search

genome / bam-readcount

Count bases in BAM/CRAM files
MIT License
298 stars 95 forks source link

Run without errors but failed to produce the site list #64

Open drtamermansour opened 5 years ago

drtamermansour commented 5 years ago

I am using the script "bam_readcount_helper.py" to run bam-readcount (installed from bioconda) to generate site list. The input VCF has ~1million line. The script runs without errors except a massage that says b'Minimum mapping quality is set to 0\n' however fails to produce to produce any output files. When I tried to run the script with a small subset of the input VCF (only 5000 lines), everything worked fine and I got the expected tsv output files

susannasiebert commented 5 years ago

I don't know if it will solve your problem, but we recently released a bugfix to the script that might not be available on bioconda. The newest version of the script is available via the mgibio/bam_readcount_helper-cwl:1.1.1 docker container. I would appreciate it, if you could run the latest version of the script to confirm whether or not the problem still persists there.

drtamermansour commented 5 years ago

Unfortunately, I can not run docker on my server

susannasiebert commented 5 years ago

You can download the latest version from GitHub as well (https://raw.githubusercontent.com/genome/docker-bam_readcount_helper-cwl/1.1.1/bam_readcount_helper.py).

drtamermansour commented 5 years ago

@susannasiebert It did not work. Same message and no output files

susannasiebert commented 5 years ago

But it ran to completion or did you have to abort it? You might be running out of memory and the process that runs bam readcount gets killed but that's just a wild guess. Without being able to reproduce the error I don't have much to go on.

drtamermansour commented 5 years ago

It runs to completion. I would expect a message with termination signal if the subprocess is killed. I will rerun in a safer environment with high allocated resources to see. Does the message of b'Minimum mapping quality is set to 0\n' indicate something bad?

susannasiebert commented 5 years ago

It just a status messages indicating that you haven't set a minimum mapping quality threshold in your command so it defaulted to 0.

kaine1973 commented 2 years ago

I have the same issue running on docker:

        "Id": "170eca85c6f857fa46e2ee88865ad50a4a3a15a20703bac7c62e807aacecdd4d",
        "Created": "2022-03-21T05:46:11.301004263Z",
        "Path": "/usr/bin/bam-readcount",
        "Args": [
            "-l",
            "test.bed",
            "-f",
            "/DATA/GATK_bundle/b37/ftp.broadinstitute.org/bundle/hg38/Homo_sapiens_assembly38.fasta",
            "YJ0227-DC-2-N099.add.sort.bam",
            "chr1:75118320-75118325"
        ],

most of them are snp positions(rows with "#N/A" values in ref column):

start   end id  chorom  ref type    observed
3337275 3337275 rs7516137   1   #N/A    SNP_001 A/C/G
35926061    35926061    rs140864    1   G   INDEL_001   -/TTC
53005761    53005761    rs2307956   1   T   INDEL_002   #N/A
61320635    61320635    rs3067397   1   T   INDEL_003   -/AGATA
68104512    68104512    rs10607699  1   C   INDEL_004   -/CCT
75118324    75118324    rs6669519   1   #N/A    SNP_002 A/T
76156113    76156113    rs142717783 1   T   INDEL_005   -/TAA
85467307    85467307    rs3054057   1   A   INDEL_006   -/AACA
91772336    91772336    rs17878444  1   A   INDEL_007   -/CCTAAACAAAAATGGGAT
93163154    93163154    rs71852971  1   A   INDEL_008   -/ACTC
102915337   102915337   rs141853979 1   T   INDEL_009   -/TTTG
118960151   118960151   rs10923710  1   #N/A    SNP_003 G/T
119135915   119135915   rs138331044 1   C   INDEL_010   -/CATATGC
166132297   166132297   rs59841142  1   C   INDEL_011   -/CTAA/TAAC
181612985   181612985   rs76941525  1   T   INDEL_012   -/TATT
194909217   194909217   rs2307924   1   G   INDEL_013   -/ATTAAATA
197539771   197539771   rs4915551   1   #N/A    SNP_004 A/G
205415467   205415467   rs10572185  1   A   INDEL_014   -/GA
241179066   241179066   rs67487831  1   T   INDEL_015   -/TCAA
1135331 1135331 rs11277697  2   T   INDEL_016   -/TTAGG
34933612    34933612    rs35635240  2   C   INDEL_017   -/AT
55541987    55541987    rs113011930 2   T   INDEL_018   -/TTCT
74356331    74356331    rs3836186   2   T   INDEL_019   -/TA
99465100    99465100    rs28369942  2   A   INDEL_020   -/GACTT
108615100   108615100   rs35484769  2   T   INDEL_021   -/GGT
108897145   108897145   rs3827760   2   #N/A    SNP_005 C/T
148653792   148653792   rs34076006  2   G   INDEL_022   -/AAG
168943764   168943764   rs2307959   2   C   INDEL_023   -/CACA/CACG/CATG/G
212199882   212199882   rs3038275   2   G   INDEL_024   -/GACT
232016261   232016261   rs12473319  2   #N/A    SNP_006 C/G
234793461   234793461   rs146875868 2   T   INDEL_025   -/TCTT
41094731    41094731    rs2067235   3   C   INDEL_026   -/CAACCTGGATT
48811704    48811704    rs57455836  3   A   INDEL_027   -/AA
58021780    58021780    rs145191158 3   T   INDEL_028   -/TTTG
97258895    97258895    rs10662588  3   C   INDEL_029   -/TCTA
113016440   113016440   rs66477007  3   A   INDEL_030   -/TCTT
136618783   136618783   rs35136650  3   T   INDEL_031   -/TTA
139220153   139220153   rs12633011  3   #N/A    SNP_008 A/G
139228026   139228026   rs12632544  3   #N/A    SNP_007 A/C/T
140459797   140459797   rs10590825  3   C   INDEL_032   -/CCT
173756134   173756134   rs147792696 3   A   INDEL_033   -/ACACAA
8376859 8376859 rs3834231   4   T   INDEL_034   -/CCTA
47898170    47898170    rs145577149 4   A   INDEL_035   -/AAAT
78858786    78858786    rs10669491  4   T   INDEL_036   -/TAAT/TTAA
86985935    86985935    rs34843628  4   A   INDEL_037   -/TGAT
102341074   102341074   rs10642484  4   G   INDEL_038   -/GA
106968615   106968615   rs2308292   4   T   INDEL_039   -/TAAGT
113582580   113582580   rs35309403  4   A   INDEL_040   -/ACTG
118108898   118108898   rs35294396  4   A   INDEL_041   -/AAC
132139036   132139036   rs3064355   4   A   INDEL_042   -/AAG
153910747   153910747   rs2045323   4   #N/A    SNP_009 A/G
894997  894997  rs66843001  5   A   INDEL_043   -/A
28042975    28042975    rs1470608   5   #N/A    SNP_012 A/C
33951588    33951588    rs16891982  5   #N/A    SNP_010 A/C/G
33958854    33958854    rs28777 5   #N/A    SNP_011 A/C
42202012    42202012    rs11279993  5   A   INDEL_044   -/CAGGCCA
43456435    43456435    rs35416543  5   T   INDEL_045   -/T
63212914    63212914    rs1610935   5   G   INDEL_046   #N/A
77449242    77449242    rs1610937   5   A   INDEL_047   -/AGGA
114472240   114472240   rs66595817  5   C   INDEL_048   -/CTTTC
117313728   117313728   rs59363699  5   T   INDEL_049   -/ATTTA
127507347   127507347   rs1611095   5   C   INDEL_050   -/CCAG
129701718   129701718   rs1160980   5   T   INDEL_051   -/GAT
156235246   156235246   rs1305056   5   C   INDEL_052   -/CTACTGAT
396321  396321  rs12203592  6   #N/A    SNP_014 C/T
457748  457748  rs4959270   6   #N/A    SNP_015 A/C/T
6445552 6445552 rs60867863  6   A   INDEL_053   -/ATTA
31093302    31093302    rs112879447 6   T   INDEL_054   -/TATAAC
33705351    33705351    rs10701651  6   C   INDEL_055   -/CT
85101948    85101948    rs147468294 6   #N/A    SNP_013 -/C
94529411    94529411    rs140762    6   T   INDEL_056   -/AAATGTAA
97010245    97010245    rs2307652   6   A   INDEL_057   -/AAGC/AGCA
126360923   126360923   rs35634111  6   T   INDEL_058   -/T
134508084   134508084   rs34067069  6   T   INDEL_059   -/TTC
162610654   162610654   rs79225518  6   A   INDEL_060   -/AAG
166105012   166105012   rs35711971  6   C   INDEL_061   -/CA
36355785    36355785    rs3217112   7   T   INDEL_062   -/TAATA
77203403    77203403    rs67426579  7   G   INDEL_063   -/GTG
80253774    80253774    rs10673591  7   A   INDEL_064   -/AGAT
95417839    95417839    rs17879936  7   A   INDEL_065   -/GTAAGCATTGT
108190900   108190900   rs35351379  7   A   INDEL_066   -/ATG
111299928   111299928   rs1611048   7   A   INDEL_067   -/TAAG
134142604   134142604   rs142221201 7   A   INDEL_068   -/AAAG
139140459   139140459   rs10632896  7   T   INDEL_069   -/TAAAAA
154612852   154612852   rs1611001   7   T   INDEL_070   -/TTGGGCTTATT
9229746 9229746 rs111847181 8   #N/A    SNP_016 -/AC
19232270    19232270    rs2308072   8   A   INDEL_071   -/AAGG
28603444    28603444    rs112456713 8   C   INDEL_072   -/CT
58130742    58130742    rs75333006  8   T   INDEL_073   -/TC
62582834    62582834    rs60564093  8   A   INDEL_074   -/TCA
66041029    66041029    rs10642965  8   A   INDEL_075   -/CCG/CTG
99066698    99066698    rs11988731  8   #N/A    SNP_017 A/C/T
113952338   113952338   rs57981446  8   A   INDEL_076   -/AGGAG
118935562   118935562   rs3081400   8   C   INDEL_077   -/CTTTC
140066260   140066260   rs67365630  8   A   INDEL_078   -/ACT
12617325    12617325    rs140847    9   A   INDEL_079   -/CGTT
12709305    12709305    rs683   9   #N/A    SNP_018 A/C
16858086    16858086    rs10756819  9   #N/A    SNP_019 A/C/G/T
20930191    20930191    rs35464887  9   T   INDEL_080   -/TTTA
23281139    23281139    rs5897043   9   T   INDEL_081   -/AAGTAA
25018530    25018530    rs76158822  9   T   INDEL_082   -/TTAAG
34310394    34310394    rs5897566   9   T   INDEL_083   -/TAAC
87809523    87809523    rs113116058 9   A   INDEL_084   -/A
96235629    96235629    rs8190570   9   T   INDEL_085   -/CCACAAAGA
106389924   106389924   rs570278618 9   A   INDEL_086   #N/A
111781629   111781629   rs146332920 9   A   INDEL_087   -/AGG
119360528   119360528   rs74615971  9   A   INDEL_088   -/AC
124303359   124303359   rs67405073  9   T   INDEL_089   -/TGA
586488  586488  rs111740146 10  C   INDEL_090   -/CCTG
13857820    13857820    rs140683187 10  A   INDEL_091   -/AAC
27672761    27672761    rs4749259   10  #N/A    SNP_020 C/T
27721676    27721676    rs12258832  10  #N/A    SNP_021 A/G
31458334    31458334    rs200364632 10  T   INDEL_092   -/TGT
98769092    98769092    rs5787309   10  T   INDEL_093   -/TTATT
105760904   105760904   rs11277790  10  T   INDEL_094   -/TCCAACT
110260060   110260060   rs34287950  10  T   INDEL_095   -/TTT
118007993   118007993   rs3740550   10  #N/A    SNP_022 A/G
127150379   127150379   rs113501732 10  C   INDEL_096   -/CCTGT
11340101    11340101    rs55757518  11  C   INDEL_097   -/ACTCA
20507456    20507456    rs67100350  11  T   INDEL_098   -/TAGT
25010685    25010685    rs35135058  11  C   INDEL_099   -/AA/TA
36029406    36029406    rs11278940  11  A   INDEL_100   -/AGGACT
84269039    84269039    rs769299    11  T   INDEL_101   -/GATA
88647370    88647370    rs76382932  11  A   INDEL_102   -/AAG
89178528    89178528    rs1042602   11  #N/A    SNP_025 A/C
89277878    89277878    rs1393350   11  #N/A    SNP_024 A/G
89284793    89284793    rs1126809   11  #N/A    SNP_023 A/G
92379690    92379690    rs35883582  11  A   INDEL_103   -/AG
99640647    99640647    rs17174476  11  T   INDEL_104   #N/A
103356515   103356515   rs3076465   11  T   INDEL_105   -/ATAA
111622715   111622715   rs35499279  11  T   INDEL_106   -/TAAA
126418977   126418977   rs33972805  11  C   INDEL_107   -/CT
21026266    21026266    rs35962397  12  T   INDEL_108   -/TT
21095647    21095647    rs75788814  12  A   INDEL_109   -/A
39772872    39772872    rs67939200  12  T   INDEL_110   -/TCA
43885415    43885415    rs63547361  12  T   INDEL_111   -/T/TT/TTT/TTTT
66466596    66466596    rs145941537 12  A   INDEL_112   -/AATT
88934558    88934558    rs12821256  12  #N/A    SNP_026 A/C/G/T
94347169    94347169    rs2307570   12  T   INDEL_113   #N/A
130458730   130458730   rs67264216  12  T   INDEL_114   -/TGTCG
27663744    27663744    rs35453727  13  A   INDEL_115   -/AGA
30754246    30754246    rs17238892  13  A   INDEL_116   -/AGAGAAAGCTGAAG
101509904   101509904   rs35065898  13  A   INDEL_117   -/ACTT
105793575   105793575   rs145040038 13  T   INDEL_118   -/TTTTTT
107215851   107215851   rs60575667  13  A   INDEL_119   -/AAG
26626846    26626846    rs34924537  14  A   INDEL_120   -/ATC
27365040    27365040    rs141910158 14  T   INDEL_121   -/TTC
57583364    57583364    rs2308163   14  T   INDEL_122   -/TAAT/TGAT
61723290    61723290    rs3059957   14  A   INDEL_123   -/ACA
66663833    66663833    rs561160795 14  T   INDEL_124   -/TGG
77482925    77482925    rs5809836   14  G   INDEL_125   -/G
91462938    91462938    rs61490765  14  T   INDEL_126   -/TTAAT
92307319    92307319    rs12896399  14  #N/A    SNP_029 G/T
92334859    92334859    rs2402130   14  #N/A    SNP_027 A/G
92416482    92416482    rs17128291  14  #N/A    SNP_028 A/G
105625407   105625407   rs35171885  14  A   INDEL_127   -/A
105666087   105666087   rs35112164  14  T   INDEL_128   -/AC
105708700   105708700   rs58621233  14  C   INDEL_129   lengthTooLong
105801333   105801333   rs571755931 14  G   INDEL_130   -/G
25871708    25871708    rs139762874 15  G   INDEL_131   -/GATA
26574760    26574760    rs11444232  15  G   INDEL_132   -/G
27942626    27942626    rs1545397   15  #N/A    SNP_039 A/T
27951891    27951891    rs1800414   15  #N/A    SNP_031 A/G/T
27985172    27985172    rs1800407   15  #N/A    SNP_033 A/G
28026629    28026629    rs12441727  15  #N/A    SNP_037 A/G
28111713    28111713    rs1129038   15  #N/A    SNP_035 A/G
28120472    28120472    rs12913832  15  #N/A    SNP_036 A/G
28208069    28208069    rs2238289   15  #N/A    SNP_034 C/T
28251049    28251049    rs6497292   15  #N/A    SNP_038 A/G
28285036    28285036    rs1667394   15  #N/A    SNP_032 A/G/T
29452599    29452599    rs34419736  15  A   INDEL_133   -/AAG
38298549    38298549    rs77635204  15  A   INDEL_134   -/AGAA
48134287    48134287    rs1426654   15  #N/A    SNP_030 A/G/T
49138327    49138327    rs34421865  15  C   INDEL_135   -/CTCT
64067957    64067957    rs58269429  15  T   INDEL_136   -/T/TT
67214196    67214196    rs66739142  15  T   INDEL_137   -/TCTTT
89321086    89321086    rs2307433   15  C   INDEL_138   -/GTAG
94535647    94535647    rs10626599  15  T   INDEL_139   -/TGTGC
4370817 4370817 rs35193388  16  C   INDEL_140   -/C/CC
17366108    17366108    rs10610201  16  T   INDEL_141   -/TCAT
55657913    55657913    rs1610905   16  T   INDEL_142   -/GCAGGACTGGGCACC
67157988    67157988    rs11282585  16  T   INDEL_143   -/TCCAG
83976701    83976701    rs10641793  16  T   INDEL_144   -/TGT
89317317    89317317    rs3114908   16  #N/A    SNP_049 A/G
89645534    89645534    rs145010051 16  G   INDEL_145   -/GGA
89768914    89768914    rs3069460   16  C   INDEL_146   -/AGTACTG
89917970    89917970    rs3212355   16  #N/A    SNP_048 C/T
89919436    89919436    rs1805005   16  #N/A    SNP_050 G/T
89919510    89919510    rs1805006   16  #N/A    SNP_045 A/C/G
89919532    89919532    rs2228479   16  #N/A    SNP_044 A/C/G
89919683    89919683    rs11547464  16  #N/A    SNP_042 A/G
89919709    89919709    rs1805007   16  #N/A    SNP_040 A/C/G/T
89919714    89919714    rs201326893 16  #N/A    SNP_052 A/C
89919722    89919722    rs1110400   16  #N/A    SNP_047 C/T
89919736    89919736    rs1805008   16  #N/A    SNP_041 C/T
89919746    89919746    rs885479    16  #N/A    SNP_043 A/G
89920138    89920138    rs1805009   16  #N/A    SNP_051 A/C/G
89957798    89957798    rs8051733   16  #N/A    SNP_046 A/G
4066839 4066839 rs2307581   17  #N/A    INDEL_147   -/TCCTATTCTACTCTGAAT
16181672    16181672    rs1305047   17  A   INDEL_148   -/CACA
20179106    20179106    rs16711 17  T   INDEL_149   -/CCTA/TTTCTTCCTA/TTTCTTTCTA
42107367    42107367    rs55830333  17  T   INDEL_150   -/A/AA/AAA/TA/TAA/TAAA/TAAAA
44114012    44114012    rs66913380  17  G   INDEL_151   -/GCCA
46737952    46737952    rs530345654 17  A   INDEL_152   lengthTooLong
53108999    53108999    rs72031009  17  T   INDEL_153   -/TAGAG
63340461    63340461    rs3833118   17  G   INDEL_154   -/C
71451565    71451565    rs8068343   17  #N/A    SNP_053 A/C/G/T
4252512 4252512 rs33979673  18  A   INDEL_155   -/A/AA
28457382    28457382    rs77206391  18  A   INDEL_156   -/ACAA
65851100    65851100    rs5825653   18  G   INDEL_157   -/A/G
15268500    15268500    rs33971783  19  T   INDEL_158   -/TGTT
16661769    16661769    rs543659729 19  T   INDEL_159   -/TA
32599329    32599329    rs72085595  19  T   INDEL_160   -/TGTC
38504108    38504108    rs34529638  19  C   INDEL_161   -/CCT
48638150    48638150    rs5828358   19  A   INDEL_162   -/CAGA
17434375    17434375    rs11471448  20  T   INDEL_163   -/GCA
25297829    25297829    rs16438 20  G   INDEL_164   -/CCCAC/CCCCA
31989531    31989531    rs59000476  20  C   INDEL_165   -/C
34077942    34077942    rs6059655   20  #N/A    SNP_054 A/G
34197406    34197406    rs6119471   20  #N/A    SNP_056 C/G
34259192    34259192    rs35455305  20  A   INDEL_166   -/AA/AG
34630286    34630286    rs2378249   20  #N/A    SNP_055 A/G
43039365    43039365    rs59586141  20  A   INDEL_167   -/AAC
60350158    60350158    rs10699638  20  A   INDEL_168   -/AC
16154963    16154963    rs71331798  21  A   INDEL_169   lengthTooLong
28469929    28469929    rs9980535   21  #N/A    SNP_057 A/G
33288451    33288451    rs8178524   21  G   INDEL_170   -/GAAGTCTGAGG/GAAGTCTGAGT
33680694    33680694    rs538690481 21  T   INDEL_171   -/TCTGAA
44937300    44937300    rs10654444  21  G   INDEL_172   -/GAG
25354850    25354850    rs16388 22  G   INDEL_173   -/ATTGCC
29160990    29160990    rs34305529  22  A   INDEL_174   -/AAAG
35305906    35305906    rs6481  22  G   INDEL_175   -/GTGGA
36873500    36873500    rs34123598  22  C   INDEL_176   -/ATCT
37013845    37013845    rs16363 22  T   INDEL_177   -/TGTTT/TGTTTTGTTT
40215285    40215285    rs34831294  22  T   INDEL_178   -/T/TT
6133168 6133168 rs35954471  X   C   INDEL_179   -/CAT
7138903 7138903 rs10671504  X   C   INDEL_180   -/CC/CCTTTTT
9795098 9795098 rs143123845 X   T   INDEL_181   lengthTooLong
10266797    10266797    rs3048996   X   A   INDEL_182   -/ATC
12554074    12554074    rs36094418  X   A   INDEL_183   -/AGA
12566942    12566942    rs79829945  X   C   INDEL_184   -/ACTAT
12894743    12894743    rs25581 X   T   INDEL_185   -/TGAGA
13693178    13693178    rs10699224  X   G   INDEL_186   -/ATTA/GTTA
13716801    13716801    rs3216913   X   T   INDEL_187   -/TTTG/TTTT
15312838    15312838    rs58595330  X   T   INDEL_188   -/CTTTAA
28965958    28965958    rs60283667  X   A   INDEL_189   -/TCAC
29139857    29139857    rs2308280   X   T   INDEL_190   -/TTA
37796483    37796483    rs35574346  X   A   INDEL_191   -/AAAC
45679953    45679953    rs4030406   X   A   INDEL_192   -/ATTA
47820987    47820987    rs16637 X   T   INDEL_193   -/CAACCAAT
77614999    77614999    rs45449991  X   G   INDEL_194   -/AAC
80684645    80684645    rs71671860  X   C   INDEL_195   -/CTT
84353649    84353649    rs34763847  X   A   INDEL_196   -/ATAG
86360699    86360699    rs199731653 X   A   INDEL_197   -/ATC
88754687    88754687    rs3215490   X   C   INDEL_198   -/GACA
94137006    94137006    rs2307707   X   C   INDEL_199   -/GTCT
97600747    97600747    rs363794    X   A   INDEL_200   -/ATA
99076816    99076816    rs11277082  X   C   INDEL_201   -/ACCTCACTCA
102020346   102020346   rs16368 X   A   INDEL_202   -/AGA
104096999   104096999   rs16367 X   A   INDEL_203   -/AAGT
104844603   104844603   rs56820033  X   A   INDEL_204   -/CAAA
113288716   113288716   rs61260787  X   T   INDEL_205   -/GTCCTT
113291823   113291823   rs3859989   X   A   INDEL_206   -/AAG
115556974   115556974   rs149102585 X   T   INDEL_207   -/TTTG
117768021   117768021   rs57608175  X   C   INDEL_208   -/GGTCATCACGAG
120704050   120704050   rs59605609  X   A   INDEL_209   -/TTAAA
125673141   125673141   rs1160845   X   C   INDEL_210   -/AGG
128824407   128824407   rs16397 X   G   INDEL_211   -/GTG
136743271   136743271   rs2308033   X   A   INDEL_212   -/CTT
138925426   138925426   rs17394 X   A   INDEL_213   -/AAAA/AAAAG
139182054   139182054   rs57843641  X   T   INDEL_214   -/ATAATA
151229201   151229201   rs3077884   X   A   INDEL_215   -/CTT
151290512   151290512   rs2307741   X   C   INDEL_216   -/CCTCTGAAC
312722  312722  rs376744795 Y   #N/A    INDEL_217   -/TACCCC/TACTCC/TATCCC
1467037 1467037 rs201342692 Y   #N/A    INDEL_218   -/ACTC/CCTC
7954743 7954743 rs771783753 Y   A   INDEL_219   -/ATC
12902575    12902575    rs2032676   Y   A   INDEL_220   -/CAAA
13396820    13396820    rs199815934 Y   C   INDEL_221   -/CTTCT
14259886    14259886    rs76041101  Y   A   INDEL_222   -/AGT
19571279    19571279    rs3908  Y   G   INDEL_223   -/G
19603426    19603426    rs759551978 Y   A   INDEL_224   -/AGAT