge
kiwisolver 1.4.5 pypi_0 pypi
krb5 1.20.1 h568e23c_1
ld_impl_linux-64 2.40 h12ee557_0
legacy-api-wrap 1.4 pypi_0 pypi
lerc 4.0.0 h6a678d5_0
libarchive 3.6.2 hb4bd9a0_1 main
libasprintf 0.22.5 h661eb56_2 conda-forge
libasprintf-devel 0.22.5 h661eb56_2 conda-forge
libblas 3.9.0 22_linux64_openblas conda-forge
libcblas 3.9.0 22_linux64_openblas conda-forge
libcurl 7.88.1 h91b91d3_2
libdb 6.2.32 h6a678d5_1
libdeflate 1.18 h0b41bf4_0 conda-forge
libedit 3.1.20230828 h5eee18b_0
libev 4.33 h7f8727e_1
libffi 3.4.4 h6a678d5_1
libgcc-devel_linux-64 13.2.0 hdb50d1a_113 conda-forge
libgcc-ng 13.2.0 h77fa898_13 conda-forge
libgettextpo 0.22.5 h59595ed_2 conda-forge
libgettextpo-devel 0.22.5 h59595ed_2 conda-forge
libgfortran-ng 13.2.0 h69a702a_13 conda-forge
libgfortran5 13.2.0 h3d2ce59_13 conda-forge
libglib 2.78.1 hebfc3b9_0 conda-forge
libgomp 13.2.0 h77fa898_13 conda-forge
libiconv 1.17 hd590300_2 conda-forge
libjpeg-turbo 2.1.5.1 hd590300_1 conda-forge
liblapack 3.9.0 22_linux64_openblas conda-forge
libmamba 1.4.1 hdb19cb5_0
libmambapy 1.4.1 py310hdb19cb5_0
libnghttp2 1.52.0 ha637b67_1
libnsl 2.0.0 h5eee18b_0
libopenblas 0.3.27 pthreads_h413a1c8_0 conda-forge
libpng 1.6.39 h5eee18b_0
libsanitizer 13.2.0 h6ddb7a1_13 conda-forge
libsolv 0.7.29 ha6fb4c9_0 conda-forge
libsqlite 3.46.0 hde9e2c9_0 conda-forge
libssh2 1.10.0 haa6b8db_3 conda-forge
libstdcxx-devel_linux-64 13.2.0 hdb50d1a_113 conda-forge
libstdcxx-ng 13.2.0 hc0a3c3a_13 conda-forge
libtiff 4.5.1 h8b53f26_1 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libwebp-base 1.3.2 h5eee18b_1
libxcb 1.16 hd590300_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxml2 2.10.3 hca2bb57_4 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
lima 2.9.0 h9ee0642_1 bioconda
llvmlite 0.42.0 pypi_0 pypi
lz4-c 1.9.4 h6a678d5_1
make 4.2.1 h1bed415_1
matplotlib 3.9.0 pypi_0 pypi
menuinst 2.0.2 py310hff52083_0 conda-forge
natsort 8.4.0 pypi_0 pypi
ncurses 6.4 h6a678d5_0
networkx 3.3 pypi_0 pypi
numba 0.59.1 pypi_0 pypi
numpy 2.0.0 py310h515e003_0 conda-forge
openjdk 11.0.13 h87a67e3_0
openssl 1.1.1w h7f8727e_0
p7zip 16.02 h6a678d5_0 anaconda
packaging 24.1 py310h06a4308_0
pandas 2.2.2 pypi_0 pypi
pango 1.50.14 hd33c08f_0 conda-forge
patsy 0.5.6 pypi_0 pypi
pbbam 2.4.0 h8db2425_0 bioconda
pbccs 6.4.0 h9ee0642_0 bioconda
pbcopper 2.3.0 h4ac6f70_3 bioconda
pbmm2 1.14.99 h9ee0642_0 bioconda
pbpigeon 1.2.0 h4ac6f70_0 bioconda
pbskera 1.2.0 hdfd78af_0 bioconda
pbtk 3.1.1 h9ee0642_0 bioconda
pcre2 10.40 hc3806b6_0 conda-forge
perl 5.32.1 7_hd590300_perl5 conda-forge
perl-b-cow 0.007 pl5321hd590300_0 conda-forge
perl-base 2.23 pl5321hd8ed1ab_0 conda-forge
perl-bioperl-core 1.7.8 pl5321hdfd78af_1 bioconda
perl-business-isbn 3.007 pl5321hd8ed1ab_0 conda-forge
perl-business-isbn-data 20210112.006 pl5321hd8ed1ab_0 conda-forge
perl-carp 1.50 pl5321hd8ed1ab_0 conda-forge
perl-class-inspector 1.36 pl5321hdfd78af_0 bioconda
perl-class-load 0.25 pl5321hdfd78af_1 bioconda
perl-class-load-xs 0.10 pl5321h0b41bf4_0 conda-forge
perl-class-methodmaker 2.24 pl5321h031d066_4 bioconda
perl-clone 0.46 pl5321h166bdaf_0 conda-forge
perl-compress-raw-zlib 2.202 pl5321h166bdaf_0 conda-forge
perl-constant 1.33 pl5321hd8ed1ab_0 conda-forge
perl-cpan-meta-check 0.014 pl5321ha770c72_0 conda-forge
perl-data-optlist 0.114 pl5321ha770c72_0 conda-forge
perl-db_file 1.858 pl5321h166bdaf_0 conda-forge
perl-devel-globaldestruction 0.14 pl5321ha770c72_0 conda-forge
perl-devel-overloadinfo 0.007 pl5321ha770c72_0 conda-forge
perl-devel-stacktrace 2.04 pl5321ha770c72_0 conda-forge
perl-digest-hmac 1.04 pl5321hdfd78af_0 bioconda
perl-digest-md5 2.58 pl5321h166bdaf_0 conda-forge
perl-dist-checkconflicts 0.11 pl5321ha770c72_0 conda-forge
perl-encode 3.21 pl5321hd590300_0 conda-forge
perl-encode-locale 1.05 pl5321hdfd78af_7 bioconda
perl-eval-closure 0.14 pl5321ha770c72_0 conda-forge
perl-exporter 5.74 pl5321hd8ed1ab_0 conda-forge
perl-exporter-tiny 1.002002 pl5321hd8ed1ab_0 conda-forge
perl-extutils-makemaker 7.70 pl5321hd8ed1ab_0 conda-forge
perl-file-listing 6.16 pl5321hdfd78af_0 bioconda
perl-file-share 0.25 pl5321hdfd78af_3 bioconda
perl-file-sharedir 1.118 pl5321hdfd78af_0 bioconda
perl-file-sharedir-install 0.13 pl5321hdfd78af_1 bioconda
perl-file-spec 3.48_01 pl5321hdfd78af_2 bioconda
perl-getopt-long 2.58 pl5321hdfd78af_0 bioconda
perl-graph 0.9728 pl5321hdfd78af_0 bioconda
perl-heap 0.80 pl5321hdfd78af_1 bioconda
perl-html-parser 3.81 pl5321h4ac6f70_1 bioconda
perl-html-tagset 3.20 pl5321hdfd78af_4 bioconda
perl-http-cookies 6.10 pl5321hdfd78af_0 bioconda
perl-http-daemon 6.16 pl5321hdfd78af_0 bioconda
perl-http-date 6.06 pl5321hdfd78af_0 bioconda
perl-http-message 6.36 pl5321hdfd78af_0 bioconda
perl-http-negotiate 6.01 pl5321hdfd78af_4 bioconda
perl-inc-latest 0.500 pl5321ha770c72_0 conda-forge
perl-io-html 1.004 pl5321hdfd78af_0 bioconda
perl-io-socket-ssl 2.075 pl5321hd8ed1ab_0 conda-forge
perl-io-tty 1.16 pl5321h166bdaf_0 conda-forge
perl-ipc-run 20200505.0 pl5321hdfd78af_0 bioconda
perl-libwww-perl 6.39 pl5321hdfd78af_1 bioconda
perl-list-moreutils 0.430 pl5321hdfd78af_0 bioconda
perl-list-moreutils-xs 0.430 pl5321h031d066_2 bioconda
perl-lwp-mediatypes 6.04 pl5321hdfd78af_1 bioconda
perl-lwp-protocol-https 6.10 pl5321hdfd78af_0 bioconda
perl-lwp-simple 6.39 pl5321h9ee0642_5 bioconda
perl-mime-base64 3.16 pl5321h166bdaf_0 conda-forge
perl-module-build 0.4232 pl5321ha770c72_0 conda-forge
perl-module-implementation 0.09 pl5321ha770c72_0 conda-forge
perl-module-runtime 0.016 pl5321ha770c72_0 conda-forge
perl-module-runtime-conflicts 0.003 pl5321ha770c72_0 conda-forge
perl-moose 2.2201 pl5321hec16e2b_2 bioconda
perl-mozilla-ca 20211001 pl5321hdfd78af_0 bioconda
perl-mro-compat 0.15 pl5321ha770c72_0 conda-forge
perl-net-http 6.22 pl5321hdfd78af_0 bioconda
perl-net-ssleay 1.92 pl5321haa6b8db_1 conda-forge
perl-ntlm 1.09 pl5321hdfd78af_5 bioconda
perl-package-deprecationmanager 0.18 pl5321ha770c72_0 conda-forge
perl-package-stash 0.40 pl5321ha770c72_0 conda-forge
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perl-safe 2.37 pl5321hdfd78af_2 bioconda
perl-scalar-list-utils 1.63 pl5321h166bdaf_0 conda-forge
perl-set-object 1.42 pl5321h031d066_3 bioconda
perl-socket 2.027 pl5321h031d066_4 bioconda
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perl-sub-exporter 0.991 pl5321ha770c72_0 conda-forge
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perl-test-harness 3.44 pl5321hd8ed1ab_0 conda-forge
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perl-test-requiresinternet 0.05 pl5321hdfd78af_1 bioconda
perl-test-warnings 0.031 pl5321ha770c72_0 conda-forge
perl-text-balanced 2.06 pl5321hdfd78af_0 bioconda
perl-text-wrap 2021.0814 pl5321hd8ed1ab_0 conda-forge
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perl-timedate 2.33 pl5321hdfd78af_2 bioconda
perl-try-tiny 0.31 pl5321ha770c72_0 conda-forge
perl-uri 5.17 pl5321ha770c72_0 conda-forge
perl-url-encode 0.03 pl5321h9ee0642_0 bioconda
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perl-www-robotrules 6.02 pl5321hdfd78af_4 bioconda
perl-yaml 1.30 pl5321hdfd78af_0 bioconda
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pip 24.0 pyhd8ed1ab_0 conda-forge
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r-tidyr 1.2.0 r42h884c59f_0
r-tidyselect 1.1.2 r42h142f84f_0
r-timedate 3043.102 r42h6115d3f_0
r-utf8 1.2.2 r42h76d94ec_0
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r-withr 2.5.0 r42h6115d3f_0
readline 8.2 h5eee18b_0
reproc 14.2.4 h6a678d5_2
reproc-cpp 14.2.4 h6a678d5_2
requests 2.32.3 py310h06a4308_1
ruamel.yaml 0.17.21 py310h5eee18b_0
ruamel.yaml.clib 0.2.8 py310h5eee18b_0
samtools 1.18 hd87286a_0 bioconda
scanpy 1.10.1 pypi_0 pypi
scikit-learn 1.5.0 pypi_0 pypi
scipy 1.14.1 pypi_0 pypi
seaborn 0.13.2 pypi_0 pypi
sed 4.8 h7b6447c_0
session-info 1.0.0 pypi_0 pypi
setuptools 69.2.0 pyhd8ed1ab_0 conda-forge
simplejson 3.19.2 py310h5eee18b_0
sinto 0.9.0 pyh086e186_0 bioconda
six 1.16.0 pyhd3eb1b0_1
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sysroot_linux-64 2.12 he073ed8_17 conda-forge
threadpoolctl 3.5.0 pypi_0 pypi
tk 8.6.14 h39e8969_0
tktable 2.10 h3d55465_1
tqdm 4.66.5 py310h2f386ee_0
truststore 0.8.0 py310h06a4308_0
tzdata 2024.1 pypi_0 pypi
umap-learn 0.5.6 pypi_0 pypi
urllib3 2.2.3 py310h06a4308_0
wheel 0.43.0 pyhd8ed1ab_1 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.1.1 hd590300_0 conda-forge
xorg-libsm 1.2.4 h7391055_0 conda-forge
xorg-libx11 1.8.9 hb711507_1 conda-forge
xorg-libxau 1.0.11 hd590300_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxt 1.3.0 hd590300_1 conda-forge
xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge
xorg-xproto 7.0.31 h27cfd23_1007
xz 5.2.10 h5eee18b_1
yaml-cpp 0.7.0 h59595ed_3 conda-forge
zipp 3.21.0 py310h06a4308_0
zlib 1.2.13 hd590300_5 conda-forge
zstandard 0.22.0 py310h2c38b39_0
zstd 1.5.5 hc292b87_0
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