Problem with running mop_preprocess.nf
Closed this issue · 1 comments
assetdaniyarov commented
Hi,
There is a problem running mop_preprocess.nf.
(drna_mop2) prom@PCT0223:/path/MOP2/mop_preprocess$ /path/nextflow run mop_preprocess.nf -with-singularity -profile local
N E X T F L O W ~ version 22.10.2
Launching `mop_preprocess.nf` [hopeful_majorana] DSL2 - revision: ec40fe0af4
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====================================================
BIOCORE@CRG Master of Pores 2. Preprocessing - N F ~ version 2.0
====================================================
conffile. : final_summary_01.txt
fast5 :
fastq : /path/**/*.fastq
reference : /data/PublicData/refSeq_transcripts/GRCh38_latest_rna.fna
annotation : /data/PublicData/refSeq_transcripts/GRCh38_latest_genomic.gff.gz
granularity. : 1
ref_type : transcriptome
pars_tools : drna_tool_splice_opt.tsv
output : /path/MOP2/mop_preprocess/output
GPU : ON
basecalling : guppy
demultiplexing : NO
demulti_fast5 : NO
filtering : nanoq
mapping : graphmap2
counting : nanocount
discovery : bambu
cram_conv : NO
subsampling_cram : 50
saveSpace : NO
email : lucacozzuto@crg.es
Sending the email to lucacozzuto@crg.es
----------------------CHECK TOOLS -----------------------------
> basecalling will be skipped
> demultiplexing will be skipped
mapping : graphmap2
filtering : nanoq
counting : nanocount
discovery : bambu
--------------------------------------------------------------
[- ] process > preprocess_simple:FASTQC:fastQC -
[- ] process > preprocess_simple:GRAPHMAP2:map -
[- ] process > preprocess_simple:FASTQC:fastQC -
[- ] process > preprocess_simple:GRAPHMAP2:map -
[- ] process > preprocess_simple:SAMTOOLS_SORT:sortAln -
[- ] process > preprocess_simple:SAMTOOLS_INDEX:indexBam -
[- ] process > preprocess_simple:bam2stats -
[- ] process > preprocess_simple:joinAlnStats -
[- ] process > preprocess_simple:NANOPLOT_QC:MOP_nanoPlot -
[- ] process > preprocess_simple:NANOCOUNT:nanoCount -
[- ] process > preprocess_simple:AssignReads -
[- ] process > preprocess_simple:countStats -
[- ] process > preprocess_simple:joinCountStats -[- ] process > preprocess_simple:MULTIQC:makeReport -
[- ] process > preprocess_simple:FASTQC:fastQC -
[- ] process > preprocess_simple:GRAPHMAP2:map -
[- ] process > preprocess_simple:SAMTOOLS_SORT:sortAln -
[- ] process > preprocess_simple:SAMTOOLS_INDEX:indexBam -
[- ] process > preprocess_simple:bam2stats -
[- ] process > preprocess_simple:joinAlnStats -[- ] process > preprocess_simple:NANOPLOT_QC:MOP_nanoPlot -
[- ] process > preprocess_simple:NANOCOUNT:nanoCount -
[- ] process > preprocess_simple:AssignReads -
[- ] process > preprocess_simple:countStats -
[- ] process > preprocess_simple:joinCountStats -
[- ] process > preprocess_simple:MULTIQC:makeReport -
Error executing process > 'preprocess_simple:FASTQC:fastQC (PAI52977_pass_d5246539_0.fastq)'
Caused by:
Failed to pull singularity image
command: singularity pull --name quay.io-biocontainers-fastqc-0.11.9--0.img.pulling.1668531299614 docker://quay.io/biocontainers/fastqc:0.11.9--0 > /dev/null
status : 255
message:
INFO: Converting OCI blobs to SIF format
INFO: Starting build...
Getting image source signatures
Copying blob sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
Copying blob sha256:77c6c00e8b61bb628567c060b85690b0b0561bb37d8ad3f3792877bddcfe2500
Copying blob sha256:3aaade50789a6510c60e536f5e75fe8b8fc84801620e575cb0435e2654ffd7f6
Copying blob sha256:00cf8b9f3d2a08745635830064530c931d16f549d031013a9b7c6535e7107b88
Copying blob sha256:7ff999a2256f84141f17d07d26539acea8a4d9c149fefbbcc9a8b4d15ea32de7
Copying blob sha256:d2ba336f2e4458a9223203bf17cc88d77e3006d9cbf4f0b24a1618d0a5b82053
Copying blob sha256:dfda3e01f2b637b7b89adb401f2f763d592fcedd2937240e2eb3286fabce55f0
Copying blob sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
Copying blob sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
Copying blob sha256:10c3bb32200bdb5006b484c59b5f0c71b4dbab611d33fca816cd44f9f5ce9e3c
Copying blob sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
Copying blob sha256:6d92b3a49ebfad5fe895550c2cb24b6370d61783aa4f979702a94892cbd19077
Copying config sha256:8b79910fc535b5dd09ef33662f939e7e51006d1ef5545c919e72cc877acbe5b1
Writing manifest to image destination
Storing signatures
2022/11/15 16:55:38 info unpack layer: sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
2022/11/15 16:55:39 info unpack layer: sha256:77c6c00e8b61bb628567c060b85690b0b0561bb37d8ad3f3792877bddcfe2500 2022/11/15 16:55:39 warn rootless{dev/console} creating empty file in place of device 5:1 2022/11/15 16:55:39 info unpack layer: sha256:3aaade50789a6510c60e536f5e75fe8b8fc84801620e575cb0435e2654ffd7f6
2022/11/15 16:55:39 info unpack layer: sha256:00cf8b9f3d2a08745635830064530c931d16f549d031013a9b7c6535e7107b88
2022/11/15 16:55:39 info unpack layer: sha256:7ff999a2256f84141f17d07d26539acea8a4d9c149fefbbcc9a8b4d15ea32de7
2022/11/15 16:55:39 info unpack layer: sha256:d2ba336f2e4458a9223203bf17cc88d77e3006d9cbf4f0b24a1618d0a5b82053
2022/11/15 16:55:39 info unpack layer: sha256:dfda3e01f2b637b7b89adb401f2f763d592fcedd2937240e2eb3286fabce55f0
2022/11/15 16:55:39 info unpack layer: sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
2022/11/15 16:55:39 info unpack layer: sha256:10c3bb32200bdb5006b484c59b5f0c71b4dbab611d33fca816cd44f9f5ce9e3c
2022/11/15 16:55:39 info unpack layer: sha256:6d92b3a49ebfad5fe895550c2cb24b6370d61783aa4f979702a94892cbd19077
INFO: Creating SIF file...
FATAL: While making image from oci registry: error fetching image to cache: while building SIF from layers: while creating SIF: while creating container: writing data object for SIF file: copying data object file to SIF file: write /home/prom/.singularity/cache/oci-tmp/tmp_223233459: no space left on device
(drna_mop2) prom@PCT0223:/path/MOP2/mop_preprocess$
(drna_mop2) prom@PCT0223:/path/MOP2/mop_preprocess$ which singularity
/usr/local/bin/singularity
(drna_mop2) prom@PCT0223:/path/MOP2/mop_preprocess$ singularity version
3.6.3
(drna_mop2) prom@PCT0223:/path/MOP2/mop_preprocess$ guppy_basecaller -v
: Guppy Basecalling Software, (C) Oxford Nanopore Technologies, Limited. Version 3.4.5+fb1fbfb
(drna_mop2) prom@PCT0223:/path/MOP2/mop_preprocess$ which guppy_basecaller
/path/MOP2/mop_preprocess/bin/ont-guppy/bin/guppy_basecaller
I attach the configuration file params.config.test:
params {
conffile = "final_summary_01.txt"
fast5 = ""
fastq = "/path/**/*.fastq"
reference = "/data/PublicData/refSeq_transcripts/GRCh38_latest_rna.fna"
annotation = "/data/PublicData/refSeq_transcripts/GRCh38_latest_genomic.gff.gz"
ref_type = "transcriptome"
pars_tools = "drna_tool_splice_opt.tsv"
output = "$baseDir/output"
qualityqc = 5
granularity = 1
basecalling = "guppy"
GPU = "ON"
demultiplexing = "NO"
demulti_fast5 = "NO"
filtering = "nanoq"
mapping = "graphmap2"
counting = "nanocount"
discovery = "bambu"
cram_conv = "NO"
subsampling_cram = 50
saveSpace = "NO"
email = "lucacozzuto@crg.es"
}
lucacozzuto commented
Hi, the problem is written in the log:
no space left on device
Luca