Error executing R script in Amber - Githubissues

hartwigmedical / hmftools

Various algorithms for analysing genomics data

GNU General Public License v3.0

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Error executing R script in Amber #393

Closed msubirana closed 1 year ago

msubirana commented 1 year ago

I'm running the pipeline using:

./pipeline/scripts/run_pipeline ./pipeline/scripts data HMFtools-Resources_dna_pipeline_v5_32_38_hmf_dna_pipeline_resources.38_v5.32 HMFtools-Resources_dna_pipeline_v5_32_hmf_dna_pipeline_tools_v5.32 NET25_TI,NET25_BL V38 WGS 10 16

But during the R runs, it breaks. I have installed all the R dependencies, but it seems that the /tmp/script17671355960897683989.R file is not present. Then, Purple does not have the .cobalt.ratio.pcf files, and it breaks. Do you have any suggestions?

11:23:42.385 INFO  [worker-0] - Executing R script via command: Rscript /tmp/script17671355960897683989.R /gpfs42/robbyfs/scratch/lab_lpasquali/shared_data/projects-data/insulinomas-genetics/output/gpl/NET25_TI/cobalt/NET25_TI.cobalt.ratio.tsv.gz tumorGCRatio /gpfs42/robbyfs/scratch/lab_lpasquali/shared_data/projects-data/insulinomas-genetics/output/gpl/NET25_TI/cobalt/NET25_TI.cobalt.ratio.pcf 100
11:23:42.385 INFO  [worker-3] - Executing R script via command: Rscript /tmp/script555115699108876182.R /gpfs42/robbyfs/scratch/lab_lpasquali/shared_data/projects-data/insulinomas-genetics/output/gpl/NET25_TI/cobalt/NET25_TI.cobalt.ratio.tsv.gz referenceGCDiploidRatio /gpfs42/robbyfs/scratch/lab_lpasquali/shared_data/projects-data/insulinomas-genetics/output/gpl/NET25_TI/cobalt/NET25_BL.cobalt.ratio.pcf 100

11:23:43.472 FATAL [worker-0] - Error executing R script. Examine error file /tmp/ratioSegmentation.R10424677975166030996.error for details.
11:23:43.472 FATAL [worker-3] - Error executing R script. Examine error file /tmp/ratioSegmentation.R14431321662434737205.error for details.
Exception in thread "main" java.util.concurrent.ExecutionException: java.io.IOException: R execution failed. Unable to complete segmentation.
    at java.base/java.util.concurrent.FutureTask.report(FutureTask.java:122)
    at java.base/java.util.concurrent.FutureTask.get(FutureTask.java:191)
    at com.hartwig.hmftools.cobalt.RatioSegmentation.applyRatioSegmentation(RatioSegmentation.java:34)
    at com.hartwig.hmftools.cobalt.CobaltApplication.run(CobaltApplication.java:133)
    at com.hartwig.hmftools.cobalt.CobaltApplication.main(CobaltApplication.java:69)
Caused by: java.io.IOException: R execution failed. Unable to complete segmentation.
    at com.hartwig.hmftools.cobalt.RatioSegmentation.ratioSegmentation(RatioSegmentation.java:48)
    at com.hartwig.hmftools.cobalt.RatioSegmentation.lambda$applyRatioSegmentation$0(RatioSegmentation.java:25)
    at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
    at java.base/java.lang.Thread.run(Thread.java:833)

hongwingl commented 1 year ago

Hi,

Do you have the files /tmp/ratioSegmentation.R14431321662434737205.error and /tmp/ratioSegmentation.R14431321662434737205.error? They should contain the actual errors.

msubirana commented 1 year ago

The files do no exists...

And the /tmp/script17671355960897683989.R also does not exist

hongwingl commented 1 year ago

I see. Is it possible that the /tmp directory is not writable?

msubirana commented 1 year ago

yes, I'm running in the cluster and I have limited rights. Is it possible to redefine the tmp path?

hongwingl commented 1 year ago

The source code uses java standard method to create a temp file. We do not explicitly control how the tmp path is managed, as it is different between operating systems, and therefore beyond our scope.

hongwingl commented 1 year ago

Would you mind pasting the command line argument for cobalt here, and also the bam file header? You can get the bam header with the command: samtools view -H <bam file>

msubirana commented 1 year ago

amber=/gpfs42/robbyfs/scratch/lab_lpasquali/msubirana/marc/refs/hmftools/amber-3.9.jar
cobalt=/gpfs42/robbyfs/scratch/lab_lpasquali/msubirana/marc/refs/hmftools/cobalt-1.14.jar

tumor_name=NET25_TI
tumor_bam=/gpfs42/robbyfs/scratch/lab_lpasquali/msubirana/marc/insulinomas/data/WGS/BAM/INS/all_ok/NET25_TI.bam
ctrl_name=NET25_BL
ctrl_bam=/gpfs42/robbyfs/scratch/lab_lpasquali/msubirana/marc/insulinomas/data/WGS/BAM/INS/all_ok/NET25_BL.bam
output_dir=/gpfs42/robbyfs/scratch/lab_lpasquali/shared_data/projects-data/insulinomas-genetics/output/hmftools
GermlineHetPon=/gpfs42/robbyfs/scratch/lab_lpasquali/msubirana/marc/refs/HMFtools-Resources_dna_pipeline_v5_32_38_hmf_dna_pipeline_resources.38_v5.32/copy_number/GermlineHetPon.38.vcf.gz
GC_profile=/gpfs42/robbyfs/scratch/lab_lpasquali/msubirana/marc/refs/HMFtools-Resources_dna_pipeline_v5_32_38_hmf_dna_pipeline_resources.38_v5.32/copy_number/GC_profile.1000bp.38.cnp
output_amber=${output_dir}/amber
output_cobalt=${output_dir}/cobalt

threads=16

mkdir -p $output_amber
mkdir -p $output_cobalt

# cobalt

java -jar -Xmx8G $cobalt -reference $ctrl_name -reference_bam $ctrl_bam -tumor $tumor_name -tumor_bam $tumor_bam -output_dir $output_cobalt -threads $threads -gc_profile $GC_profile

@HD VN:1.6  SO:coordinate
@SQ SN:chr1 LN:248956422
@SQ SN:chr2 LN:242193529
@SQ SN:chr3 LN:198295559
@SQ SN:chr4 LN:190214555
@SQ SN:chr5 LN:181538259
@SQ SN:chr6 LN:170805979
@SQ SN:chr7 LN:159345973
@SQ SN:chr8 LN:145138636
@SQ SN:chr9 LN:138394717
@SQ SN:chr10    LN:133797422
@SQ SN:chr11    LN:135086622
@SQ SN:chr12    LN:133275309
@SQ SN:chr13    LN:114364328
@SQ SN:chr14    LN:107043718
@SQ SN:chr15    LN:101991189
@SQ SN:chr16    LN:90338345
@SQ SN:chr17    LN:83257441
@SQ SN:chr18    LN:80373285
@SQ SN:chr19    LN:58617616
@SQ SN:chr20    LN:64444167
@SQ SN:chr21    LN:46709983
@SQ SN:chr22    LN:50818468
@SQ SN:chrX LN:156040895
@SQ SN:chrY LN:57227415
@SQ SN:chrM LN:16569
@SQ SN:chr1_KI270706v1_random   LN:175055
@SQ SN:chr1_KI270707v1_random   LN:32032
@SQ SN:chr1_KI270708v1_random   LN:127682
@SQ SN:chr1_KI270709v1_random   LN:66860
@SQ SN:chr1_KI270710v1_random   LN:40176
@SQ SN:chr1_KI270711v1_random   LN:42210
@SQ SN:chr1_KI270712v1_random   LN:176043
@SQ SN:chr1_KI270713v1_random   LN:40745
@SQ SN:chr1_KI270714v1_random   LN:41717
@SQ SN:chr2_KI270715v1_random   LN:161471
@SQ SN:chr2_KI270716v1_random   LN:153799
@SQ SN:chr3_GL000221v1_random   LN:155397
@SQ SN:chr4_GL000008v2_random   LN:209709
@SQ SN:chr5_GL000208v1_random   LN:92689
@SQ SN:chr9_KI270717v1_random   LN:40062
@SQ SN:chr9_KI270718v1_random   LN:38054
@SQ SN:chr9_KI270719v1_random   LN:176845
@SQ SN:chr9_KI270720v1_random   LN:39050
@SQ SN:chr11_KI270721v1_random  LN:100316
@SQ SN:chr14_GL000009v2_random  LN:201709
@SQ SN:chr14_GL000225v1_random  LN:211173
@SQ SN:chr14_KI270722v1_random  LN:194050
@SQ SN:chr14_GL000194v1_random  LN:191469
@SQ SN:chr14_KI270723v1_random  LN:38115
@SQ SN:chr14_KI270724v1_random  LN:39555
@SQ SN:chr14_KI270725v1_random  LN:172810
@SQ SN:chr14_KI270726v1_random  LN:43739
@SQ SN:chr15_KI270727v1_random  LN:448248
@SQ SN:chr16_KI270728v1_random  LN:1872759
@SQ SN:chr17_GL000205v2_random  LN:185591
@SQ SN:chr17_KI270729v1_random  LN:280839
@SQ SN:chr17_KI270730v1_random  LN:112551
@SQ SN:chr22_KI270731v1_random  LN:150754
@SQ SN:chr22_KI270732v1_random  LN:41543
@SQ SN:chr22_KI270733v1_random  LN:179772
@SQ SN:chr22_KI270734v1_random  LN:165050
@SQ SN:chr22_KI270735v1_random  LN:42811
@SQ SN:chr22_KI270736v1_random  LN:181920
@SQ SN:chr22_KI270737v1_random  LN:103838
@SQ SN:chr22_KI270738v1_random  LN:99375
@SQ SN:chr22_KI270739v1_random  LN:73985
@SQ SN:chrY_KI270740v1_random   LN:37240
@SQ SN:chrUn_KI270302v1 LN:2274
@SQ SN:chrUn_KI270304v1 LN:2165
@SQ SN:chrUn_KI270303v1 LN:1942
@SQ SN:chrUn_KI270305v1 LN:1472
@SQ SN:chrUn_KI270322v1 LN:21476
@SQ SN:chrUn_KI270320v1 LN:4416
@SQ SN:chrUn_KI270310v1 LN:1201
@SQ SN:chrUn_KI270316v1 LN:1444
@SQ SN:chrUn_KI270315v1 LN:2276
@SQ SN:chrUn_KI270312v1 LN:998
@SQ SN:chrUn_KI270311v1 LN:12399
@SQ SN:chrUn_KI270317v1 LN:37690
@SQ SN:chrUn_KI270412v1 LN:1179
@SQ SN:chrUn_KI270411v1 LN:2646
@SQ SN:chrUn_KI270414v1 LN:2489
@SQ SN:chrUn_KI270419v1 LN:1029
@SQ SN:chrUn_KI270418v1 LN:2145
@SQ SN:chrUn_KI270420v1 LN:2321
@SQ SN:chrUn_KI270424v1 LN:2140
@SQ SN:chrUn_KI270417v1 LN:2043
@SQ SN:chrUn_KI270422v1 LN:1445
@SQ SN:chrUn_KI270423v1 LN:981
@SQ SN:chrUn_KI270425v1 LN:1884
@SQ SN:chrUn_KI270429v1 LN:1361
@SQ SN:chrUn_KI270442v1 LN:392061
@SQ SN:chrUn_KI270466v1 LN:1233
@SQ SN:chrUn_KI270465v1 LN:1774
@SQ SN:chrUn_KI270467v1 LN:3920
@SQ SN:chrUn_KI270435v1 LN:92983
@SQ SN:chrUn_KI270438v1 LN:112505
@SQ SN:chrUn_KI270468v1 LN:4055
@SQ SN:chrUn_KI270510v1 LN:2415
@SQ SN:chrUn_KI270509v1 LN:2318
@SQ SN:chrUn_KI270518v1 LN:2186
@SQ SN:chrUn_KI270508v1 LN:1951
@SQ SN:chrUn_KI270516v1 LN:1300
@SQ SN:chrUn_KI270512v1 LN:22689
@SQ SN:chrUn_KI270519v1 LN:138126
@SQ SN:chrUn_KI270522v1 LN:5674
@SQ SN:chrUn_KI270511v1 LN:8127
@SQ SN:chrUn_KI270515v1 LN:6361
@SQ SN:chrUn_KI270507v1 LN:5353
@SQ SN:chrUn_KI270517v1 LN:3253
@SQ SN:chrUn_KI270529v1 LN:1899
@SQ SN:chrUn_KI270528v1 LN:2983
@SQ SN:chrUn_KI270530v1 LN:2168
@SQ SN:chrUn_KI270539v1 LN:993
@SQ SN:chrUn_KI270538v1 LN:91309
@SQ SN:chrUn_KI270544v1 LN:1202
@SQ SN:chrUn_KI270548v1 LN:1599
@SQ SN:chrUn_KI270583v1 LN:1400
@SQ SN:chrUn_KI270587v1 LN:2969
@SQ SN:chrUn_KI270580v1 LN:1553
@SQ SN:chrUn_KI270581v1 LN:7046
@SQ SN:chrUn_KI270579v1 LN:31033
@SQ SN:chrUn_KI270589v1 LN:44474
@SQ SN:chrUn_KI270590v1 LN:4685
@SQ SN:chrUn_KI270584v1 LN:4513
@SQ SN:chrUn_KI270582v1 LN:6504
@SQ SN:chrUn_KI270588v1 LN:6158
@SQ SN:chrUn_KI270593v1 LN:3041
@SQ SN:chrUn_KI270591v1 LN:5796
@SQ SN:chrUn_KI270330v1 LN:1652
@SQ SN:chrUn_KI270329v1 LN:1040
@SQ SN:chrUn_KI270334v1 LN:1368
@SQ SN:chrUn_KI270333v1 LN:2699
@SQ SN:chrUn_KI270335v1 LN:1048
@SQ SN:chrUn_KI270338v1 LN:1428
@SQ SN:chrUn_KI270340v1 LN:1428
@SQ SN:chrUn_KI270336v1 LN:1026
@SQ SN:chrUn_KI270337v1 LN:1121
@SQ SN:chrUn_KI270363v1 LN:1803
@SQ SN:chrUn_KI270364v1 LN:2855
@SQ SN:chrUn_KI270362v1 LN:3530
@SQ SN:chrUn_KI270366v1 LN:8320
@SQ SN:chrUn_KI270378v1 LN:1048
@SQ SN:chrUn_KI270379v1 LN:1045
@SQ SN:chrUn_KI270389v1 LN:1298
@SQ SN:chrUn_KI270390v1 LN:2387
@SQ SN:chrUn_KI270387v1 LN:1537
@SQ SN:chrUn_KI270395v1 LN:1143
@SQ SN:chrUn_KI270396v1 LN:1880
@SQ SN:chrUn_KI270388v1 LN:1216
@SQ SN:chrUn_KI270394v1 LN:970
@SQ SN:chrUn_KI270386v1 LN:1788
@SQ SN:chrUn_KI270391v1 LN:1484
@SQ SN:chrUn_KI270383v1 LN:1750
@SQ SN:chrUn_KI270393v1 LN:1308
@SQ SN:chrUn_KI270384v1 LN:1658
@SQ SN:chrUn_KI270392v1 LN:971
@SQ SN:chrUn_KI270381v1 LN:1930
@SQ SN:chrUn_KI270385v1 LN:990
@SQ SN:chrUn_KI270382v1 LN:4215
@SQ SN:chrUn_KI270376v1 LN:1136
@SQ SN:chrUn_KI270374v1 LN:2656
@SQ SN:chrUn_KI270372v1 LN:1650
@SQ SN:chrUn_KI270373v1 LN:1451
@SQ SN:chrUn_KI270375v1 LN:2378
@SQ SN:chrUn_KI270371v1 LN:2805
@SQ SN:chrUn_KI270448v1 LN:7992
@SQ SN:chrUn_KI270521v1 LN:7642
@SQ SN:chrUn_GL000195v1 LN:182896
@SQ SN:chrUn_GL000219v1 LN:179198
@SQ SN:chrUn_GL000220v1 LN:161802
@SQ SN:chrUn_GL000224v1 LN:179693
@SQ SN:chrUn_KI270741v1 LN:157432
@SQ SN:chrUn_GL000226v1 LN:15008
@SQ SN:chrUn_GL000213v1 LN:164239
@SQ SN:chrUn_KI270743v1 LN:210658
@SQ SN:chrUn_KI270744v1 LN:168472
@SQ SN:chrUn_KI270745v1 LN:41891
@SQ SN:chrUn_KI270746v1 LN:66486
@SQ SN:chrUn_KI270747v1 LN:198735
@SQ SN:chrUn_KI270748v1 LN:93321
@SQ SN:chrUn_KI270749v1 LN:158759
@SQ SN:chrUn_KI270750v1 LN:148850
@SQ SN:chrUn_KI270751v1 LN:150742
@SQ SN:chrUn_KI270752v1 LN:27745
@SQ SN:chrUn_KI270753v1 LN:62944
@SQ SN:chrUn_KI270754v1 LN:40191
@SQ SN:chrUn_KI270755v1 LN:36723
@SQ SN:chrUn_KI270756v1 LN:79590
@SQ SN:chrUn_KI270757v1 LN:71251
@SQ SN:chrUn_GL000214v1 LN:137718
@SQ SN:chrUn_KI270742v1 LN:186739
@SQ SN:chrUn_GL000216v2 LN:176608
@SQ SN:chrUn_GL000218v1 LN:161147
@SQ SN:chrEBV   LN:171823
@RG ID:NET25_BL PL:ILLUMINA PU:1    SM:NET25_BL
@PG ID:bwa  PN:bwa  VN:0.7.17-r1194-dirty   CL:bwa mem -M -t 48 -R @RG\tID:NET25_BL\tPL:ILLUMINA\tPU:1\tSM:NET25_BL /gpfs42/robbyfs/scratch/lab_lpasquali/msubirana/ref/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa /gpfs42/robbyfs/scratch/lab_lpasquali/msubirana/marc/insulinomas/data/WGS/BAM/toDo/NET25_BL_R1.fq /gpfs42/robbyfs/scratch/lab_lpasquali/msubirana/marc/insulinomas/data/WGS/BAM/toDo/NET25_BL_R2.fq
@PG ID:SAMBLASTER   VN:0.1.24   CL:samblaster -i stdin -o stdout -M
@PG ID:samtools PN:samtools PP:SAMBLASTER   VN:1.12 CL:samtools view -H /gpfs42/robbyfs/scratch/lab_lpasquali/msubirana/marc/insulinomas/data/WGS/BAM/INS/all_ok/NET25_BL.bam

@HD VN:1.6  SO:coordinate
@SQ SN:chr1 LN:248956422
@SQ SN:chr2 LN:242193529
@SQ SN:chr3 LN:198295559
@SQ SN:chr4 LN:190214555
@SQ SN:chr5 LN:181538259
@SQ SN:chr6 LN:170805979
@SQ SN:chr7 LN:159345973
@SQ SN:chr8 LN:145138636
@SQ SN:chr9 LN:138394717
@SQ SN:chr10    LN:133797422
@SQ SN:chr11    LN:135086622
@SQ SN:chr12    LN:133275309
@SQ SN:chr13    LN:114364328
@SQ SN:chr14    LN:107043718
@SQ SN:chr15    LN:101991189
@SQ SN:chr16    LN:90338345
@SQ SN:chr17    LN:83257441
@SQ SN:chr18    LN:80373285
@SQ SN:chr19    LN:58617616
@SQ SN:chr20    LN:64444167
@SQ SN:chr21    LN:46709983
@SQ SN:chr22    LN:50818468
@SQ SN:chrX LN:156040895
@SQ SN:chrY LN:57227415
@SQ SN:chrM LN:16569
@SQ SN:chr1_KI270706v1_random   LN:175055
@SQ SN:chr1_KI270707v1_random   LN:32032
@SQ SN:chr1_KI270708v1_random   LN:127682
@SQ SN:chr1_KI270709v1_random   LN:66860
@SQ SN:chr1_KI270710v1_random   LN:40176
@SQ SN:chr1_KI270711v1_random   LN:42210
@SQ SN:chr1_KI270712v1_random   LN:176043
@SQ SN:chr1_KI270713v1_random   LN:40745
@SQ SN:chr1_KI270714v1_random   LN:41717
@SQ SN:chr2_KI270715v1_random   LN:161471
@SQ SN:chr2_KI270716v1_random   LN:153799
@SQ SN:chr3_GL000221v1_random   LN:155397
@SQ SN:chr4_GL000008v2_random   LN:209709
@SQ SN:chr5_GL000208v1_random   LN:92689
@SQ SN:chr9_KI270717v1_random   LN:40062
@SQ SN:chr9_KI270718v1_random   LN:38054
@SQ SN:chr9_KI270719v1_random   LN:176845
@SQ SN:chr9_KI270720v1_random   LN:39050
@SQ SN:chr11_KI270721v1_random  LN:100316
@SQ SN:chr14_GL000009v2_random  LN:201709
@SQ SN:chr14_GL000225v1_random  LN:211173
@SQ SN:chr14_KI270722v1_random  LN:194050
@SQ SN:chr14_GL000194v1_random  LN:191469
@SQ SN:chr14_KI270723v1_random  LN:38115
@SQ SN:chr14_KI270724v1_random  LN:39555
@SQ SN:chr14_KI270725v1_random  LN:172810
@SQ SN:chr14_KI270726v1_random  LN:43739
@SQ SN:chr15_KI270727v1_random  LN:448248
@SQ SN:chr16_KI270728v1_random  LN:1872759
@SQ SN:chr17_GL000205v2_random  LN:185591
@SQ SN:chr17_KI270729v1_random  LN:280839
@SQ SN:chr17_KI270730v1_random  LN:112551
@SQ SN:chr22_KI270731v1_random  LN:150754
@SQ SN:chr22_KI270732v1_random  LN:41543
@SQ SN:chr22_KI270733v1_random  LN:179772
@SQ SN:chr22_KI270734v1_random  LN:165050
@SQ SN:chr22_KI270735v1_random  LN:42811
@SQ SN:chr22_KI270736v1_random  LN:181920
@SQ SN:chr22_KI270737v1_random  LN:103838
@SQ SN:chr22_KI270738v1_random  LN:99375
@SQ SN:chr22_KI270739v1_random  LN:73985
@SQ SN:chrY_KI270740v1_random   LN:37240
@SQ SN:chrUn_KI270302v1 LN:2274
@SQ SN:chrUn_KI270304v1 LN:2165
@SQ SN:chrUn_KI270303v1 LN:1942
@SQ SN:chrUn_KI270305v1 LN:1472
@SQ SN:chrUn_KI270322v1 LN:21476
@SQ SN:chrUn_KI270320v1 LN:4416
@SQ SN:chrUn_KI270310v1 LN:1201
@SQ SN:chrUn_KI270316v1 LN:1444
@SQ SN:chrUn_KI270315v1 LN:2276
@SQ SN:chrUn_KI270312v1 LN:998
@SQ SN:chrUn_KI270311v1 LN:12399
@SQ SN:chrUn_KI270317v1 LN:37690
@SQ SN:chrUn_KI270412v1 LN:1179
@SQ SN:chrUn_KI270411v1 LN:2646
@SQ SN:chrUn_KI270414v1 LN:2489
@SQ SN:chrUn_KI270419v1 LN:1029
@SQ SN:chrUn_KI270418v1 LN:2145
@SQ SN:chrUn_KI270420v1 LN:2321
@SQ SN:chrUn_KI270424v1 LN:2140
@SQ SN:chrUn_KI270417v1 LN:2043
@SQ SN:chrUn_KI270422v1 LN:1445
@SQ SN:chrUn_KI270423v1 LN:981
@SQ SN:chrUn_KI270425v1 LN:1884
@SQ SN:chrUn_KI270429v1 LN:1361
@SQ SN:chrUn_KI270442v1 LN:392061
@SQ SN:chrUn_KI270466v1 LN:1233
@SQ SN:chrUn_KI270465v1 LN:1774
@SQ SN:chrUn_KI270467v1 LN:3920
@SQ SN:chrUn_KI270435v1 LN:92983
@SQ SN:chrUn_KI270438v1 LN:112505
@SQ SN:chrUn_KI270468v1 LN:4055
@SQ SN:chrUn_KI270510v1 LN:2415
@SQ SN:chrUn_KI270509v1 LN:2318
@SQ SN:chrUn_KI270518v1 LN:2186
@SQ SN:chrUn_KI270508v1 LN:1951
@SQ SN:chrUn_KI270516v1 LN:1300
@SQ SN:chrUn_KI270512v1 LN:22689
@SQ SN:chrUn_KI270519v1 LN:138126
@SQ SN:chrUn_KI270522v1 LN:5674
@SQ SN:chrUn_KI270511v1 LN:8127
@SQ SN:chrUn_KI270515v1 LN:6361
@SQ SN:chrUn_KI270507v1 LN:5353
@SQ SN:chrUn_KI270517v1 LN:3253
@SQ SN:chrUn_KI270529v1 LN:1899
@SQ SN:chrUn_KI270528v1 LN:2983
@SQ SN:chrUn_KI270530v1 LN:2168
@SQ SN:chrUn_KI270539v1 LN:993
@SQ SN:chrUn_KI270538v1 LN:91309
@SQ SN:chrUn_KI270544v1 LN:1202
@SQ SN:chrUn_KI270548v1 LN:1599
@SQ SN:chrUn_KI270583v1 LN:1400
@SQ SN:chrUn_KI270587v1 LN:2969
@SQ SN:chrUn_KI270580v1 LN:1553
@SQ SN:chrUn_KI270581v1 LN:7046
@SQ SN:chrUn_KI270579v1 LN:31033
@SQ SN:chrUn_KI270589v1 LN:44474
@SQ SN:chrUn_KI270590v1 LN:4685
@SQ SN:chrUn_KI270584v1 LN:4513
@SQ SN:chrUn_KI270582v1 LN:6504
@SQ SN:chrUn_KI270588v1 LN:6158
@SQ SN:chrUn_KI270593v1 LN:3041
@SQ SN:chrUn_KI270591v1 LN:5796
@SQ SN:chrUn_KI270330v1 LN:1652
@SQ SN:chrUn_KI270329v1 LN:1040
@SQ SN:chrUn_KI270334v1 LN:1368
@SQ SN:chrUn_KI270333v1 LN:2699
@SQ SN:chrUn_KI270335v1 LN:1048
@SQ SN:chrUn_KI270338v1 LN:1428
@SQ SN:chrUn_KI270340v1 LN:1428
@SQ SN:chrUn_KI270336v1 LN:1026
@SQ SN:chrUn_KI270337v1 LN:1121
@SQ SN:chrUn_KI270363v1 LN:1803
@SQ SN:chrUn_KI270364v1 LN:2855
@SQ SN:chrUn_KI270362v1 LN:3530
@SQ SN:chrUn_KI270366v1 LN:8320
@SQ SN:chrUn_KI270378v1 LN:1048
@SQ SN:chrUn_KI270379v1 LN:1045
@SQ SN:chrUn_KI270389v1 LN:1298
@SQ SN:chrUn_KI270390v1 LN:2387
@SQ SN:chrUn_KI270387v1 LN:1537
@SQ SN:chrUn_KI270395v1 LN:1143
@SQ SN:chrUn_KI270396v1 LN:1880
@SQ SN:chrUn_KI270388v1 LN:1216
@SQ SN:chrUn_KI270394v1 LN:970
@SQ SN:chrUn_KI270386v1 LN:1788
@SQ SN:chrUn_KI270391v1 LN:1484
@SQ SN:chrUn_KI270383v1 LN:1750
@SQ SN:chrUn_KI270393v1 LN:1308
@SQ SN:chrUn_KI270384v1 LN:1658
@SQ SN:chrUn_KI270392v1 LN:971
@SQ SN:chrUn_KI270381v1 LN:1930
@SQ SN:chrUn_KI270385v1 LN:990
@SQ SN:chrUn_KI270382v1 LN:4215
@SQ SN:chrUn_KI270376v1 LN:1136
@SQ SN:chrUn_KI270374v1 LN:2656
@SQ SN:chrUn_KI270372v1 LN:1650
@SQ SN:chrUn_KI270373v1 LN:1451
@SQ SN:chrUn_KI270375v1 LN:2378
@SQ SN:chrUn_KI270371v1 LN:2805
@SQ SN:chrUn_KI270448v1 LN:7992
@SQ SN:chrUn_KI270521v1 LN:7642
@SQ SN:chrUn_GL000195v1 LN:182896
@SQ SN:chrUn_GL000219v1 LN:179198
@SQ SN:chrUn_GL000220v1 LN:161802
@SQ SN:chrUn_GL000224v1 LN:179693
@SQ SN:chrUn_KI270741v1 LN:157432
@SQ SN:chrUn_GL000226v1 LN:15008
@SQ SN:chrUn_GL000213v1 LN:164239
@SQ SN:chrUn_KI270743v1 LN:210658
@SQ SN:chrUn_KI270744v1 LN:168472
@SQ SN:chrUn_KI270745v1 LN:41891
@SQ SN:chrUn_KI270746v1 LN:66486
@SQ SN:chrUn_KI270747v1 LN:198735
@SQ SN:chrUn_KI270748v1 LN:93321
@SQ SN:chrUn_KI270749v1 LN:158759
@SQ SN:chrUn_KI270750v1 LN:148850
@SQ SN:chrUn_KI270751v1 LN:150742
@SQ SN:chrUn_KI270752v1 LN:27745
@SQ SN:chrUn_KI270753v1 LN:62944
@SQ SN:chrUn_KI270754v1 LN:40191
@SQ SN:chrUn_KI270755v1 LN:36723
@SQ SN:chrUn_KI270756v1 LN:79590
@SQ SN:chrUn_KI270757v1 LN:71251
@SQ SN:chrUn_GL000214v1 LN:137718
@SQ SN:chrUn_KI270742v1 LN:186739
@SQ SN:chrUn_GL000216v2 LN:176608
@SQ SN:chrUn_GL000218v1 LN:161147
@SQ SN:chrEBV   LN:171823
@RG ID:NET25_TI PL:ILLUMINA PU:1    SM:NET25_TI
@PG ID:bwa  PN:bwa  VN:0.7.17-r1194-dirty   CL:bwa mem -M -t 48 -R @RG\tID:NET25_TI\tPL:ILLUMINA\tPU:1\tSM:NET25_TI /gpfs42/robbyfs/scratch/lab_lpasquali/msubirana/ref/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa /gpfs42/robbyfs/scratch/lab_lpasquali/msubirana/marc/insulinomas/data/WGS/BAM/toDo/NET25_TI_R1.fq /gpfs42/robbyfs/scratch/lab_lpasquali/msubirana/marc/insulinomas/data/WGS/BAM/toDo/NET25_TI_R2.fq
@PG ID:SAMBLASTER   VN:0.1.24   CL:samblaster -i stdin -o stdout -M
@PG ID:samtools PN:samtools PP:SAMBLASTER   VN:1.12 CL:samtools view -H /gpfs42/robbyfs/scratch/lab_lpasquali/msubirana/marc/insulinomas/data/WGS/BAM/INS/all_ok/NET25_TI.bam

hongwingl commented 1 year ago

Thanks. This all seem fine to me. Would you be able try running it on a machine with writable /tmp directory and see if it works? Just want to make sure the /tmp is the issue here.

msubirana commented 1 year ago

Is it possible to run the R script separately to have all the files that purple requires from cobalt and amber?

hongwingl commented 1 year ago

You can extract the script out from the repo and run them manually. Though I suspect making /tmp writable would be a much simpler option?

hongwingl commented 1 year ago

Are you able to try running the R script manually and see if it works?

Download https://raw.githubusercontent.com/hartwigmedical/hmftools/master/cobalt/src/main/resources/r/ratioSegmentation.R
Run the following

Rscript ratioSegmentation.R /gpfs42/robbyfs/scratch/lab_lpasquali/shared_data/projects-data/insulinomas-genetics/output/gpl/NET25_TI/cobalt/NET25_TI.cobalt.ratio.tsv.gz tumorGCRatio /gpfs42/robbyfs/scratch/lab_lpasquali/shared_data/projects-data/insulinomas-genetics/output/gpl/NET25_TI/cobalt/NET25_TI.cobalt.ratio.pcf 100

hongwingl commented 1 year ago

I just found out that there is indeed a way to set the tmp directory for java process, when executing the java command, add the following -Djava.io.tmpdir=<new temp dir>, i.e.

java -Djava.io.tmpdir=/path/to/tmpdir -jar cobalt.jar ...

msubirana commented 1 year ago

sorry for the late replay, I tested the ratioSegmentation.R from the repo and the copynumber dependence was not correctly installed, after check all the dependencies it works! thanks for all the feedback!