zuberlab / crispr-mageck-nf Goto Github PK
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License: MIT License
Analyze CRISPR and shRNA functional genetic screening data
License: MIT License
N E X T F L O W ~ version 19.01.0
Launching `zuberlab/crispr-mageck-nf` [jovial_engelbart] - revision: 3b2575bbe5 [master]
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$mageck = <value>` with a process selector
[warm up] executor > slurm
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$postprocess = <value>` with a process selector
[74/c8674e] Submitted process > mageck (48hIFNG_d04_HLA_high_vs_NoIFNG_d0)
ERROR ~ Error executing process > 'mageck (48hIFNG_d04_HLA_high_vs_NoIFNG_d0)'
Caused by:
Process `mageck (48hIFNG_d04_HLA_high_vs_NoIFNG_d0)` terminated with an error exit status (1)
Command executed:
prefilter_counts.R counts_mageck_ctrls-grouped.txt "pmax(48hIFNG_d04_HLA_high,NoIFNG_d0)" 50 > counts_filtered.txt
VERSION=$(mageck -v 2>&1 >/dev/null)
if [ $VERSION = "0.5.5" ]; then
mageck test --output-prefix 48hIFNG_d04_HLA_high_vs_NoIFNG_d0 --count-table counts_filtered.txt --control-id NoIFNG_d0 --treatment-id 48hIFNG_d04_HLA_high --norm-method median --adjust-method fdr --gene-lfc-method mean --normcounts-to-file
else
mageck test --output-prefix 48hIFNG_d04_HLA_high_vs_NoIFNG_d0 --count-table counts_filtered.txt --control-id NoIFNG_d0 --treatment-id 48hIFNG_d04_HLA_high --norm-method median --adjust-method fdr --gene-lfc-method mean --normcounts-to-file
fi
Command exit status:
1
Command output:
(empty)
Command error:
.command.stub: line 45: ps: command not found
.command.stub: line 45: ps: command not found
.command.stub: line 45: ps: command not found
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
Parsed with column specification:
cols(
.default = col_integer(),
id = col_character(),
group = col_character()
)
See spec(...) for full column specifications.
Error in parse(text = x) : <text>:1:8: unexpected symbol
1: pmax(48hIFNG_d04_HLA_high
^
Calls: %>% ... eval_bare -> .Call -> parse_expr -> parse_exprs -> parse
Execution halted
Work dir:
/groups/zuber/zubarchive/USERS/Kimon/markus/HLA1_staggered/work/74/c8674eaf6ff6d7d550c57c867ad3d3
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
FAILED
If I edit the counts table and contrasts table to rename the offending sample as h48IFNG_d04_HLA_high
instead, the pipeline works fine.
Hi, thanks for putting this together.
I'm trying to understand the contrasts.txt file and how to indicate my design matrix for the analysis. How does one specify baseline (time 0), for the treatment and control conditions? Also, why do some entries in the table take a list of multiple samples?
Why not stick with the design matrix format that mageck normally takes as input?
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