wangdatou2009
commented
6 years ago And if I tried nextflow run YAMP.nf --reads1 ./data/ERR011089_1.fastq.gz --reads2 ./data/ERR011089_2.fastq.gz --prefix Meta_HIT_ERR011089 --outdir ./data --mode complete -with-docker docker://alesssia/yampdocker
basically the same
N E X T F L O W ~ version 0.28.0
Launching YAMP.nf [cocky_lovelace] - revision: 8ed2c9d795
[warm up] executor > local
[5d/aef143] Submitted process > dedup
[6c/5db1ee] Submitted process > qualityAssessment (1)
[51/90f83d] Submitted process > qualityAssessment (2)
ERROR ~ Error executing process > 'dedup'
Caused by:
Process dedup terminated with an error exit status (125)
Command executed:
Measures execution time
sysdate=$(date) starttime=$(date +%s.%N) echo "Performing Quality Control. STEP 1 [De-duplication] at $sysdate" > .log.2 echo " " >> .log.2
Sets the maximum memory to the value requested in the config file
maxmem=$(echo "32 GB" | sed 's/ //g' | sed 's/B//g')
Defines command for de-duplication
if [ "paired" = "paired" ]; then CMD="clumpify.sh -Xmx"$maxmem" in1=ERR011089_1.fastq.gz in2=ERR011089_2.fastq.gz out1=Meta_HIT_ERR011089_dedupe_R1.fq.gz out2=Meta_HIT_ERR011089_dedupe_R2.fq.gz qin=33 dedupe subs=0 threads=4" else CMD="clumpify.sh -Xmx"$maxmem" in=ERR011089_1.fastq.gz out=Meta_HIT_ERR011089_dedupe.fq.gz qin=33 dedupe subs=0 threads=4" fi
Logs version of the software and executed command (BBmap prints on stderr)
version=$(clumpify.sh --version 2>&1 >/dev/null | grep "BBMap version") echo "Using clumpify.sh in $version " >> .log.2 echo "Executing command: $CMD " >> .log.2 echo " " >> .log.2
De-duplicates
exec $CMD 2>&1 | tee tmp.log
Logs some figures about sequences passing de-duplication
echo "Clumpify's de-duplication stats: " >> .log.2 echo " " >> .log.2 sed -n '/Reads In:/,/Duplicates Found:/p' tmp.log >> .log.2 echo " " >> .log.2 totR=$(grep "Reads In:" tmp.log | cut -f 1 | cut -d: -f 2 | sed 's/ //g') remR=$(grep "Duplicates Found:" tmp.log | cut -f 1 | cut -d: -f 2 | sed 's/ //g') survivedR=$(($totR-$remR)) percentage=$(echo $survivedR $totR | awk '{print $1/$2*100}' ) echo "$survivedR out of $totR paired reads survived de-duplication ($percentage%, $remR reads removed)" >> .log.2 echo " " >> .log.2
Measures and logs execution time
endtime=$(date +%s.%N) exectime=$(echo "$endtime $starttime" | awk '{print $1-$2}') sysdate=$(date) echo "STEP 1 (Quality control) terminated at $sysdate ($exectime seconds)" >> .log.2 echo " " >> .log.2 echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++" >> .log.2 echo " " >> .log.2
Command exit status: 125
Command output: (empty)
Command error: docker: Error parsing reference: "docker://alesssia/yampdocker" is not a valid repository/tag: invalid reference format. See 'docker run --help'.
Work dir: ......................YAMP/work/5d/aef143354299874734a019ccc6a418
Tip: when you have fixed the problem you can continue the execution appending to the nextflow command line the option -resume
-- Check '.nextflow.log' file for details WARN: Killing pending tasks (1)
alesssia
Hi Alessia, I tried to use docker and run locally in linux 16.04, I tried steps like below, and what's wrong with the error ? the docker image was pulled completely, but the system still unable to find image 'yampdocker:latest' locally
Error N E X T F L O W ~ version 0.28.0 Launching
YAMP.nf[angry_shockley] - revision: 8ed2c9d795 [warm up] executor > local [ff/30bff9] Submitted process > dedup [78/3e0203] Submitted process > qualityAssessment (1) [51/e88aa9] Submitted process > qualityAssessment (2) ERROR ~ Error executing process > 'dedup'Caused by: Process
dedupterminated with an error exit status (125)Command executed:
Measures execution time
sysdate=$(date) starttime=$(date +%s.%N) echo "Performing Quality Control. STEP 1 [De-duplication] at $sysdate" > .log.2 echo " " >> .log.2
Sets the maximum memory to the value requested in the config file
maxmem=$(echo "32 GB" | sed 's/ //g' | sed 's/B//g')
Defines command for de-duplication
if [ "paired" = "paired" ]; then CMD="clumpify.sh -Xmx"$maxmem" in1=ERR011089_1.fastq.gz in2=ERR011089_2.fastq.gz out1=Meta_HIT_ERR011089_dedupe_R1.fq.gz out2=Meta_HIT_ERR011089_dedupe_R2.fq.gz qin=33 dedupe subs=0 threads=4" else CMD="clumpify.sh -Xmx"$maxmem" in=ERR011089_1.fastq.gz out=Meta_HIT_ERR011089_dedupe.fq.gz qin=33 dedupe subs=0 threads=4" fi
Logs version of the software and executed command (BBmap prints on stderr)
version=$(clumpify.sh --version 2>&1 >/dev/null | grep "BBMap version") echo "Using clumpify.sh in $version " >> .log.2 echo "Executing command: $CMD " >> .log.2 echo " " >> .log.2
De-duplicates
exec $CMD 2>&1 | tee tmp.log
Logs some figures about sequences passing de-duplication
echo "Clumpify's de-duplication stats: " >> .log.2 echo " " >> .log.2 sed -n '/Reads In:/,/Duplicates Found:/p' tmp.log >> .log.2 echo " " >> .log.2 totR=$(grep "Reads In:" tmp.log | cut -f 1 | cut -d: -f 2 | sed 's/ //g') remR=$(grep "Duplicates Found:" tmp.log | cut -f 1 | cut -d: -f 2 | sed 's/ //g') survivedR=$(($totR-$remR)) percentage=$(echo $survivedR $totR | awk '{print $1/$2*100}' ) echo "$survivedR out of $totR paired reads survived de-duplication ($percentage%, $remR reads removed)" >> .log.2 echo " " >> .log.2
Measures and logs execution time
endtime=$(date +%s.%N) exectime=$(echo "$endtime $starttime" | awk '{print $1-$2}') sysdate=$(date) echo "STEP 1 (Quality control) terminated at $sysdate ($exectime seconds)" >> .log.2 echo " " >> .log.2 echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++" >> .log.2 echo " " >> .log.2
Command exit status: 125
Command output: (empty)
Command error: Unable to find image 'yampdocker:latest' locally docker: Error response from daemon: repository yampdocker not found: does not exist or no pull access. See 'docker run --help'.
Work dir: .....................YAMP/work/ff/30bff9a2c9c06f891f279d055ca0b3
Tip: view the complete command output by changing to the process work dir and entering the command
cat .command.out-- Check '.nextflow.log' file for details WARN: Killing pending tasks (2)