.command.sh: line 2: repmask_vcf.sh: command not found #56
Comments
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Can you install Nextflow without conda?
In the past, people reported issues when things were installed via conda.
…-------- Original Message --------
On 2/7/25 1:32 PM, Will Tyler wrote:
Description
I am trying to run the test dataset and failing with the error below. I think repmask_vcf.sh is in the bin folder, but I am not sure how to fix this because I am new to Nextflow and Apptainer. I reset my Nextflow and Apptainer cache prior to running the command below.
Command
nextflow run https://github.com/cgroza/GraffiTE --reference hs37d5.chr22.fa --assemblies assemblies.csv --reads reads.csv --TE_library human_DFAM3.6.fasta
Output
N E X T F L O W ~ version 24.10.4
Pulling cgroza/GraffiTE ...
downloaded from https://github.com/cgroza/GraffiTE.git
Launching `https://github.com/cgroza/GraffiTE` [sleepy_lamport] DSL2 - revision: 2f5a1bd [main]
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V . 2f5a1bd
Find and Genotype Transposable Elements Insertion Polymorphisms
in Genome Assemblies using a Pangenomic Approach
Authors: Cristian Groza and Clément Goubert
Bug/issues: https://github.com/cgroza/GraffiTE/issues
WARN: Access to undefined parameter `bams` -- Initialise it to a default value eg. `params.bams = some_value`
[- ] process > map_asm -
executor > local (5)
[a6/e5a214] process > map_asm (1) [100%] 1 of 1 ✔
executor > local (5)
[a6/e5a214] process > map_asm (1) [100%] 1 of 1 ✔
[ab/658322] process > svim_asm (1) [100%] 1 of 1 ✔
[fc/e4eb59] process > survivor_merge [100%] 1 of 1 ✔
[a8/8e8e64] process > split_repeatmask [100%] 1 of 1 ✔
[09/4ea3f8] process > repeatmask_VCF (1) [100%] 1 of 1, failed: 1 ✘
[- ] process > tsd_prep -
[- ] process > tsd_search -
[- ] process > tsd_report -
[- ] process > concat_repeatmask -
[- ] process > pangenie -
[- ] process > merge_VCFs -
ERROR ~ Error executing process > 'repeatmask_VCF (1)'
Caused by:
Process `repeatmask_VCF (1)` terminated with an error exit status (127)
Command executed:
repmask_vcf.sh genotypes.vcf genotypes_repmasked.vcf.gz human_DFAM3.6.fasta
bcftools view -G genotypes_repmasked.vcf.gz | awk -v FS=' ' -v OFS=' ' '{if($0 ~ /#CHROM/) {$9 = "FORMAT"; $10 = "ref"; print $0} else if(substr($0, 1, 1) == "#") {print $0} else {$9 = "GT"; $10 = "1|0"; print $0}}' | awk 'NR==1{print; print "##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">"} NR!=1' | bcftools view -i 'INFO/total_match_span > 0.80' -o genotypes_repmasked_temp.vcf
fix_vcf.py --ref hs37d5.chr22.fa --vcf_in genotypes_repmasked_temp.vcf --vcf_out genotypes_repmasked_filtered.vcf
Command exit status:
127
Command output:
(empty)
Command error:
INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
.command.sh: line 2: repmask_vcf.sh: command not found
Work dir:
/N/slate/tylerwi/GraffiTE_testset/work/09/4ea3f82e3ab078efe4ef0c9cb3b099
Container:
/N/slate/tylerwi/GraffiTE_testset/work/singularity/cgroza-collection-graffite-latest.img
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
-- Check '.nextflow.log' file for details
System details
uname -a
Linux c30.quartz.uits.iu.edu 4.18.0-553.16.1.el8_10.x86_64 #1 SMP Thu Aug 1 04:16:12 EDT 2024 x86_64 GNU/Linux
I loaded Apptainer as a module available on my university's computing system.
module list
Currently Loaded Modules:
1) gnu/9.3.0 2) quota/1.9 3) xalt/3.0.3 4) mvapich/2.3.5 5) StdEnv 6) conda/24.1.2 7) apptainer/1.1.9 8) singularity/apptainer/1.1.9
I installed Nextflow through a conda environment.
conda env export
name: graffite
channels:
- defaults
- bioconda
- conda-forge
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=2_gnu
- _sysroot_linux-64_curr_repodata_hack=3=haa98f57_10
- alsa-lib=1.2.13=hb9d3cd8_0
- bzip2=1.0.8=h5eee18b_6
- c-ares=1.34.4=hb9d3cd8_0
- ca-certificates=2024.12.31=h06a4308_0
- cairo=1.18.0=hbb29018_2
- coreutils=8.25=1
- curl=8.11.1=h332b0f4_0
- font-ttf-dejavu-sans-mono=2.37=hd3eb1b0_0
- font-ttf-inconsolata=2.001=hcb22688_0
- font-ttf-source-code-pro=2.030=hd3eb1b0_0
- font-ttf-ubuntu=0.83=h8b1ccd4_0
- fontconfig=2.15.0=h7e30c49_1
- fonts-anaconda=1=h8fa9717_0
- fonts-conda-ecosystem=1=hd3eb1b0_0
- freetype=2.12.1=h267a509_2
- giflib=5.2.2=h5eee18b_0
- graphite2=1.3.14=h295c915_1
- harfbuzz=8.5.0=hfac3d4d_0
- icu=73.2=h59595ed_0
- k8=1.2=he8db53b_5
- kernel-headers_linux-64=3.10.0=h57e8cba_10
- krb5=1.21.3=h143b758_0
- lcms2=2.16=hb7c19ff_0
- lerc=4.0.0=h6a678d5_0
- libcups=2.3.3=h4637d8d_4
- libcurl=8.11.1=h332b0f4_0
- libdeflate=1.23=h4ddbbb0_0
- libedit=3.1.20230828=h5eee18b_0
- libev=4.33=h7f8727e_1
- libexpat=2.6.4=h5888daf_0
- libffi=3.4.4=h6a678d5_1
- libgcc=14.2.0=h77fa898_1
- libgcc-ng=14.2.0=h69a702a_1
- libglib=2.82.2=h2ff4ddf_1
- libgomp=14.2.0=h77fa898_1
- libiconv=1.17=hd590300_2
- libjpeg-turbo=3.0.3=h5eee18b_0
- liblzma=5.6.4=hb9d3cd8_0
- libnghttp2=1.64.0=h161d5f1_0
- libpng=1.6.46=h943b412_0
- libssh2=1.11.1=hf672d98_0
- libstdcxx=14.2.0=hc0a3c3a_1
- libstdcxx-ng=14.2.0=h4852527_1
- libtiff=4.7.0=hd9ff511_3
- libuuid=2.38.1=h0b41bf4_0
- libwebp-base=1.5.0=h851e524_0
- libxcb=1.17.0=h8a09558_0
- libzlib=1.3.1=hb9d3cd8_2
- minimap2=2.28=h577a1d6_4
- ncurses=6.4=h6a678d5_0
- nextflow=24.10.4=hdfd78af_0
- openjdk=21.0.0=haa376d0_0
- openssl=3.4.0=h7b32b05_1
- pcre2=10.44=hba22ea6_2
- pixman=0.44.2=h29eaf8c_0
- pthread-stubs=0.3=h0ce48e5_1
- python_abi=3.13=0_cp313
- sysroot_linux-64=2.17=h57e8cba_10
- xorg-libice=1.1.2=hb9d3cd8_0
- xorg-libsm=1.2.5=he73a12e_0
- xorg-libx11=1.8.11=h4f16b4b_0
- xorg-libxau=1.0.12=hb9d3cd8_0
- xorg-libxdmcp=1.1.5=hb9d3cd8_0
- xorg-libxext=1.3.6=hb9d3cd8_0
- xorg-libxfixes=6.0.1=hb9d3cd8_0
- xorg-libxi=1.8.2=hb9d3cd8_0
- xorg-libxrender=0.9.12=hb9d3cd8_0
- xorg-libxt=1.3.1=hb9d3cd8_0
- xorg-libxtst=1.2.5=hb9d3cd8_3
- zlib=1.3.1=hb9d3cd8_2
- zstd=1.5.6=ha6fb4c9_0
prefix: /N/u/tylerwi/Quartz/.conda/envs/graffite
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I tried reinstalling Nextflow (with |
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Somehow the PATH environment variable is not being configured properly in your case.
I never had to mess with this myself, it was always handled for me by Nextflow and singularity.
Normally, nextflow should add the bin directory to the PATH in the execution environment.
This directory is cloned from the GraffiTE repository and contains all the scripts the pipeline needs.
…On Friday, February 7th, 2025 at 2:01 PM, Will Tyler ***@***.***> wrote:
I tried reinstalling Nextflow (with curl -s https://get.nextflow.io | bash). I then cleaned the Nextflow cache and Apptainer cache. I am still getting the same issue.
/N/slate/tylerwi/nextflow run https://github.com/cgroza/GraffiTE --reference hs37d5.chr22.fa --assemblies assemblies.csv --reads reads.csv --TE_library human_DFAM3.6.fasta
N E X T F L O W ~ version 24.10.4
Launching `https://github.com/cgroza/GraffiTE` [lonely_lovelace] DSL2 - revision: 2f5a1bd [main]
▄████ ██▀███ ▄▄▄ █████▒ █████▒██▓▄▄▄█████▓▓█████
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░ ░ ░ ░░ ░ ░ ▒ ░ ░ ░ ░ ▒ ░ ░ ░
░ ░ ░ ░ ░ ░ ░
V . 2f5a1bd
Find and Genotype Transposable Elements Insertion Polymorphisms
in Genome Assemblies using a Pangenomic Approach
Authors: Cristian Groza and Clément Goubert
Bug/issues: https://github.com/cgroza/GraffiTE/issues
WARN: Access to undefined parameter `bams` -- Initialise it to a default value eg. `params.bams = some_value`
executor > local (5)
[57/b1c625] process > map_asm (1) [100%] 1 of 1 ✔
executor > local (5)
[57/b1c625] process > map_asm (1) [100%] 1 of 1 ✔
[28/5b1510] process > svim_asm (1) [100%] 1 of 1 ✔
[99/f6a463] process > survivor_merge [100%] 1 of 1 ✔
[3d/468777] process > split_repeatmask [100%] 1 of 1 ✔
[ee/a0cb12] process > repeatmask_VCF (1) [100%] 1 of 1, failed: 1 ✘
[- ] process > tsd_prep -
[- ] process > tsd_search -
[- ] process > tsd_report -
[- ] process > concat_repeatmask -
[- ] process > pangenie -
[- ] process > merge_VCFs -
ERROR ~ Error executing process > 'repeatmask_VCF (1)'
Caused by:
Process `repeatmask_VCF (1)` terminated with an error exit status (127)
Command executed:
repmask_vcf.sh genotypes.vcf genotypes_repmasked.vcf.gz human_DFAM3.6.fasta
bcftools view -G genotypes_repmasked.vcf.gz | awk -v FS=' ' -v OFS=' ' '{if($0 ~ /#CHROM/) {$9 = "FORMAT"; $10 = "ref"; print $0} else if(substr($0, 1, 1) == "#") {print $0} else {$9 = "GT"; $10 = "1|0"; print $0}}' | awk 'NR==1{print; print "##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">"} NR!=1' | bcftools view -i 'INFO/total_match_span > 0.80' -o genotypes_repmasked_temp.vcf
fix_vcf.py --ref hs37d5.chr22.fa --vcf_in genotypes_repmasked_temp.vcf --vcf_out genotypes_repmasked_filtered.vcf
Command exit status:
127
Command output:
(empty)
Command error:
INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
.command.sh: line 2: repmask_vcf.sh: command not found
Work dir:
/N/slate/tylerwi/GraffiTE_testset/work/ee/a0cb12ef77128b6f3b069e32150589
Container:
/N/slate/tylerwi/GraffiTE_testset/work/singularity/cgroza-collection-graffite-latest.img
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
-- Check '.nextflow.log' file for details
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I am able to get through the |
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So I attempted to replicate your scenario and it works fine on my end. |
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Description
I am trying to run the test dataset and failing with the error below. I think
repmask_vcf.shis in thebinfolder, but I am not sure how to fix this because I am new to Nextflow and Apptainer. I reset my Nextflow and Apptainer cache prior to running the command below.Command
Output
System details
I loaded Apptainer as a module available on my university's computing system.
I installed Nextflow through a conda environment.
The text was updated successfully, but these errors were encountered: