Workflow specification is complete?: False

[t-neumann]

Dear Manta Team,

I'm having reproducible issues that identically processed datasets are stuck in Manta with the following status messages that are updated hourly but it never runs through:

[2018-08-08T11:55:56.989475Z] [cn-11] [4907_1] [WorkflowRunner] [StatusUpdate] ===== MantaWorkflow StatusUpdate =====
[2018-08-08T11:55:56.995621Z] [cn-11] [4907_1] [WorkflowRunner] [StatusUpdate] Workflow specification is complete?: False
[2018-08-08T11:55:56.996339Z] [cn-11] [4907_1] [WorkflowRunner] [StatusUpdate] Task status (waiting/queued/running/complete/error): 11849/0/1/1/0
[2018-08-08T11:55:56.996960Z] [cn-11] [4907_1] [WorkflowRunner] [StatusUpdate] Longest ongoing queued task time (hrs): 0.0000
[2018-08-08T11:55:56.997640Z] [cn-11] [4907_1] [WorkflowRunner] [StatusUpdate] Longest ongoing queued task name: ''
[2018-08-08T11:55:56.998454Z] [cn-11] [4907_1] [WorkflowRunner] [StatusUpdate] Longest ongoing running task time (hrs): 0.9997
[2018-08-08T11:55:56.999157Z] [cn-11] [4907_1] [WorkflowRunner] [StatusUpdate] Longest ongoing running task name: 'getAlignmentStats_generateStats_000'
[2018-08-08T12:55:57.163218Z] [cn-11] [4907_1] [WorkflowRunner] [StatusUpdate] ===== MantaWorkflow StatusUpdate =====
[2018-08-08T12:55:57.181497Z] [cn-11] [4907_1] [WorkflowRunner] [StatusUpdate] Workflow specification is complete?: False
[2018-08-08T12:55:57.182282Z] [cn-11] [4907_1] [WorkflowRunner] [StatusUpdate] Task status (waiting/queued/running/complete/error): 11849/0/1/1/0
[2018-08-08T12:55:57.183055Z] [cn-11] [4907_1] [WorkflowRunner] [StatusUpdate] Longest ongoing queued task time (hrs): 0.0000
[2018-08-08T12:55:57.183700Z] [cn-11] [4907_1] [WorkflowRunner] [StatusUpdate] Longest ongoing queued task name: ''
[2018-08-08T12:55:57.184375Z] [cn-11] [4907_1] [WorkflowRunner] [StatusUpdate] Longest ongoing running task time (hrs): 2.0000
[2018-08-08T12:55:57.186269Z] [cn-11] [4907_1] [WorkflowRunner] [StatusUpdate] Longest ongoing running task name: 'getAlignmentStats_generateStats_000'

I ran two testfiles produced by bwa - one was a paired-end WGS dataset, the other RNA-seq. But both processed identically, same modules, same resources, same node.

module load samtools/1.4-foss-2017a bwa/0.7.15-foss-2017a

bwa mem -M -R '@RG\tID:MCC_1T\tPL:illumina\tSM:MCC_1T' -t 20 /groups/obenauf/Software/indices/virus/Centrifuge/bwa/p+h+v_unique.fa /groups/obenauf/NGS_data/Leiendecker_MCC/WGS/FASTQ/LP2100019-DNA_A01_1.fastq.gz /groups/obenauf/NGS_data/Leiendecker_MCC/WGS/FASTQ/LP2100019-DNA_A01_2.fastq.gz | samtools view -b - | samtools sort -@ 4 -o MCC_1T.virus.bam

bwa mem -M -R '@RG\tID:MCC_1T\tPL:illumina\tSM:MCC_1T' -t 20 /groups/obenauf/Software/indices/virus/Centrifuge/bwa/p+h+v_unique.fa /scratch-ii2/users/tobias.neumann/95/4f153e2c9c8d88ed3a80209f6e8046/CAFW2ANXX_6#RNAseq-MCC-25-1-GCCACA_1.fq /scratch-ii2/users/tobias.neumann/95/4f153e2c9c8d88ed3a80209f6e8046/CAFW2ANXX_6#RNAseq-MCC-25-1-GCCACA_2.fq | samtools view -b - | samtools sort -@ 4 -o MCC-25-1.virus.bam

Then I run manta out of the official Docker container. the MCC_1T (WGS 157 GB) passes after a couple of hours successfully. The MCC-25 sample (RNA-seq 1.5 GB) is looping with the bespoke message.

singularity exec docker://quay.io/biocontainers/manta:1.4.0--py27_1 configManta.py --bam ../bwa/MCC_1T.virus.bam --referenceFasta /groups/obenauf/Software/indices/virus/Centrifuge/bwa/p+h+v_unique.fa --runDir MCC_1T_manta
singularity exec docker://quay.io/biocontainers/manta:1.4.0--py27_1 MCC_1T_manta/runWorkflow.py -m local -j 24 -g 100

singularity exec docker://quay.io/biocontainers/manta:1.4.0--py27_1 configManta.py --bam ../bwa/MCC-25-1.virus.bam --referenceFasta /groups/obenauf/Software/indices/virus/Centrifuge/bwa/p+h+v_unique.fa --runDir testrun_self
singularity exec docker://quay.io/biocontainers/manta:1.4.0--py27_1 testrun_self/runWorkflow.py -m local -j 24 -g 100

I also tried running the RNA-seq sample with the --rna flag, but that didn't help.

Can you help me on this? I'm out of options.

[x-chen]

Yes, RNA-seq sample need be run with --rna option.

Manta seemed to choke at the stats generation step, which essentially subsample reads and estimate insertion size from the input bam. Could you describe more about the RNA-seq bam? Are they paired-end reads?

My intuition is that there might be some unexpected characteristics of the RNA bam. If that's not easy to identify, I would need a sample of your bam files to debug. Is it possible to share a bamlet that can demonstrate the same problem?

[t-neumann]

Yes they are paired-end reads. Could you provide me with an email adress, then I could send you an example bam via file-share links.

[t-neumann]

Dear @x-chen. I sent you some testdata last week and just was wondering whether you need anything in addition?

[x-chen]

I was on vacation last week. And I will take a look once time allows.

[x-chen]

There was a bug in stats generation that was triggered by reference sequences smaller than 100bp. I just created a branch bug-MANTA-1459 with the bug fixed.
https://github.com/Illumina/manta/tree/bug-MANTA-1459

I have tested it against the test data you provided, and the bug fix will be rolled in the next release.

[x-chen]

The bug fix is now in v1.5.0