Error running example PBMC data using nextflow

[bapoorva]

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 ?