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velocyto-team / velocyto.py

RNA velocity estimation in Python
http://velocyto.org/velocyto.py/
BSD 2-Clause "Simplified" License
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error that occurred when I ran velocyto on bam files #301

Open gabriellayi opened 3 years ago

gabriellayi commented 3 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

GouQiao commented 2 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

Hi ,

I met same problem. Did you solve this matter?

Best.