v1.4 works, but v1.5 not work

[ybdong919]

In my end, v1.4 has been working but v1.5 not work. The error of v1.5 is below:

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.

[jwarnn]

I ran into the same issue in a linux and cloud environment. As a work around I created an empty directory in the launch folder called tmp. That fixed the issue in both environments. Try that and see if it works. Then maybe we could do a PR and get that added into the workflow.

[urbagal]

Yes, creating a tmp sub-folder within mycosnp folder will resolve the issue. In the newer version, an empty folder will be added.

[hgibling]

EDIT: This must have been a local issue for me. Retested and found that the tmp dir is only needed in the main software folder.

@urbagal A note that adding the empty tmp folder in the mycosnp-nf folder alone did not solve this issue for me, I also had to put an empty tmp folder in the launch directory, as jwarnn mentioned above.

This was the case with the mycosnp version at commit 41b3656be38eecf0f7639f1d449dc8af888c5408, singularity 3.10.0, and either nextflow 23.10.1.5891 or 23.04.1.5866 (both were tested).