pySCENIC
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Published
20 hours ago •
aertslab
aertslab
Error running example PBMC data using nextflow
Hi,
Following this protocol here to run pyscenic on the test pbmc dataset but its failing with this error
nextflow run aertslab/SCENICprotocol \ -profile docker,test
> -profile docker,test
CAPSULE: Downloading dependency org.slf4j:log4j-over-slf4j:jar:1.7.25
CAPSULE: Downloading dependency org.multiverse:multiverse-core:jar:0.7.0
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-xml:jar:3.0.7
CAPSULE: Downloading dependency org.checkerframework:checker-compat-qual:jar:2.0.0
CAPSULE: Downloading dependency io.nextflow:nextflow:jar:21.04.3
CAPSULE: Downloading dependency org.codehaus.mojo:animal-sniffer-annotations:jar:1.14
CAPSULE: Downloading dependency com.google.errorprone:error_prone_annotations:jar:2.1.3
CAPSULE: Downloading dependency com.google.guava:guava:jar:24.1.1-jre
CAPSULE: Downloading dependency org.codehaus.jsr166-mirror:jsr166y:jar:1.7.0
CAPSULE: Downloading dependency org.slf4j:slf4j-api:jar:1.7.25
CAPSULE: Downloading dependency io.nextflow:nf-commons:jar:21.04.3
CAPSULE: Downloading dependency com.beust:jcommander:jar:1.35
CAPSULE: Downloading dependency org.jsoup:jsoup:jar:1.11.2
CAPSULE: Downloading dependency com.google.j2objc:j2objc-annotations:jar:1.1
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-templates:jar:3.0.7
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-json:jar:3.0.7
CAPSULE: Downloading dependency ch.qos.logback:logback-core:jar:1.1.11
CAPSULE: Downloading dependency ch.grengine:grengine:jar:1.3.0
CAPSULE: Downloading dependency jline:jline:jar:2.9
CAPSULE: Downloading dependency com.github.zafarkhaja:java-semver:jar:0.9.0
CAPSULE: Downloading dependency javax.mail:mail:jar:1.4.7
CAPSULE: Downloading dependency org.slf4j:jul-to-slf4j:jar:1.7.25
CAPSULE: Downloading dependency ch.qos.logback:logback-classic:jar:1.1.11
CAPSULE: Downloading dependency commons-lang:commons-lang:jar:2.6
CAPSULE: Downloading dependency org.iq80.leveldb:leveldb-api:jar:0.12
CAPSULE: Downloading dependency org.codehaus.gpars:gpars:jar:1.2.1
CAPSULE: Downloading dependency com.google.code.findbugs:jsr305:jar:1.3.9
CAPSULE: Downloading dependency io.nextflow:nf-httpfs:jar:21.04.3
CAPSULE: Downloading dependency org.objenesis:objenesis:jar:2.1
CAPSULE: Downloading dependency org.yaml:snakeyaml:jar:1.18
CAPSULE: Downloading dependency com.esotericsoftware.kryo:kryo:jar:2.24.0
CAPSULE: Downloading dependency org.slf4j:jcl-over-slf4j:jar:1.7.25
CAPSULE: Downloading dependency org.apache.ivy:ivy:jar:2.3.0
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-nio:jar:3.0.7
CAPSULE: Downloading dependency com.googlecode.javaewah:JavaEWAH:jar:1.1.6
CAPSULE: Downloading dependency javax.activation:activation:jar:1.1.1
CAPSULE: Downloading dependency com.jcraft:jsch:jar:0.1.54
CAPSULE: Downloading dependency org.pf4j:pf4j:jar:3.4.1
CAPSULE: Downloading dependency org.iq80.leveldb:leveldb:jar:0.12
CAPSULE: Downloading dependency org.codehaus.groovy:groovy:jar:3.0.7
CAPSULE: Downloading dependency com.jcraft:jzlib:jar:1.1.1
CAPSULE: Downloading dependency com.google.code.gson:gson:jar:2.2.4
CAPSULE: Downloading dependency org.eclipse.jgit:org.eclipse.jgit:jar:5.2.1.201812262042-r
CAPSULE: Downloading dependency org.pf4j:pf4j-update:jar:2.3.0
CAPSULE: Downloading dependency commons-codec:commons-codec:jar:1.10
N E X T F L O W ~ version 21.04.3
Pulling aertslab/SCENICprotocol ...
downloaded from https://github.com/aertslab/SCENICprotocol.git
Launching `aertslab/SCENICprotocol` [suspicious_hamilton] - revision: 37e555c112 [master]
***
Project name: SCENIC Protocol
Project dir : /home/bapoorva/.nextflow/assets/aertslab/SCENICprotocol
Git info: https://github.com/aertslab/SCENICprotocol - master [37e555c112cc4f55a26ef3f7c232ffe9238ae476]
Cmd line: nextflow run aertslab/SCENICprotocol -profile docker,test
Pipeline version: 0.2.0
***
Parameters in use:
loom_input=https://raw.githubusercontent.com/aertslab/SCENICprotocol/master/example/expr_mat_tiny.loom
loom_filtered=filtered.loom
loom_output=pyscenic_integrated-output.loom
thr_min_genes=1
thr_min_cells=1
thr_n_genes=5000
thr_pct_mito=0.25
outdir=output
threads=6
TFs=https://raw.githubusercontent.com/aertslab/SCENICprotocol/master/example/test_TFs_tiny.txt
motifs=https://raw.githubusercontent.com/aertslab/SCENICprotocol/master/example/motifs.tbl
db=https://raw.githubusercontent.com/aertslab/SCENICprotocol/master/example/genome-ranking.feather
pyscenic_output=pyscenic_output.loom
grn=grnboost2
cell_id_attribute=CellID
gene_attribute=Gene
pyscenic_container=aertslab/pyscenic:0.9.19
seed=777
***
WARNING: only using a single feather database:
/aertslab/SCENICprotocol/master/example/genome-ranking.feather.
To include all database files using pattern matching, make sure the value for the '--db' parameter is enclosed in quotes!
***
executor > local (1)
[b1/133606] process > filter [ 0%] 0 of 1
[- ] process > preprocess -
[- ] process > pca -
[- ] process > visualize -
[- ] process > cluster -
[- ] process > GRNinference -
[- ] process > cisTarget -
[- ] process > AUCell -
[- ] process > visualizeAUC -
[- ] process > integrateOutput -
executor > local (1)
[b1/133606] process > filter [100%] 1 of 1, failed: 1 ✘
[- ] process > preprocess -
[- ] process > pca -
[- ] process > visualize -
[- ] process > cluster -
[- ] process > GRNinference -
[- ] process > cisTarget -
[- ] process > AUCell -
[- ] process > visualizeAUC -
[- ] process > integrateOutput -
Error executing process > 'filter'
Caused by:
Process `filter` terminated with an error exit status (127)
Command executed:
filtering-basic.py --loom_input expr_mat_tiny.loom --loom_filtered filtered.loom --thr_min_genes 1 --thr_min_cells 1 --thr_n_genes 5000 --thr_pct_mito 0.25
Command exit status:
127
Command output:
(empty)
Command error:
.command.run: line 72: docker: command not found
Work dir:
/project/labprojects/projects/Morrisey/Maria/lungMAP/Pediatric/Prox_3/scenic/work/b1/133606672916b4e8fab0df7f0a790f
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
It is basically failing at the filtration step. What am i doing wrong here ?
Sorry my bad. I have singularity installed. So now i gave it the command
nextflow run aertslab/SCENICprotocol -profile singularity,test
Still getting an error
N E X T F L O W ~ version 21.04.3
Launching `aertslab/SCENICprotocol` [disturbed_mahavira] - revision: 37e555c112 [master]
***
Project name: SCENIC Protocol
Project dir : /home/bapoorva/.nextflow/assets/aertslab/SCENICprotocol
Git info: https://github.com/aertslab/SCENICprotocol - master [37e555c112cc4f55a26ef3f7c232ffe9238ae476]
Cmd line: nextflow run aertslab/SCENICprotocol -profile singularity,test
Pipeline version: 0.2.0
***
Parameters in use:
loom_input=https://raw.githubusercontent.com/aertslab/SCENICprotocol/master/example/expr_mat_tiny.loom
loom_filtered=filtered.loom
loom_output=pyscenic_integrated-output.loom
thr_min_genes=1
thr_min_cells=1
thr_n_genes=5000
thr_pct_mito=0.25
outdir=output
threads=6
TFs=https://raw.githubusercontent.com/aertslab/SCENICprotocol/master/example/test_TFs_tiny.txt
motifs=https://raw.githubusercontent.com/aertslab/SCENICprotocol/master/example/motifs.tbl
db=https://raw.githubusercontent.com/aertslab/SCENICprotocol/master/example/genome-ranking.feather
pyscenic_output=pyscenic_output.loom
grn=grnboost2
cell_id_attribute=CellID
gene_attribute=Gene
pyscenic_container=aertslab/pyscenic:0.9.19
seed=777
***
WARNING: only using a single feather database:
/aertslab/SCENICprotocol/master/example/genome-ranking.feather.
To include all database files using pattern matching, make sure the value for the '--db' parameter is enclosed in quotes!
***
[- ] process > filter -
[- ] process > preprocess -
[- ] process > pca -
[- ] process > filter -
[- ] process > preprocess -
[- ] process > pca -
[- ] process > visualize -
[- ] process > cluster -
[- ] process > GRNinference -
[- ] process > cisTarget -
[- ] process > AUCell -
[- ] process > visualizeAUC -
[- ] process > filter -
[- ] process > preprocess -
[- ] process > pca -
[- ] process > visualize -
[- ] process > cluster -
[- ] process > GRNinference -
[- ] process > cisTarget -
[- ] process > AUCell -
[- ] process > visualizeAUC -
[- ] process > integrateOutput -
Pulling Singularity image docker://aertslab/pyscenic:0.9.19 [cache /project/labprojects/projects/Morrisey/Maria/lungMAP/Pediatric/old/Prox_3/scenic/work/singularity/aertslab-pyscenic-0.9.19.img]
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /project/labprojects/scenic/work/singularity -- Use env variable NXF_SINGULARITY_CACHEDIR to specify a different location
Error executing process > 'filter'
Caused by:
Failed to pull singularity image
command: singularity pull --name aertslab-pyscenic-0.9.19.img.pulling.1668094117397 docker://aertslab/pyscenic:0.9.19 > /dev/null
status : 255
message:
INFO: Converting OCI blobs to SIF format
FATAL: While making image from oci registry: error fetching image to cache: while building SIF from layers: unable to create new build: while searching for mksquashfs: exec: "mksquashfs": executable file not found in $PATH
Hello, bapoorva,
The same happen on my own data.
have you found any soulution?
regards,
Erfan
