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This repository has been archived by the owner on Jun 13, 2024. It is now read-only.
I try to run scflow and got this error:
Would you please have a look? When I run the command view manifest.txt, I don't have the number 1 and 2 before each row. Thank you so much! nextflow run nf-core/scflow \--manifest manifest.txt \--input sample_sheet.tsv \-c scflow_analysis.config \-profile singularity -r dev
ERROR ~ Error executing process > 'SCFLOW:SCFLOW_CHECKINPUTS (SCFLOW_CHECKINPUTS)'
Caused by:
Process `SCFLOW:SCFLOW_CHECKINPUTS (SCFLOW_CHECKINPUTS)` terminated with an error exit status (1)
Command executed:
check_inputs.r \
--input sample_sheet.tsv --manifest manifest.txt
scflow_version=$(Rscript -e 'cat(as.character(utils::packageVersion("scFlow")))'); echo "scFlow ${scflow_version}" > "scFlow_${scflow_version}.version.txt"
Command exit status:
1
Command output:
The following paths were not found: -
key filepath
1 wt /labs/chris/sn_mouse/wt/filtered_feature_bc_matrix
2 mt /labs/chris/sn_mouse/ko/filtered_feature_bc_matrix
Command error:
/apps/modules/lmod/lmod/init/bash: line 16: __lmod_vx: unbound variable
INFO: Converting SIF file to temporary sandbox...
Warning message:
In read.table(file = file, header = header, sep = sep, quote = quote, :
incomplete final line found by readTableHeader on 'sample_sheet.tsv' (edited)
Hello,
I see two bits. The trivial one is that you likely miss a terminal newline in your sample_sheet.tsv file, which would make that warning disappear. When editing files in Windows this commonly happens.
The not so trivial part (for me) is that
INFO: Converting SIF file to temporary sandbox...
warning. This likely means that your singularity box cannot access anything outside of what is local to it in the file tree. I tried multiple things
add containerOptions flag with -B /labs
set environment variable SINGULARITY_BIND
but in the end it only helped to copy/move the data to a local subdirectory and then adjust the paths.
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Hi there!
I try to run scflow and got this error:
Would you please have a look? When I run the command view manifest.txt, I don't have the number 1 and 2 before each row. Thank you so much!
nextflow run nf-core/scflow \--manifest manifest.txt \--input sample_sheet.tsv \-c scflow_analysis.config \-profile singularity -r dev
manifest.txt
key filepath
wt /labs/chris/sn_mouse/WT/filtered_feature_bc_matrix
mt /labs/chris/sn_mouse/KO/filtered_feature_bc_matrix
sample_sheet.txt
individual group diagnosis manifest
1 wt wt wt
2 ko ko ko
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