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CDCgov/mycosnp-nf
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NFCORE_MYCOSNP:MYCOSNP:FASTQC_RAW (ERR2172266) fail #110

Closed ybdong919 closed 10 months ago

ybdong919 commented 1 year ago

executor > local (21) [7f/bfa9f3] process > NFCORE_MYCOSNP:MYCOSNP:INPUT_CHECK:LANE_MERGE (ERR2172267) [100%] 3 of 3 ✔ [2b/4e2547] process > NFCORE_MYCOSNP:MYCOSNP:BWA_REFERENCE:INPUT_PROC [100%] 1 of 1 ✔ [b5/98c466] process > NFCORE_MYCOSNP:MYCOSNP:BWA_REFERENCE:NUCMER (reference) [100%] 1 of 1 ✔ [1d/ff2b7b] process > NFCORE_MYCOSNP:MYCOSNP:BWA_REFERENCE:COORDSTOBED (reference) [100%] 1 of 1 ✔ [53/1f9437] process > NFCORE_MYCOSNP:MYCOSNP:BWA_REFERENCE:BEDTOOLS_MASKFASTA (reference) [100%] 1 of 1 ✔ [be/d2e52a] process > NFCORE_MYCOSNP:MYCOSNP:BWA_REFERENCE:BWA_INDEX (reference.fa) [100%] 1 of 1 ✔ [91/5a4153] process > NFCORE_MYCOSNP:MYCOSNP:BWA_REFERENCE:SAMTOOLS_FAIDX (reference.fa) [100%] 1 of 1 ✔ [- ] process > NFCORE_MYCOSNP:MYCOSNP:BWA_REFERENCE:PICARD_CREATESEQUENCEDICTIONARY - [1f/8a1505] process > NFCORE_MYCOSNP:MYCOSNP:BWA_PREPROCESS:SEQKIT_PAIR (ERR2172267) [100%] 3 of 3 ✔ [06/2af72b] process > NFCORE_MYCOSNP:MYCOSNP:BWA_PREPROCESS:FAQCS (ERR2172267) [100%] 3 of 3 ✔ [- ] process > NFCORE_MYCOSNP:MYCOSNP:BWA_PREPROCESS:BWA_MEM - [- ] process > NFCORE_MYCOSNP:MYCOSNP:BWA_PREPROCESS:PICARD_MARKDUPLICATES - [- ] process > NFCORE_MYCOSNP:MYCOSNP:BWA_PREPROCESS:PICARD_CLEANSAM - [- ] process > NFCORE_MYCOSNP:MYCOSNP:BWA_PREPROCESS:PICARD_FIXMATEINFORMATION - [- ] process > NFCORE_MYCOSNP:MYCOSNP:BWA_PREPROCESS:PICARD_ADDORREPLACEREADGROUPS - [- ] process > NFCORE_MYCOSNP:MYCOSNP:BWA_PREPROCESS:SAMTOOLS_INDEX - [91/8ddfea] process > NFCORE_MYCOSNP:MYCOSNP:BWA_PREPROCESS:FASTQC_POST (ERR2172267) [ 0%] 0 of 3 [- ] process > NFCORE_MYCOSNP:MYCOSNP:BWA_PREPROCESS:QUALIMAP_BAMQC - [- ] process > NFCORE_MYCOSNP:MYCOSNP:BWA_PREPROCESS:SAMTOOLS_STATS - [- ] process > NFCORE_MYCOSNP:MYCOSNP:BWA_PREPROCESS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_MYCOSNP:MYCOSNP:BWA_PREPROCESS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_MYCOSNP:MYCOSNP:BWA_PREPROCESS:QC_REPORT - [- ] process > NFCORE_MYCOSNP:MYCOSNP:QC_REPORTSHEET - [- ] process > NFCORE_MYCOSNP:MYCOSNP:GATK4_HAPLOTYPECALLER - [- ] process > NFCORE_MYCOSNP:MYCOSNP:GATK4_LOCALCOMBINEGVCFS - [- ] process > NFCORE_MYCOSNP:MYCOSNP:GATK_VARIANTS:GATK4_GENOTYPEGVCFS - [- ] process > NFCORE_MYCOSNP:MYCOSNP:GATK_VARIANTS:GATK4_VARIANTFILTRATION - [- ] process > NFCORE_MYCOSNP:MYCOSNP:GATK_VARIANTS:GATK4_SELECTVARIANTS - [- ] process > NFCORE_MYCOSNP:MYCOSNP:GATK_VARIANTS:FILTER_GATK_GENOTYPES - [- ] process > NFCORE_MYCOSNP:MYCOSNP:GATK_VARIANTS:BCFTOOLS_VIEW_CONVERT - [- ] process > NFCORE_MYCOSNP:MYCOSNP:GATK_VARIANTS:BCFTOOLS_INDEX - [- ] process > NFCORE_MYCOSNP:MYCOSNP:GATK_VARIANTS:SPLIT_VCF - [- ] process > NFCORE_MYCOSNP:MYCOSNP:GATK_VARIANTS:VCF_CONSENSUS - [- ] process > NFCORE_MYCOSNP:MYCOSNP:GATK_VARIANTS:VCF_TO_FASTA - [- ] process > NFCORE_MYCOSNP:MYCOSNP:GATK_VARIANTS:VCF_QC - [- ] process > NFCORE_MYCOSNP:MYCOSNP:SEQKIT_REPLACE - [- ] process > NFCORE_MYCOSNP:MYCOSNP:SNPDISTS - [- ] process > NFCORE_MYCOSNP:MYCOSNP:CREATE_PHYLOGENY:RAPIDNJ - [- ] process > NFCORE_MYCOSNP:MYCOSNP:CREATE_PHYLOGENY:FASTTREE - [- ] process > NFCORE_MYCOSNP:MYCOSNP:CREATE_PHYLOGENY:QUICKSNP - [- ] process > NFCORE_MYCOSNP:MYCOSNP:CUSTOM_DUMPSOFTWAREVERSIONS - [b7/200515] process > NFCORE_MYCOSNP:MYCOSNP:FASTQC_RAW (ERR2172266) [ 33%] 1 of 3, failed: 1 [- ] process > NFCORE_MYCOSNP:MYCOSNP:MULTIQC - Pulling Singularity image https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0 [cache /blue/bphl-florida/dongyibo/MycoSNP_Test/test/work/singularity/depot.galaxyproject.org-singularity-bedtools-2.30.0--hc088bd4_0.img] Pulling Singularity image https://depot.galaxyproject.org/singularity/bwa:0.7.17--hed695b0_7 [cache /blue/bphl-florida/dongyibo/MycoSNP_Test/test/work/singularity/depot.galaxyproject.org-singularity-bwa-0.7.17--hed695b0_7.img] Pulling Singularity image https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1 [cache /blue/bphl-florida/dongyibo/MycoSNP_Test/test/work/singularity/depot.galaxyproject.org-singularity-samtools-1.15--h1170115_1.img] Pulling Singularity image https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0 [cache /blue/bphl-florida/dongyibo/MycoSNP_Test/test/work/singularity/depot.galaxyproject.org-singularity-picard-2.26.10--hdfd78af_0.img] Execution cancelled -- Finishing pending tasks before exit ERROR ~ Error executing process > 'NFCORE_MYCOSNP:MYCOSNP:FASTQC_RAW (ERR2172266)'

Caused by: Missing output file(s) *.html expected by process NFCORE_MYCOSNP:MYCOSNP:FASTQC_RAW (ERR2172266)

Command executed:

[ ! -f ERR2172266.raw_1.fastq.gz ] && ln -s ERR2172266_R1.fastq.gz ERR2172266.raw_1.fastq.gz [ ! -f ERR2172266.raw_2.fastq.gz ] && ln -s ERR2172266_R2.fastq.gz ERR2172266.raw_2.fastq.gz fastqc --quiet --dir . --threads 2 ERR2172266.raw_1.fastq.gz ERR2172266.raw_2.fastq.gz

cat <<-END_VERSIONS > versions.yml "NFCORE_MYCOSNP:MYCOSNP:FASTQC_RAW": fastqc: $( fastqc --version | sed -e "s/FastQC v//g" ) END_VERSIONS

Command exit status: 0

Command output: (empty)

Command error: ... 6 more Failed to process file ERR2172266.raw_1.fastq.gz javax.imageio.IIOException: Can't create cache file! at java.desktop/javax.imageio.ImageIO.createImageOutputStream(ImageIO.java:423) at java.desktop/javax.imageio.ImageIO.write(ImageIO.java:1589) at uk.ac.babraham.FastQC.Modules.AbstractQCModule.writeDefaultImage(AbstractQCModule.java:72) at uk.ac.babraham.FastQC.Modules.PerBaseQualityScores.makeReport(PerBaseQualityScores.java:199) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.(HTMLReportArchive.java:131) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:185) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123) at java.base/java.lang.Thread.run(Thread.java:834) Caused by: java.nio.file.NoSuchFileException: /blue/bphl-florida/dongyibo/MycoSNP_Test/test/mycosnp-nf/tmp/imageio3321702396665602365.tmp at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:92) at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111) at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:116) at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:215) at java.base/java.nio.file.Files.newByteChannel(Files.java:370) at java.base/java.nio.file.Files.createFile(Files.java:647) at java.base/java.nio.file.TempFileHelper.create(TempFileHelper.java:137) at java.base/java.nio.file.TempFileHelper.createTempFile(TempFileHelper.java:160) at java.base/java.nio.file.Files.createTempFile(Files.java:912) at java.desktop/javax.imageio.stream.FileCacheImageOutputStream.(FileCacheImageOutputStream.java:88) at java.desktop/com.sun.imageio.spi.OutputStreamImageOutputStreamSpi.createOutputStreamInstance(OutputStreamImageOutputStreamSpi.java:68) at java.desktop/javax.imageio.ImageIO.createImageOutputStream(ImageIO.java:419) ... 7 more Failed to process file ERR2172266.raw_2.fastq.gz javax.imageio.IIOException: Can't create cache file! at java.desktop/javax.imageio.ImageIO.createImageOutputStream(ImageIO.java:423) at java.desktop/javax.imageio.ImageIO.write(ImageIO.java:1589) at uk.ac.babraham.FastQC.Modules.AbstractQCModule.writeDefaultImage(AbstractQCModule.java:72) at uk.ac.babraham.FastQC.Modules.PerBaseQualityScores.makeReport(PerBaseQualityScores.java:199)Describe the bug A clear and concise description of what feature is not working.

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urbagal commented 10 months ago

A tmp subfolder in the Mycosnp folder should help resolve this issue.