manta path error

[egenomics]

Description of the bug

Manta fails with a path error:

  error [java.lang.InterruptedException]: java.lang.InterruptedException
Jan-16 03:00:07.184 [Actor Thread 16] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA (1)'

Caused by:
  Path value cannot be null

Command used and terminal output

nextflow run /playground/nf-core-raredisease_1.1.1/1_1_1/      -profile singularity     --input /playground/dataset_cnvs/samplesheet.csv     --skip_snv_annotation     --skip_sv_annotation     --skip_cnv_calling     --outdir /playground/dataset_cnvs/results     --intervals_wgs /playground/dataset_cnvs/Illumina-truseq-rapid-exome_v1.2_hg38_target_orig.interval_list     --intervals_y /playground/dataset_cnvs/Illumina-truseq-rapid-exome_v1.2_hg38_target_orig.interval_list     --skip_mt_analysis     --skip_vep_filter     --target_bed /playground/dataset_cnvs/Illumina-truseq-rapid-exome_v1.2_hg38_target_orig.bed     --variant_catalog /playground/dataset_cnvs/variant_catalog.json

Relevant files

nextflow.log

System information

nextflow version 23.10.0.5889
Workstation
local (singularity)
Ubuntu 22.04.03 LTS
raredisease 1.1.1

[egenomics]

-resume [name_run] also doesn't seem to work, as it does not recover the bwa-mem2 or fastqc processes, that were finished.

[jemten]

Hi @egenomics,
I've also noticed that -resume and I'm currently looking into that.
Are these exome samples?

[egenomics]

yes, they are exomes (it's been modified in the nextflow.config, analysis_type = 'wes'). I managed to have -resume working but it gets the same error: path value cannot be null error in manta :(

[egenomics]

Any idea where the error might be?

[jemten]

Hmm something seems to be off when combining the channels for going from a sample to case. From looking at the logs it looks like the samples aren't related in any way. Is that correct?

[egenomics]

Yes, in theory they are not related. Should I process every "case" separately in a difference nextflow run - samplesheet instance?

[jemten]

I think it's worth trying to do that while we are trying to nail down why the first setup doesn't work. Also, if possible, could you share your samplesheet?

[egenomics]

I will try to do it separately, but I need to process ~120 exomes with certain urgency.

This is one of the samplesheets

cat samplesheet_R1080.csv 
sample,lane,fastq_1,fastq_2,sex,phenotype,paternal_id,maternal_id,case_id
200851803,1,/playground/fastq/R1080/200851803_S1_R1_001.fastq.gz,/playground/fastq/R1080/200851803_S1_R2_001.fastq.gz,other,2,0,0,200851803
192631319,1,/playground/fastq/R1080/192631319_S2_R1_001.fastq.gz,/playground/fastq/R1080/192631319_S2_R2_001.fastq.gz,2,2,0,0,192631319
192629071,1,/playground/fastq/R1080/192629071_S3_R1_001.fastq.gz,/playground/fastq/R1080/192629071_S3_R2_001.fastq.gz,1,2,0,0,192629071
192629059,1,/playground/fastq/R1080/192629059_S4_R1_001.fastq.gz,/playground/fastq/R1080/192629059_S4_R2_001.fastq.gz,2,2,0,0,192629059
192637663,1,/playground/fastq/R1080/192637663_S5_R1_001.fastq.gz,/playground/fastq/R1080/192637663_S5_R2_001.fastq.gz,1,2,0,0,192637663
192606791,1,/playground/fastq/R1080/192606791_S6_R1_001.fastq.gz,/playground/fastq/R1080/192606791_S6_R2_001.fastq.gz,2,2,0,0,192606791
192641178,1,/playground/fastq/R1080/192641178_S7_R1_001.fastq.gz,/playground/fastq/R1080/192641178_S7_R2_001.fastq.gz,2,2,0,0,192641178
192610990,1,/playground/fastq/R1080/192610990_S8_R1_001.fastq.gz,/playground/fastq/R1080/192610990_S8_R2_001.fastq.gz,1,2,0,0,192610990
192643630,1,/playground/fastq/R1080/192643630_S9_R1_001.fastq.gz,/playground/fastq/R1080/192643630_S9_R2_001.fastq.gz,1,2,0,0,192643630
190846474,1,/playground/fastq/R1080/190846474_S10_R1_001.fastq.gz,/playground/fastq/R1080/190846474_S10_R2_001.fastq.gz,1,2,0,0,190846474
190846477,1,/playground/fastq/R1080/190846477_S11_R1_001.fastq.gz,/playground/fastq/R1080/190846477_S11_R2_001.fastq.gz,1,2,0,0,190846477

[jemten]

Try to start one and see if the error persists. The pipeline should be compatible with your setup, and otherwise we'll try to fix it. We are working to get a new release out in a couple of week so it would be good to get a grip on the issue.

[egenomics]

Hi,
I get a different error when processing samples one by one (error at the end).

The command is this one

nextflow run /playground/nf-core-raredisease_1.1.1/1_1_1/ -profile singularity \
--input /playground/dataset_cnvs/samplesheets_raredisease/samplesheet_$sample.csv --skip_snv_annotation --skip_sv_annotation --skip_cnv_calling \
--outdir /playground/dataset_cnvs/results/$sample --intervals_wgs /playground/dataset_cnvs/Illumina-truseq-rapid-exome_v1.2_hg38_target_orig.interval_list \
 --intervals_y /playground/dataset_cnvs/Illumina-truseq-rapid-exome_v1.2_hg38_target_orig.interval_list --skip_mt_analysis --skip_vep_filter \
 --target_bed /playground/dataset_cnvs/Illumina-truseq-rapid-exome_v1.2_hg38_target_orig.bed \
 --variant_catalog /playground/dataset_cnvs/variant_catalog.json \
 --analysis_type wes

ERROR ~ Error executing process > 'NFCORE_RAREDISEASE:RAREDISEASE:PREPARE_REFERENCES:GATK_BILT (playground)'

Caused by:
  Process `NFCORE_RAREDISEASE:RAREDISEASE:PREPARE_REFERENCES:GATK_BILT (playground)` terminated with an error exit status (3)

Command executed:

  gatk --java-options "-Xmx24576M" BedToIntervalList \
      --INPUT Illumina-truseq-rapid-exome_v1.2_hg38_target_orig.bed \
      --OUTPUT playground_target.interval_list \
      --SEQUENCE_DICTIONARY genome.dict \
      --TMP_DIR . \
  
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RAREDISEASE:RAREDISEASE:PREPARE_REFERENCES:GATK_BILT":
      gatk4: $(echo $(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*$//')
  END_VERSIONS

Command exit status:
  3

Command output:
  (empty)

Command error:
  Using GATK jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar
  Running:
      java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx24576M -jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar BedToIntervalList --INPUT Illumina-truseq-rapid-exome_v1.2_hg38_target_orig.bed --OUTPUT playground_target.interval_list --SEQUENCE_DICTIONARY genome.dict --TMP_DIR .
  08:58:38.845 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
  [Fri Jan 26 08:58:38 GMT 2024] BedToIntervalList --INPUT Illumina-truseq-rapid-exome_v1.2_hg38_target_orig.bed --SEQUENCE_DICTIONARY genome.dict --OUTPUT playground_target.interval_list --TMP_DIR . --SORT true --UNIQUE false --DROP_MISSING_CONTIGS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
  [Fri Jan 26 08:58:38 GMT 2024] Executing as jlvillanueva@HCP14035 on Linux 6.5.0-14-generic amd64; OpenJDK 64-Bit Server VM 17.0.3-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.4.0.0
  [Fri Jan 26 08:58:39 GMT 2024] picard.util.BedToIntervalList done. Elapsed time: 0.00 minutes.
  Runtime.totalMemory()=285212672
  To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
  picard.PicardException: Start on sequence 'chr4' was past the end: 112788531 < 112904435
  	at picard.util.BedToIntervalList.doWork(BedToIntervalList.java:160)
  	at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:289)
  	at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:37)
  	at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
  	at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
  	at org.broadinstitute.hellbender.Main.main(Main.java:289)

Work dir:
  /playground/work/66/42850f2837916a14b7ce930937ae25

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- Check '.nextflow.log' file for details

[ramprasadn]

This looks like an issue with your bed file, where the start location is greater than the end location for chr4. Could you check if that is the case?

[egenomics]

Hi,
The coordinates where the pipeline complains are right in the middle of chromosome 4.

This is the bed file:
[...]
chr4 112654064 112654163
chr4 112657238 112657337
chr4 112904434 112904592 <<---------------
chr4 113049678 113049863
chr4 113106860 113106959
[...]

[ramprasadn]

hmmm.. Would it be possible for you to share your bed file and your dictionary file?

[egenomics]

Here
Illumina-truseq-rapid-exome_v1.2_hg38_target_orig.zip