Entering edit mode
3.1 years ago
Hi guys,
I'm running velocyto on bam files via ssh. One sample was succeeded, but when I started running the other two samples, I saw this error showed up over and over again, at the beginning, I thought something was wrong with my bam files, so I re-transferred them to the server, and changed the memory in the bash file, as these two samples are bigger than the first sample, but I still see the same error:
File "/wynton/home/anderson/yiwang/.local/bin/velocyto", line 11, in <module>
load_entry_point('velocyto==0.17.17', 'console_scripts', 'velocyto')()
File "/wynton/home/anderson/yiwang/.local/lib/python3.6/site-packages/click/core.py", line 829, in __call__
return self.main(*args, **kwargs)
File "/wynton/home/anderson/yiwang/.local/lib/python3.6/site-packages/click/core.py", line 782, in main
rv = self.invoke(ctx)
File "/wynton/home/anderson/yiwang/.local/lib/python3.6/site-packages/click/core.py", line 1259, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/wynton/home/anderson/yiwang/.local/lib/python3.6/site-packages/click/core.py", line 1066, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/wynton/home/anderson/yiwang/.local/lib/python3.6/site-packages/click/core.py", line 610, in invoke
return callback(*args, **kwargs)
File "/wynton/home/anderson/yiwang/.local/lib/python3.6/site-packages/velocyto/commands/run.py", line 116, in run
samtools_memory=samtools_memory, dump=dump, loom_numeric_dtype=dtype, verbose=verbose, additional_ca=additional_ca)
File "/wynton/home/anderson/yiwang/.local/lib/python3.6/site-packages/velocyto/commands/_run.py", line 229, in _run
results = exincounter.count(bamfile_cellsorted, multimap=multimap) # NOTE: we would avoid some millions of if statements evaluations if we write two function count and count_with output
File "/wynton/home/anderson/yiwang/.local/lib/python3.6/site-packages/velocyto/counter.py", line 756, in count
for r in self.iter_alignments(bamfile, unique=not multimap):
File "/wynton/home/anderson/yiwang/.local/lib/python3.6/site-packages/velocyto/counter.py", line 251, in iter_alignments
fin = pysam.AlignmentFile(bamfile) # type: pysam.AlignmentFile
File "pysam/libcalignmentfile.pyx", line 742, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 952, in pysam.libcalignmentfile.AlignmentFile._open
File "pysam/libchtslib.pyx", line 365, in pysam.libchtslib.HTSFile.check_truncation
OSError: no BGZF EOF marker; file may be truncated
I googled, I found ppl had the same error as me, they suggested checking the bam files with samtools, I did, but I can't tell if it's correct or not:
samtools view GW_possorted_genome_bam.bam | tail
A00269:304:H2MKKDSXY:4:2141:9218:28166 4 * 0 0 * * 0 0 CTGTGCACCCCGAATCTGCCCCTATCCCCTTCTCTGCTTCCTGCACTGCACACCTGCTAGTCCCAGACCCCTCCCCCAAATAAACGTGAGGGTTAAAAGTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:FFF:FFF:F:F:::F:FFF:FFFF,F:FFFF:FFFFFFFFFFFFFFFFFFF:FFFFFF:FF:F:FFFFFFF: NH:i:0 HI:i:0 AS:i:91 nM:i:0 uT:A:1 xf:i:0 li:i:0 BC:Z:TTGCCGGA QT:Z:FFFFFFF: CR:Z:TTTGTTGTCTTCACGC CY:Z:FFFFFFFFFFFFFFFF CB:Z:TTTGTTGTCTTCACGC-1 UR:Z:AGGTTTGGATTG UY:Z:FFFFFFFFFFFF UB:Z:AGGTTTGGATTG RG:Z:test:0:1:H2MKKDSXY:4
A00269:304:H2MKKDSXY:4:2344:12192:34601 4 * 0 0 * * 0 0 CCCGCCCCTGTCCCCTAGCCGCCGCTCCGGGCTCTGCTCGCCCTCCTACGTTGCGGTCACACCCTTCTCCCTTCGGGGAGACAACGACGGCGGTGGCGGGAGCTTCTCCACGGCCGACCAGCTGGAGATGGTGACCGAGCTGCTGGGAGG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFF:FFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:F:FF:FFFFFFFFFFFF NH:i:0 HI:i:0 AS:i:49 nM:i:4 uT:A:1 xf:i:0 li:i:0 BC:Z:GCCAATCC QT:Z:FFFF,FFF CR:Z:TTTGTTGTCTTCGTAT CY:Z:FFFFFFFFFFFFFFFF CB:Z:TTTGTTGTCTTCGTAT-1 UR:Z:ACTCCGCTGTCG UY:Z:FFFFFFFFFFFF UB:Z:ACTCCGCTGTCG RG:Z:test:0:1:H2MKKDSXY:4
A00269:304:H2MKKDSXY:4:1242:8223:3865 4 * 0 0 * * 0 0 CTGAAAAGGGCTTCCAGTCCCGTCACCTTGCCTGCCTGCCTCGGGAGCCAGGGCTGTGCACCTGGCAGTCCCTGCGGTCCCAGATAGCCTGAATCCTGCCCGGAGTGGAAGCTGAAGCCTGCACAGTGTCCACCCTGTTCCCACTCCCAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFF:FFF:FFFFFFFFFFF:F:FFFF::FFFFFFFFF:FFFFF:FFFFFFFFF:FFFFFFFFFFFFF NH:i:0 HI:i:0 AS:i:20 nM:i:1 uT:A:1 xf:i:0 li:i:0 BC:Z:AGTTGCAG QT:Z:FFFFFFFF CR:Z:TTTGTTGTCTTCGTAT CY:Z::FFFFFFFFFFFFFFF CB:Z:TTTGTTGTCTTCGTAT-1 UR:Z:AGTGACCATTCC UY:Z:FFFFFF:FFFFF UB:Z:AGTGACCATTCC RG:Z:test:0:1:H2MKKDSXY:4
A00269:304:H2MKKDSXY:4:2632:25880:13401 4 * 0 0 * * 0 0 CACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGATTAACCCAANTCAATAGAAGCCGGCGTAAAGAGTGTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF::FFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFF#FFFFFFFFF:FFFFFFFFFFFFFFFFF NH:i:0 HI:i:0 AS:i:62 nM:i:9 uT:A:1 xf:i:0 li:i:0 BC:Z:NTGCCGGA QT:Z:#FFFFFFF CR:Z:TTTGTTGTCTTCGTAT CY:Z:FFFFFFFFFFFFFFFF CB:Z:TTTGTTGTCTTCGTAT-1 UR:Z:CACTTATGTGAT UY:Z:FFFFFFFFFFFF UB:Z:CACTTATGTGAT RG:Z:test:0:1:H2MKKDSXY:4
A00269:304:H2MKKDSXY:4:1573:13621:26522 4 * 0 0 * * 0 0 AAAAATGCCCTAGCCCACTTCTTACCACAAGGCACACCTACACCCCTTATCCCCATACTAGTTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGTACGCCTAACCGCTAACATTACTGCAGGCCACCTACTCATG FFFFFFFFFFFFFFFFFF:FFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFF:FFFFFFFFFFFF:FFFFFFF:,FF:F:FFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFF,FFFFFF NH:i:0 HI:i:0 AS:i:19 nM:i:4 uT:A:1 xf:i:0 li:i:0 BC:Z:GCCATTCC QT:Z:FFFFFFFF CR:Z:TTTGTTGTCTTCGTAT CY:Z::FFFFFFFFFFFFFFF CB:Z:TTTGTTGTCTTCGTAT-1 UR:Z:CTGTTTAATTAG UY:Z:FFFFFFFFFFFF UB:Z:CTGTTTAATTAG RG:Z:test:0:1:H2MKKDSXY:4
A00269:304:H2MKKDSXY:4:1638:20934:35462 4 * 0 0 * * 0 0 GGCGGATACCATCAAAGCTATTAAGGAAAATCTACCCAAGAAACGCCACACTTTACTGTTCTCAGCCACACAGACCAAAACTCTCAAGGACCAGCCGCGCTGTGGTGGGAAAGACCCTGAGTATGTCTGGGTTCATGAAAAAGCAAAATA ,FF,FF,:,FF,,:F,FF,:,,:,,,F:FFFFF,:FFFFFF,FFFF:,,,FFF,FFFFFF:FFF:FF,FFFF:FFF::,,FF,F,,::,FFF,,,,,FFF:,,,,F,,::FFF:F,F,FF:FFF,,F,F:FFFFF,,F::FF:FF:FF,F NH:i:0 HI:i:0 AS:i:69 nM:i:10 uT:A:1 xf:i:0 li:i:0 BC:Z:AGTTGCAG QT:Z::FFFFFFF CR:Z:TTTGTTGGCTTCTCAA CY:Z:,FF:,F,:F:,FFFFF CB:Z:TTTGTTGTCTTCTCAA-1 UR:Z:AATGGAAAACAG UY:Z::F,F,FFFFFF, UB:Z:AATGGAAAACAG RG:Z:test:0:1:H2MKKDSXY:4
A00269:304:H2MKKDSXY:4:1137:1443:18145 4 * 0 0 * * 0 0 TCCCAAGAGAGCATCTGTCAGTTGTTGGCAAAATGATAAAGACATTTGAAAATCTGTCTTCTGACAAATAAAAAGCATTTATTTCACTGCACAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACGCGGGGTTGGGAAAAAAAACA FFFF,FFFFFFFFFFFFFF,F:FF,FFFFF,FFFFFF,:FFFF,FFFFF,:FFFFFFFFFFFFFF,,FF:FFFFFF,FFFFFFFF,FFFFF,FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF,,F,,F:F,,:F,,,:::F,,,F NH:i:0 HI:i:0 AS:i:89 nM:i:0 uT:A:1 xf:i:0 li:i:0 BC:Z:TTGCCGGA QT:Z:FFFFFFFF CR:Z:TTTGTTGTCTTCTGTA CY:Z::FFFFFFFFFFFFFFF CB:Z:TTTGTTGTCTTCTGTA-1 UR:Z:CTCAATCCGACG UY:Z:FF:FFFFFFFFF UB:Z:CTCAATCCGACG RG:Z:test:0:1:H2MKKDSXY:4
A00269:304:H2MKKDSXY:4:1542:18267:19758 4 * 0 0 * * 0 0 AAAACTAGTTAAGTTTGGGAAAATGAGCTCATGTCTGAAATGAGAAAGTAATTTATAATTTGGTTTATGGGACGGACAGGAAGGAGAAGGAGCACCACTTCTTCCTCAAGTGGAGTGTTTACACCTTGCTGTAACATTTGAACTTTCACA F:FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFF,FFFFFFFFFF,FFF:FFFFF,F,F:FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFF NH:i:0 HI:i:0 AS:i:87 nM:i:0 uT:A:1 xf:i:0 li:i:0 BC:Z:AGTTGCAG QT:Z:FFFFFFFF CR:Z:TTTGTTGTCTTGAGCA CY:Z:FFFFFFFFFFFFFFFF CB:Z:TTTGTTGTCTTGAGCA-1 UR:Z:GTAGGTTTCAAC UY:Z:FFFFFFFFFFFF UB:Z:GTAGGTTTCAAC RG:Z:test:0:1:H2MKKDSXY:4
A00269:304:H2MKKDSXY:4:1278:32570:14278 4 * 0 0 * * 0 0 ATATAGTGCTTAAGATAGGGCTGAAAATTCTAGAGGAAATTCAGGACAGTCTATCAGAAGTAAAGCGGGGAGAGAGAGTAGGAGCAAGGAGAAACGGTAAGTATACAGGCCTTTCCAAGGGTCTTGAACCCGAGGAAAAGTTAAGGTCAG FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF:FF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF,::,F::FFF:FF,FFFF:F:FFFF NH:i:0 HI:i:0 AS:i:148 nM:i:0 uT:A:3 xf:i:0 li:i:0 BC:Z:TTGCCGGA QT:Z:FFFFFFFF CR:Z:TTTGTTGTCTTTCTAG CY:Z:FFFFFFFFFFFFFFFF CB:Z:TTTGTTGTCTTTCTAG-1 UR:Z:GCTCGACATCTT UY:Z:FFFFFFFFFFFF UB:Z:GCTCGACATCTT RG:Z:test:0:1:H2MKKDSXY:4
A00269:304:H2MKKDSXY:4:2477:17743:31344 4 * 0 0 * * 0 0 GGAGAGAGAGTAGGAGCAAGGAGAAACGGTAAGTATACAGGCCTTTCCAAGGGTCTTGAACCCGAGGAAAAGTTAAGGTCAGGTAGGAATACCTGGAGAGAGATTAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGTGGGGGAGGA FFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFF:FFF,FFFFFFFFF::FFFFFFFFFFFFFFFFFF,FFFFF,FFFFF:FFF:FFFFFFFFFF:FFF:F:FFFF,FFF,::FFFFFFFF:F:FFF::,FFFFFFFF,,,,,,,,,,,, NH:i:0 HI:i:0 AS:i:122 nM:i:7 uT:A:3 xf:i:0 li:i:0 BC:Z:AGTTGCAG QT:Z::FFFFFFF CR:Z:TTTGTTGTCTTTCTAG CY:Z:FFFFFFFFFFFFFFFF CB:Z:TTTGTTGTCTTTCTAG-1 UR:Z:GCTCGACATCTT UY:Z:FFFFFFFFFFFF UB:Z:GCTCGACATCTT RG:Z:test:0:1:H2MKKDSXY:4
[yiwang@dev3 bam_files]$ samtools view WT_possorted_genome_bam.bam | tail
A00269:200:HJ7CYDMXX:2:2145:7039:32910 4 * 0 0 * * 0 0 AAGCAGTGGTATCAACGCAGAGTACATGGGAAAAATTTGTTTCTGTGTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFF:FFFFF:F:F::F NH:i:0 HI:i:0 AS:i:46 nM:i:1 uT:A:1 xf:i:0 li:i:0 BC:Z:TGTAGAAGQT:Z:FFFFF:FF CR:Z:TTTGTTGTCTTCGGTC CY:Z:FFFFFFFFFFFFFFFF CB:Z:TTTGTTGTCTTCGGTC-1 UR:Z:TTGTCACCATTT UY:Z:FFFFFFFFFFFF UB:Z:TTGTCACCATTT RG:Z:e771c0c8-efbc-45b4-a2f6-c50d2e847e34:0:1:HJ7CYDMXX:2
A00269:200:HJ7CYDMXX:2:2443:9507:13761 4 * 0 0 * * 0 0 AAGCAGTGGTATCAACGCAGAGTACATGGGATTTGGAATAAAAATTGAATTTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFF,FF:F,:FFF:FF NH:i:0 HI:i:0 AS:i:48 nM:i:3 uT:A:1 xf:i:0 li:i:0 BC:Z:TGTAGAAGQT:Z:FFFFF:FF CR:Z:TTTGTTGTCTTCGGTC CY:Z:FFFFFFFFFFFFFFFF CB:Z:TTTGTTGTCTTCGGTC-1 UR:Z:TTTAAAAACTGC UY:Z:FFFFFFFFFFFF UB:Z:TTTAAAAACTGC RG:Z:e771c0c8-efbc-45b4-a2f6-c50d2e847e34:0:1:HJ7CYDMXX:2
A00269:200:HJ7CYDMXX:1:1239:23375:31234 4 * 0 0 * * 0 0 CTCGGGGTCGGGGGTGCGTGGCGGGGGCCCGTCCCCCGCCTCCCCTCCGCGCGCCGGGTTTCGCCCCCGCGGCGTCGGGCCCCGCGGACGC FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF NH:i:0 HI:i:0 AS:i:54 nM:i:10 uT:A:1 xf:i:0 li:i:0 BC:Z:CTGGACTCQT:Z:FFFFFFFF CR:Z:TTTGTTGTCTTCGGTC CY:Z:::FFFFFFF,FFFFFF CB:Z:TTTGTTGTCTTCGGTC-1 UR:Z:TTTCTGCACATC UY:Z:F:FFFFFFFFFF UB:Z:TTTCTGCACATC RG:Z:e771c0c8-efbc-45b4-a2f6-c50d2e847e34:0:1:HJ7CYDMXX:1
A00269:200:HJ7CYDMXX:1:1181:15736:1626 4 * 0 0 * * 0 0 AAGCAGTGGTATCAACGCAGAGTACATGGGGTCAAAAGTTTTCCTGCATCTATTAAGATAACCATGGGATTTATGTCCTTGAGATCATTTA FFFFFFFFFFFFFFFFFFFFFFFFFF:FF:F:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:FFFFF:F,F,FFFFFFF:FFFFFFFF NH:i:0 HI:i:0 AS:i:58 nM:i:1 uT:A:1 xf:i:0 li:i:0 BC:Z:CTGGACTCQT:Z:,F:F:F:: CR:Z:TTAGTTGTCTTCGGTC CY:Z:F:,:FFF:FFF:::FF CB:Z:TTTGTTGTCTTCGGTC-1 UR:Z:TTTGGTCTTTTT UY:Z:F:FF:FFF::F, UB:Z:TTTGGTCTTTTT RG:Z:e771c0c8-efbc-45b4-a2f6-c50d2e847e34:0:1:HJ7CYDMXX:1
A00269:200:HJ7CYDMXX:2:1108:14172:13041 4 * 0 0 * * 0 0 AAGCAGTGGTATCAACGCAGAGTACATGGGGGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFF:::FF:F:FFFFFFFF NH:i:0 HI:i:0 AS:i:60 nM:i:0 uT:A:3 xf:i:0 li:i:0 BC:Z:AAACCTCAQT:Z:FFFFFFFF CR:Z:TTTGTTGTCTTCGGTC CY:Z:FFFFFFFFFFFFFFFF CB:Z:TTTGTTGTCTTCGGTC-1 UR:Z:TTTTATACCAAT UY:Z:FFFFFFFFFFFF UB:Z:TTTTATACCAAT RG:Z:e771c0c8-efbc-45b4-a2f6-c50d2e847e34:0:1:HJ7CYDMXX:2
A00269:200:HJ7CYDMXX:2:2108:19551:18161 4 * 0 0 * * 0 0 AAGCAGTGGTATCAACGCAGAGTACATGGGGGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:F,FF,FFFFFFFFF:F NH:i:0 HI:i:0 AS:i:60 nM:i:0 uT:A:3 xf:i:0 li:i:0 BC:Z:AAACCTCAQT:Z:FFFFFFFF CR:Z:TTTGTTGTCTTCGGTC CY:Z:FFFFFFFFFFFFFFFF CB:Z:TTTGTTGTCTTCGGTC-1 UR:Z:TTTTATACCAAT UY:Z:FFFFFFFFFFFF UB:Z:TTTTATACCAAT RG:Z:e771c0c8-efbc-45b4-a2f6-c50d2e847e34:0:1:HJ7CYDMXX:2
A00269:200:HJ7CYDMXX:2:2173:30553:22717 4 * 0 0 * * 0 0 AAGCAGTGGTATCAACGCAGAGTACATGGGGTCCCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF,FFFF,FFF:FFFF NH:i:0 HI:i:0 AS:i:57 nM:i:0 uT:A:1 xf:i:0 li:i:0 BC:Z:CTGGACTCQT:Z:F:FFFFFF CR:Z:TTTGTTGTCTTCGGTC CY:Z:FFFFFFFFFFFFFFFF CB:Z:TTTGTTGTCTTCGGTC-1 UR:Z:TTTTCTACTTGG UY:Z:FFFFFFFFFFFF UB:Z:TTTTCTACTTGG RG:Z:e771c0c8-efbc-45b4-a2f6-c50d2e847e34:0:1:HJ7CYDMXX:2
A00269:200:HJ7CYDMXX:2:2173:30798:22764 4 * 0 0 * * 0 0 AAGCAGTGGTATCAACGCAGAGTACATGGGGTCCCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFFFF:FFFFF:,FFFFF:FFFFFFF NH:i:0 HI:i:0 AS:i:57 nM:i:0 uT:A:1 xf:i:0 li:i:0 BC:Z:CTGGACTCQT:Z:FFFFFFFF CR:Z:TTTGTTGTCTTCGGTC CY:Z:FFFFFFFFFFFFFFFF CB:Z:TTTGTTGTCTTCGGTC-1 UR:Z:TTTTCTACTTGG UY:Z:FFFFFFFFFFFF UB:Z:TTTTCTACTTGG RG:Z:e771c0c8-efbc-45b4-a2f6-c50d2e847e34:0:1:HJ7CYDMXX:2
A00269:200:HJ7CYDMXX:1:2435:31403:9502 4 * 0 0 * * 0 0 GCTGGGACAGCCCCGCTCCCAGATGTAAAGAACGCGACTTCCACAAACCTGGATTTTTTATGTACAACCCTGACCGTGACCGTTTGCTATA :,FFFFF:F:FFFFFFFFFFF:FF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFF:FFF,FFFFFFFFFFF:FFFFFFFFFFFFFFFF NH:i:0 HI:i:0 AS:i:20 nM:i:0 uT:A:1 xf:i:0 li:i:0 BC:Z:GCCTTGGTQT:Z:FFFF:FFF CR:Z:TTTGTTGTCTTGGATG CY:Z:FFFFF:FFFFFF::FF CB:Z:TTTGTTGTCTTGGATG-1 UR:Z:AATTCACGTACT UY:Z:FFFFFFFFFFFF UB:Z:AATTCACGTACT RG:Z:e771c0c8-efbc-45b4-a2f6-c50d2e847e34:0:1:HJ7CYDMXX:1
A00269:200:HJ7CYDMXX:2:2457:17743:34507 4 * 0 0 * * 0 0 AAGCAGTGGTATCATCGCAGATTACATGGGCAATTTCACTAATTCCAATACTTATTATGATTGAAACAATTAGACTATGTCTTCAACCAAT ::FFFFFFFFFFFF,FFFFFF,,FFFF,F:FFFF:F:FFFFFFFF,,FFFF:F,F,FF:FFF,F,FFFFFFFF,FFFF,:FF,FFFFF,F: NH:i:0 HI:i:0 AS:i:52 nM:i:4 uT:A:1 xf:i:0 li:i:0 BC:Z:GCCATGGTQT:Z:,,F,:F,: CR:Z:TTTGTTGTCTTTGGAG CY:Z:FF:F:FFF,F,,,FF: CB:Z:TTTGTTGTCTTTGGAG-1 UR:Z:CATGTTCCGTCC UY:Z:FFFF:,,::FFF UB:Z:CATGTTCCGTCC RG:Z:e771c0c8-efbc-45b4-a2f6-c50d2e847e34:0:1:HJ7CYDMXX:2
Could you please help me with this issue?
Thanks in advance! Yi
This means that the BAM file is corrupted. This is then either bam from cellranger, indicating that cellranger crashes, or the intermediate files from velocyto, meaning that it crashes. This could be a memory shortage. In a nutshell, I discourage custom manipulatuion with files. If cellranger bam is corrupted then rerun cellranger, if velocyto crashed with a proper bam from cellranger (samtools quickcheck -qvvv can check basic integrity of bam files) then review velocyto settings, for example allocated memory.