search

phasegenomics / matlock

Simple tools for working with Hi-C data
GNU Affero General Public License v3.0
16 stars 1 forks source link

FATAL: add_link when running matlock bam2 counts #7

Open TomHarrop opened 4 years ago

TomHarrop commented 4 years ago

Hi,

We're getting an error FATAL:add_link running matlock from commit 9fe3fdd, as follows:

$ matlock bam2 counts my.bam links.out
INFO: converting bam to lachesis on my.bam
INFO: detected bam filetype
INFO: reading file "my.bam"
FATAL: add_link

Here's the body of my.bam (this is a subset of a larger HiC BAM), happy to send it for troubleshooting if that helps

GWNJ-0850:669:GW1911032620th:6:1101:18304:1590  117 Scaffold23667   14021   0   *=  14021   0   TTCACTAGGGAGAATATAACTTTTGTTTAATTGTAGTTATATATAGTAGAAGATCTATTAAGCATGGATTTTATTATGTCCAGCTGTCAGAATTCACTTCTTTAATATAATTAATATTTTTTGTTTTACCAGAACTCATTCATCTAACAN<<-A--7--7<-FA----7-<--<F7A-7-7---7--J-F7-7-<--A-77-A<---7--7--7-7-A77--7-7-A-7--A7-FAA-A<<---<FAJF<JJF<--JJ<-F7<---7FJFJ<-F7AFAFA-A7F7<AJAA7-FAFA<AA#    MC:Z:150M   AS:i:0XS:i:0    RG:Z:a
GWNJ-0850:669:GW1911032620th:6:1101:18304:1590  185 Scaffold23667   14021   60  150M    =   14021   0   TTCTTTTTAATGGATTTATTTTCGTAACAACATGGCCAATGTTAAGGTCATTGAAATCATTATGAGGACAAAATGTTTTTGATATTCATTATAATTATTATAAACAATAAATATTTGTGTGTGTGTGTCAATTATTGATGAAAAAAATTN  JF<F-F<F<--7--AF<-JF<A-7A<-FA<7FJ7A---A7-7--7-7-7-<7-A<7-<FF7FFAF-<A-FA-A<77---7-FA-JA7<-FA-JJJJJJJ<<-<<<---JJF-A<FF-JAJFF7FJJJJJFJ<JFJFJJF-JJAFF-FAA#  NM:i:17MD:Z:4C13A22A0C2T1G8A19G11G2G9T2A12C1A13G11T3G0  AS:i:70 XS:i:21 RG:Z:a
GWNJ-0850:669:GW1911032620th:6:1101:7050:1713   81  Scaffold2303    9825    60  24M4D126M   =   9767    -212    CTTTGTTGTAATAAACATCTTGAGAATATTGATCAAATAATAAATAATAATAACGCATATATATATTATATATAAGTAAACAAATAAAATCTTGTTTACAGAATCACCTAATTTGTCATCAGTCACTTCAATACTCGAAAAGTACGTGTN  J<----FAF<7-7-A<F<A--77--JFA-7--7-F<7-JA7FA-<FA7JA-JF<-7F7FFJJAFF7F7-JFF7AFFJJJJJJJF<JJFFAF<-FF<FF<F-FFJJJJJ-JF<-<AJJJJJJJAJJJFA7JAFAFFJAJJJFFFFFAAAA#NM:i:9    MD:Z:24^GCTC0C6T4T6T105A0   MC:Z:83M4D67M   AS:i:119    XS:i:21 RG:Z:a
GWNJ-0850:669:GW1911032620th:6:1101:7050:1713   161 Scaffold2303    9767    60  83M4D67M    =   9825    212 NGTCAAACCAAATATCTACTACAAAAAAAAAATAATCTCACAGTTTCAATGTATTCTGCTTTGTTGTAATAAACATCTTGAGGATATTGTTCAATTAATAATTAATAATAACGCATTTATATATTATATATAAGTAATCAAATTAAATTT  #AAAAFFFAF<JJJJJA<-F-<<A--7F<FJJJJFJ-F<-FJFFJF<-<AFJ<7JAJJ-FFF7-AFJ-777-A--<-<A-77AAFJJFFJJ<-7AJJJF<-AA--A-77--7<7-7-7<F-A7AF-<7A--A--7<J-7-AA<-<-<<-<  NM:i:9MD:Z:0A82^CTCC33A20A5A4C1 MC:Z:24M4D126M  AS:i:122    XS:i:21 RG:Z:a
GWNJ-0850:669:GW1911032620th:6:1101:4137:1731   117 Scaffold39011   3930    0   *=  3930    0   GTTTTGAGAGACATCTCTCAACTATATGTTTTCAGCTCGATCCAGCAAATAACGTCATGATCAAGTTGCACGTGGGACACATAAACTGTGTAAACATGTATCCGAGGCCCTCATTGTAAAACCTGTGAACACTAGTTCGCGCGTGCGTAN---A7----<--A------7--77-AJA77----A7-A-777A-A-<7-AAFF7--<---<-7-----7-7--7----A7----A7-<A-F-A-F7---------7-----<-<---AA7-7FF<J--<F<F77<F-A7JJJFFFA<AA#    MC:Z:5S79M66S   AS:i:0XS:i:0    RG:Z:a
GWNJ-0850:669:GW1911032620th:6:1101:4137:1731   185 Scaffold39011   3930    60  5S79M66S    =   3930    0   TATTAAAGGAAGCCCTCGCATATATGGTTATAGACTTTATGCGTCACACATATCAATTGCTTTTCTCGCTGGTTACAGGATCGATCTGAAAACATATATTTCTTTCATTAGTTGCAGTACAAGAAAAATTAGATATGCTTACTATTATTN  7-77-<-7-7)-)A)A-7---------F--<7-7--7--7--7-------7--F<A7A7-7-FA-AA--<--7A<---7<-FJAAA-<----JAJFJ<-<-<-A7---<----<--<-----JFA-7F--F7J-JAF<-FJFJJF-AA<#  NM:i:6MD:Z:21T5C8T17A8T1A13 AS:i:49 XS:i:0  RG:Z:a
GWNJ-0850:669:GW1911032620th:6:1101:8156:1801   81  Scaffold13304   2184    60  74S76M  =   2130    -130    GGGACTCGCCACAAATGATCTTCTACCACCACCATACACATTTCGTATATCGACTGCATAGCGCGGTCCAGGTGTTGTATAACAGTGTAGGAGCAAGAGACAGCTGTGCCCACGCACAGTTTTTTCCTCTCTCGTTCTCATAGCTAGTGC  <))<))<--7---777----7---7A-777--7F7--7---7---7-<-77--77-7-<7--7-77----77--A-F-JF-AA<-7F-A-<7-AJA-A-<77---JFAA<7--<--JJF-F<-<7AF<-AAA-<7AA7JJFA7JFFAFAA  NM:i:0MD:Z:76   MC:Z:90S60M AS:i:76 XS:i:54 RG:Z:a
GWNJ-0850:669:GW1911032620th:6:1101:8156:1801   161 Scaffold13304   2130    60  90S60M  =   2184    130 NTCATGATAAGGGTAAAAGAACTAATGCAAATGGATGTTTTGATATATTTTTTCCATTGAATTGATTGTTGGGGGTCGCCGAAAATGATGTTCTCCCACCTCCATTTATGTTTCGTATATCTACGGCATAGCGAGGACTATGGTTTGTAT  #AA<FJAFJJ7FFFJJFA-7-FFJ-<<J--<JJJFFA<A-JJA--<FA-<--<-<FJ<-<7<J-<AAAJJ-F-<--7AA-AA<JAFF-F-AJ-FJ-F-77-A<-77---7<J-A-A-7F-FFFA-<)))--A7A<)AF---7-7--<--7  NM:i:1MD:Z:10G49    MC:Z:74S76M AS:i:55 XS:i:25 RG:Z:a
GWNJ-0850:669:GW1911032620th:6:1101:14316:1854  77  *   0   0   *   *0  0   GCATGTATGTTGCTATTGTTGTAGGGATCGTGACGCGATTCATGTTGCTGTGGACTACGTGTATTTATTTTTGTACTTGTCTTTTATGCTGATGTTGGAGTGCACGAGTTGAGAATGGGTATCGTATGTCGTCTTGGTGTTGGGATAATT  <AAAAJ<AAJJ-AJ-AFAJJ777-FJ-7--<F----7-7--<<-<FA---<7-<--<-<<<<<-<7-AFFA--<---<A--<7---<--7--<77----7---7-7-7---77--77-7-----7--------7<----7-7-)----7A  AS:i:0  XS:i:0  RG:Z:a
GWNJ-0850:669:GW1911032620th:6:1101:14316:1854  141 *   0   0   *   *0  0   NTTTAACATTAATTTCACGTGTTTCTTTGCATTATGAATGTTGTCTGGATCGCTGTGTCGCGTGGAGCGTGCAGGCTTGTGTGTTTTACACGTTTGATGATTCCGGCGACTCGCGTCGTTTAGGTTTCGGTGGTAGCTGTGTTTTTATTT  #AA<<A-A-A-A----A-<<A-<<F-FJF-7-<-<<--<--<<F---7-<--7<--7---7--7---7-77--7A-777F-<-<A-7-----<-7F7-7-7---7--77-7-7--F)-)-7---7-7--7<)-F-7--777--777----  AS:i:0  XS:i:0  RG:Z:a
shawnpg commented 4 years ago

Hi Tom,

Thanks for letting us know about this issue! Can you send the complete BAM file so we can debug why it is crashing?

Thanks,

Shawn

TomHarrop commented 4 years ago

Hi Shawn, here it is. Sorry about the gzipped bamfile (?), github wouldn't accept .bam. Thanks!

my.bam.gz