Singularity image: bam output of alignment workflow?

[mncfletcher]

Hello,

I'm trying to run the DNA alignment pipeline on some WES data and... I appear to have lost the output bam files?

Where should they end up? If I check the output directory I think they should be in - $GLASSMOUNTS/disk2/glassdata/flowr/flowr_aln_fqs_wes-H043-0ZQU-B1-D1-20181112-15-26-49-3jo7u2wU - I don't see the final bams, only intermediate sams...

I'm running Singularity v 2.6.0

Here's the info on the Singularity container:

===
{
"WEBSITE": "https://docker.glass-consortium.org",
"org.label-schema.usage.singularity.deffile.bootstrap": "docker",
"MAINTAINER": "Samir B. Amin, tweet: sbamin, web: https://sbamin.com",
"NAME": "glasstools:beta",
"LICENSE": "https://github.com/glass-consortium/glasstools/blob/master/LICENSE",
"org.label-schema.usage": "/.singularity.d/runscript.help",
"org.label-schema.schema-version": "1.0",
"org.label-schema.build-date": "2017-11-18T13:35:49+00:00",
"org.label-schema.usage.singularity.deffile.includecmd": "no",
"VERSION": "v1.1.2s2",
"org.label-schema.usage.singularity.deffile.from": "ubuntu:16.04",
"org.label-schema.usage.singularity.deffile": "Singularity.beta",
"SOURCECODE": "https://github.com/glass-consortium/glasstools",
"org.label-schema.usage.singularity.runscript.help": "/.singularity.d/runscript.help",
"org.label-schema.usage.singularity.version": "2.4-feature-squashbuild-secbuild.g818b648",
"CONTACT": "Roel Verhaak, tweet: roelverhaak, web: https://www.jax.org/verhaak-lab",
"org.label-schema.build-size": "3629MB",
"ISSUES": "https://github.com/glass-consortium/glassdocs/issues",
"DESCRIPTION": "Singularity image to run GLASS consortium workflows"
}

Here's the flowr log:

cat H043-0ZQU-B1-D1_12Nov18_152637UTC.log

confs
/home/fletcher/.flowr.conf
/opt/miniconda/lib/R/library/flowr/conf/flowr.conf
flowr_aln_fqs_wes.conf

---

cmd = /opt/miniconda/bin/bwa mem -M -t 12 -R "@rg\tID:run150313_SN7001177_0239_AC69N1ACXX_L005_CTTGTA\tPL:illumina\tPU:AC69N1ACXX.5.CTTGTA\tLB:H043-0ZQU-B1-D1\tPI:0\tDT:2018-11-12T15:26:46+0000\tSM:H043-0ZQU\tCN:dkfz" /mnt/scratch/refdata/bundle/human_g1k_v37_decoy.fasta /mnt/glassdata/inputs/fqs/H043-0ZQU-B1-D1/H043-0ZQU-B1-D1_CTTGTA_L005_R1_complete_filtered.fastq /mnt/glassdata/inputs/fqs/H043-0ZQU-B1-D1/H043-0ZQU-B1-D1_CTTGTA_L005_R2_complete_filtered.fastq > tmp_H043-0ZQU-B1-D1/H043-0ZQU-run150313_SN7001177_0239_AC69N1ACXX_L005_CTTGTA.aln.sam
stepchecklog_path = logs/stepcheck_02_H043-0ZQU-run150313_SN7001177_0239_AC69N1ACXX_L005_CTTGTA.aln.sam.log
input = /mnt/glassdata/inputs/fqs/H043-0ZQU-B1-D1/H043-0ZQU-B1-D1_CTTGTA_L005_R1_complete_filtered.fastq
output = tmp_H043-0ZQU-B1-D1/H043-0ZQU-run150313_SN7001177_0239_AC69N1ACXX_L005_CTTGTA.aln.sam
output2 or paired fastq =
DEL = FALSE

---

cmd = /opt/miniconda/bin/bwa mem -M -t 12 -R "@rg\tID:run150313_SN7001177_0239_AC69N1ACXX_L006_CTTGTA\tPL:illumina\tPU:AC69N1ACXX.6.CTTGTA\tLB:H043-0ZQU-B1-D1\tPI:0\tDT:2018-11-12T15:26:46+0000\tSM:H043-0ZQU\tCN:dkfz" /mnt/scratch/refdata/bundle/human_g1k_v37_decoy.fasta /mnt/glassdata/inputs/fqs/H043-0ZQU-B1-D1/H043-0ZQU-B1-D1_CTTGTA_L006_R1_complete_filtered.fastq /mnt/glassdata/inputs/fqs/H043-0ZQU-B1-D1/H043-0ZQU-B1-D1_CTTGTA_L006_R2_complete_filtered.fastq > tmp_H043-0ZQU-B1-D1/H043-0ZQU-run150313_SN7001177_0239_AC69N1ACXX_L006_CTTGTA.aln.sam
stepchecklog_path = logs/stepcheck_02_H043-0ZQU-run150313_SN7001177_0239_AC69N1ACXX_L006_CTTGTA.aln.sam.log
input = /mnt/glassdata/inputs/fqs/H043-0ZQU-B1-D1/H043-0ZQU-B1-D1_CTTGTA_L006_R1_complete_filtered.fastq
output = tmp_H043-0ZQU-B1-D1/H043-0ZQU-run150313_SN7001177_0239_AC69N1ACXX_L006_CTTGTA.aln.sam
output2 or paired fastq =
DEL = FALSE

---

cmd = /opt/miniconda/bin/bwa mem -M -t 12 -R "@rg\tID:run150313_SN7001177_0239_AC69N1ACXX_L007_CTTGTA\tPL:illumina\tPU:AC69N1ACXX.7.CTTGTA\tLB:H043-0ZQU-B1-D1\tPI:0\tDT:2018-11-12T15:26:46+0000\tSM:H043-0ZQU\tCN:dkfz" /mnt/scratch/refdata/bundle/human_g1k_v37_decoy.fasta /mnt/glassdata/inputs/fqs/H043-0ZQU-B1-D1/H043-0ZQU-B1-D1_CTTGTA_L007_R1_complete_filtered.fastq /mnt/glassdata/inputs/fqs/H043-0ZQU-B1-D1/H043-0ZQU-B1-D1_CTTGTA_L007_R2_complete_filtered.fastq > tmp_H043-0ZQU-B1-D1/H043-0ZQU-run150313_SN7001177_0239_AC69N1ACXX_L007_CTTGTA.aln.sam
stepchecklog_path = logs/stepcheck_02_H043-0ZQU-run150313_SN7001177_0239_AC69N1ACXX_L007_CTTGTA.aln.sam.log
input = /mnt/glassdata/inputs/fqs/H043-0ZQU-B1-D1/H043-0ZQU-B1-D1_CTTGTA_L007_R1_complete_filtered.fastq
output = tmp_H043-0ZQU-B1-D1/H043-0ZQU-run150313_SN7001177_0239_AC69N1ACXX_L007_CTTGTA.aln.sam
output2 or paired fastq =
DEL = FALSE

---

cmd = /opt/java/jdk8/bin/java -Xmx52g -Djava.io.tmpdir=/mnt/glassdata/tmp -jar /opt/jars/picard.jar SortSam SO=coordinate INPUT=tmp_H043-0ZQU-B1-D1/H043-0ZQU-run150313_SN7001177_0239_AC69N1ACXX_L005_CTTGTA.aln.sam OUTPUT=tmp_H043-0ZQU-B1-D1/H043-0ZQU-run150313_SN7001177_0239_AC69N1ACXX_L005_CTTGTA.aln.bam VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=true
stepchecklog_path = logs/stepcheck_03_H043-0ZQU-run150313_SN7001177_0239_AC69N1ACXX_L005_CTTGTA.aln.bam.log
input = tmp_H043-0ZQU-B1-D1/H043-0ZQU-run150313_SN7001177_0239_AC69N1ACXX_L005_CTTGTA.aln.sam
output = tmp_H043-0ZQU-B1-D1/H043-0ZQU-run150313_SN7001177_0239_AC69N1ACXX_L005_CTTGTA.aln.bam
output2 or paired fastq =
DEL = TRUE

---

cmd = /opt/java/jdk8/bin/java -Xmx52g -Djava.io.tmpdir=/mnt/glassdata/tmp -jar /opt/jars/picard.jar SortSam SO=coordinate INPUT=tmp_H043-0ZQU-B1-D1/H043-0ZQU-run150313_SN7001177_0239_AC69N1ACXX_L006_CTTGTA.aln.sam OUTPUT=tmp_H043-0ZQU-B1-D1/H043-0ZQU-run150313_SN7001177_0239_AC69N1ACXX_L006_CTTGTA.aln.bam VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=true
stepchecklog_path = logs/stepcheck_03_H043-0ZQU-run150313_SN7001177_0239_AC69N1ACXX_L006_CTTGTA.aln.bam.log
input = tmp_H043-0ZQU-B1-D1/H043-0ZQU-run150313_SN7001177_0239_AC69N1ACXX_L006_CTTGTA.aln.sam
output = tmp_H043-0ZQU-B1-D1/H043-0ZQU-run150313_SN7001177_0239_AC69N1ACXX_L006_CTTGTA.aln.bam
output2 or paired fastq =
DEL = TRUE

---

cmd = /opt/java/jdk8/bin/java -Xmx52g -Djava.io.tmpdir=/mnt/glassdata/tmp -jar /opt/jars/picard.jar SortSam SO=coordinate INPUT=tmp_H043-0ZQU-B1-D1/H043-0ZQU-run150313_SN7001177_0239_AC69N1ACXX_L007_CTTGTA.aln.sam OUTPUT=tmp_H043-0ZQU-B1-D1/H043-0ZQU-run150313_SN7001177_0239_AC69N1ACXX_L007_CTTGTA.aln.bam VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=true
stepchecklog_path = logs/stepcheck_03_H043-0ZQU-run150313_SN7001177_0239_AC69N1ACXX_L007_CTTGTA.aln.bam.log
input = tmp_H043-0ZQU-B1-D1/H043-0ZQU-run150313_SN7001177_0239_AC69N1ACXX_L007_CTTGTA.aln.sam
output = tmp_H043-0ZQU-B1-D1/H043-0ZQU-run150313_SN7001177_0239_AC69N1ACXX_L007_CTTGTA.aln.bam
output2 or paired fastq =
DEL = TRUE

---

cmd = /opt/java/jdk8/bin/java -Xmx52g -Djava.io.tmpdir=/mnt/glassdata/tmp -jar /opt/jars/picard.jar MarkDuplicates OUTPUT=tmp_H043-0ZQU-B1-D1/H043-0ZQU-B1-D1.aln.dup.bam METRICS_FILE=tmp_H043-0ZQU-B1-D1/H043-0ZQU-B1-D1.metrics.txt CREATE_INDEX=true INPUT=tmp_H043-0ZQU-B1-D1/H043-0ZQU-run150313_SN7001177_0239_AC69N1ACXX_L005_CTTGTA.aln.bam INPUT=tmp_H043-0ZQU-B1-D1/H043-0ZQU-run150313_SN7001177_0239_AC69N1ACXX_L006_CTTGTA.aln.bam INPUT=tmp_H043-0ZQU-B1-D1/H043-0ZQU-run150313_SN7001177_0239_AC69N1ACXX_L007_CTTGTA.aln.bam
stepchecklog_path = logs/stepcheck_04_H043-0ZQU-B1-D1.aln.dup.bam.log
input = tmp_H043-0ZQU-B1-D1/H043-0ZQU-run150313_SN7001177_0239_AC69N1ACXX_L005_CTTGTA.aln.bam
output = tmp_H043-0ZQU-B1-D1/H043-0ZQU-B1-D1.aln.dup.bam
output2 or paired fastq = tmp_H043-0ZQU-B1-D1/H043-0ZQU-B1-D1.metrics.txt
DEL = TRUE

---

cmd = /opt/java/jdk8/bin/java -Xmx8g -jar /opt/jars/GenomeAnalysisTK.jar -nt 8 -l INFO -T RealignerTargetCreator -R /mnt/scratch/refdata/bundle/human_g1k_v37_decoy.fasta -I tmp_H043-0ZQU-B1-D1/H043-0ZQU-B1-D1.aln.dup.bam -known /mnt/scratch/refdata/bundle/1000G_phase1.indels.b37.vcf -o tmp_H043-0ZQU-B1-D1/H043-0ZQU-B1-D1.target_intervals.list
stepchecklog_path = logs/stepcheck_05_H043-0ZQU-B1-D1.target_intervals.list.log
input = tmp_H043-0ZQU-B1-D1/H043-0ZQU-B1-D1.aln.dup.bam
output = tmp_H043-0ZQU-B1-D1/H043-0ZQU-B1-D1.target_intervals.list
output2 or paired fastq =
DEL = FALSE

---

cmd = /opt/java/jdk8/bin/java -Xmx72g -jar /opt/jars/GenomeAnalysisTK.jar -T IndelRealigner -R /mnt/scratch/refdata/bundle/human_g1k_v37_decoy.fasta -I tmp_H043-0ZQU-B1-D1/H043-0ZQU-B1-D1.aln.dup.bam -known /mnt/scratch/refdata/bundle/1000G_phase1.indels.b37.vcf -targetIntervals tmp_H043-0ZQU-B1-D1/H043-0ZQU-B1-D1.target_intervals.list -o tmp_H043-0ZQU-B1-D1/H043-0ZQU-B1-D1.aln.dup.realn.bam
stepchecklog_path = logs/stepcheck_06_H043-0ZQU-B1-D1.aln.dup.realn.bam.log
input = tmp_H043-0ZQU-B1-D1/H043-0ZQU-B1-D1.aln.dup.bam
output = tmp_H043-0ZQU-B1-D1/H043-0ZQU-B1-D1.aln.dup.realn.bam
output2 or paired fastq =
DEL = TRUE

---

cmd = /opt/java/jdk8/bin/java -Xmx8g -jar /opt/jars/GenomeAnalysisTK.jar -nct 8 -l WARN -T BaseRecalibrator -R /mnt/scratch/refdata/bundle/human_g1k_v37_decoy.fasta -I tmp_H043-0ZQU-B1-D1/H043-0ZQU-B1-D1.aln.dup.realn.bam --knownSites /mnt/scratch/refdata/bundle/dbsnp_138.b37.vcf -o tmp_H043-0ZQU-B1-D1/H043-0ZQU-B1-D1.recal_data.table
stepchecklog_path = logs/stepcheck_07_H043-0ZQU-B1-D1.recal_data.table.log
input = tmp_H043-0ZQU-B1-D1/H043-0ZQU-B1-D1.aln.dup.realn.bam
output = tmp_H043-0ZQU-B1-D1/H043-0ZQU-B1-D1.recal_data.table
output2 or paired fastq =
DEL = FALSE

---

cmd = /opt/java/jdk8/bin/java -Xmx8g -jar /opt/jars/GenomeAnalysisTK.jar -T PrintReads -nct 8 -R /mnt/scratch/refdata/bundle/human_g1k_v37_decoy.fasta -I tmp_H043-0ZQU-B1-D1/H043-0ZQU-B1-D1.aln.dup.realn.bam -BQSR tmp_H043-0ZQU-B1-D1/H043-0ZQU-B1-D1.recal_data.table -o tmp_H043-0ZQU-B1-D1/H043-0ZQU-B1-D1.aln.dup.realn.recal.bam
stepchecklog_path = logs/stepcheck_08_H043-0ZQU-B1-D1.aln.dup.realn.recal.bam.log
input = tmp_H043-0ZQU-B1-D1/H043-0ZQU-B1-D1.aln.dup.realn.bam
output = tmp_H043-0ZQU-B1-D1/H043-0ZQU-B1-D1.aln.dup.realn.recal.bam
output2 or paired fastq =
DEL = TRUE

---

cmd = rm -f tmp_H043-0ZQU-B1-D1/reference.dict && /opt/java/jdk8/bin/java -Xmx26g -Djava.io.tmpdir=/mnt/glassdata/tmp -jar /opt/jars/picard.jar CreateSequenceDictionary R=/mnt/scratch/refdata/bundle/human_g1k_v37_decoy.fasta O=tmp_H043-0ZQU-B1-D1/reference.dict GENOME_ASSEMBLY=GRCH37 SPECIES=Homo_sapiens && rm -f tmp_H043-0ZQU-B1-D1/header.txt && samtools view -H tmp_H043-0ZQU-B1-D1/H043-0ZQU-B1-D1.aln.dup.realn.recal.bam | grep -v "^@sq" >| tmp_H043-0ZQU-B1-D1/header.txt && cat tmp_H043-0ZQU-B1-D1/reference.dict >> tmp_H043-0ZQU-B1-D1/header.txt && /opt/java/jdk8/bin/java -Xmx26g -Djava.io.tmpdir=/mnt/glassdata/tmp -jar /opt/jars/picard.jar ReplaceSamHeader I=tmp_H043-0ZQU-B1-D1/H043-0ZQU-B1-D1.aln.dup.realn.recal.bam HEADER=tmp_H043-0ZQU-B1-D1/header.txt O=H043-0ZQU-B1-D1.aln.dup.realn.recal.rp.bam && Rscript /mnt/glasscore/workflows/glass_docker_dnaseq_alignment/runner/check_SQ_order.R --samtools samtools --oldbam tmp_H043-0ZQU-B1-D1/H043-0ZQU-B1-D1.aln.dup.realn.recal.bam --newbam H043-0ZQU-B1-D1.aln.dup.realn.recal.rp.bam
stepchecklog_path = logs/stepcheck_09_H043-0ZQU-B1-D1.aln.dup.realn.recal.rp.bam.log
input = tmp_H043-0ZQU-B1-D1/H043-0ZQU-B1-D1.aln.dup.realn.recal.bam
output = H043-0ZQU-B1-D1.aln.dup.realn.recal.rp.bam
output2 or paired fastq =
DEL = FALSE

---

cmd = samtools index H043-0ZQU-B1-D1.aln.dup.realn.recal.rp.bam
stepchecklog_path = logs/stepcheck_09_H043-0ZQU-B1-D1.aln.dup.realn.recal.rp.bam.log
input = tmp_H043-0ZQU-B1-D1/H043-0ZQU-B1-D1.aln.dup.realn.recal.bam
output = H043-0ZQU-B1-D1.aln.dup.realn.recal.rp.bam
output2 or paired fastq =
DEL = TRUE

---

cmd = /opt/java/jdk8/bin/java -Xmx48g -jar /opt/jars/picard.jar CollectHsMetrics R=/mnt/scratch/refdata/bundle/human_g1k_v37_decoy.fasta O=coverage-E4_sureSelectV5_hg19.interval_list/H043-0ZQU-B1-D1.aln.dup.realn.recal.rp.coverage I=H043-0ZQU-B1-D1.aln.dup.realn.recal.rp.bam BAIT_INTERVALS=/mnt/scratch/refdata/E4_sureSelectV5_hg19.interval_list TARGET_INTERVALS=/mnt/scratch/refdata/E4_sureSelectV5_hg19.interval_list
stepchecklog_path = logs/stepcheck_10_H043-0ZQU-B1-D1.aln.dup.realn.recal.rp.bam.log
input =
output = H043-0ZQU-B1-D1.aln.dup.realn.recal.rp.bam
output2 or paired fastq =
DEL = FALSE

---

cmd = Rscript /mnt/glasscore/workflows/glass_docker_dnaseq_alignment/runner/get_wd_size.R
stepchecklog_path = logs/stepcheck_11_H043-0ZQU-B1-D1.aln.dup.realn.recal.rp.bam.log
input =
output = H043-0ZQU-B1-D1.aln.dup.realn.recal.rp.bam
output2 or paired fastq =
DEL = FALSE

---

cmd = ls -alh tmp_H043-0ZQU-B1-D1/.bam && rm -fv tmp_H043-0ZQU-B1-D1/.bam & sleep 5 && echo -e "DONE at $(date)" >| finishflag.txt
stepchecklog_path = logs/stepcheck_12_tmp_H043-0ZQU-B1-D1_cleanup.log
input =
output = H043-0ZQU-B1-D1.aln.dup.realn.recal.rp.bam
output2 or paired fastq =
DEL = FALSE

|======================================================================| 100%

[sbamin]

Hi @fletcher-m,

Sorry for tardy reply. Looking quickly at log file, volume mounts seems ok but there could be file/dir permission issues that is preventing output files to be written on the host file system.

Anyways, I should note that we have now moved to updated version of GLASS workflow, based on snakemake. So, glass-consortium github site and documentation is outdated. I should have noted that on website earlier. If you are part of GLASS consortium lab, please wait until this weekend when GLASS website will reflect links to updated code and data resource.

Hope that helps,
Samir