Error executing process > 'dedup' with message Command output empty #16
Description
Hi, I'm running YAMP using singularity container. I'm not sure if I missed any step during the setup but I seem to have trouble in running dedup process. The error message it shows is "Command output - empty" but don't know which one specifically it is referring to. Thank you advance for your help. let me know if I can provide with any other information.
WARN: Killing pending tasks (1)
Error executing process > 'dedup'
Caused by:
Process dedup terminated with an error exit status (1)
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 "64 GB" | sed 's/ //g' | sed 's/B//g')
#Defines command for de-duplication
if [ "paired" = "paired" ]; then
(emptyCMD="clumpify.sh -Xmx"$maxmem" in1=DR3_Female_After_Co-housing_15-N714S505_S143_L007_R1_001.fastq.gz in2=DR3_Female_After_Co-housing_15-N714S505_S143_L007_R2_001.fastq.gz out1=DR3_test_dedupe_R1.fq out2=DR3_test_dedupe_R2.fq qin=33 dedupe subs=0 threads=16"
else
/UsersCMD="clumpify.sh -Xmx"$maxmem" in=DR3_Female_After_Co-housing_15-N714S505_S143_L007_R1_001.fastq.gz out=DR3_test_dedupe.fq qin=33 dedupe subs=0 threads=16"
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:
1
Command output:
(empty)
Work dir:
/Users/rsompallae/work/4f/42cd1c844676374d9d66b1f84a4ad0
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh