Example fails

[Lila14]

I tried to run the example on the AWS instance. The genome indexing worked, but the second command failed.

I ran the command provided, though I reduced the ram usage to fit the limits of my free AWS account: pipeline.py -m gmap -g chr9_fa -c /home/ubuntu/projects/example/config.txt -q htseq-count -i example --cluster aws --ram 5 -cpu 2

The output was:

INFO:root:Staring pipeline INFO:root:Collecting input files INFO:root:Found: /home/ubuntu/projects//example/raw/SingleTestCell#2_1.fq /home/ubuntu/projects//example/raw/SingleTestCell#1_1.fq /home/ubuntu/projects//example/raw/SingleTestCell#2_2.fq /home/ubuntu/projects//example/raw/SingleTestCell#3_2.fq /home/ubuntu/projects//example/raw/SingleTestCell#3_1.fq /home/ubuntu/projects//example/raw/SingleTestCell#1_2.fq INFO:root:Paired:True INFO:root:Read-length:75 INFO:root:Mapping started INFO:root:Mapper: gmap INFO:root:Passed parameters: INFO:root:Executed Command: /home/ubuntu/tools/mapper//gmap/gsnap -A sam -B 5 -t 2 -d chr9_fa -D /home/ubuntu/references/chr9_fa/gmap /home/ubuntu/projects//example/raw/SingleTestCell#{#}1.fq /home/ubuntu/projects//example/raw/SingleTestCell#{#}2.fq > /home/ubuntu/temp/example/output/mapped/sam/example{#}.sam INFO:root:Parallel command submitted: exec /bin/bash -c ' wrapper_func() { /home/ubuntu/tools/mapper//gmap/gsnap -A sam -B 5 -t 2 -d chr9_fa -D /home/ubuntu/references/chr9_fa/gmap /home/ubuntu/projects//example/raw/SingleTestCell#$1_1.fq /home/ubuntu/projects//example/raw/SingleTestCell#$1_2.fq > /home/ubuntu/temp/example/output/mapped/sam/example$1.sam ; }; export -f wrapper_func; parallel -j2 --retries 3 --halt soon,fail=20% --memfree 5M "wrapper_func {} > /home/ubuntu/temp/example/output/mapped/sam/example_{}.mapping.log 2>&1" ::: {1..3}' parallel: This job failed: wrapper_func 1 > /home/ubuntu/temp/example/output/mapped/sam/example_1.mapping.log 2>&1 parallel: Starting no more jobs. Waiting for 1 jobs to finish. parallel: This job failed: wrapper_func 2 > /home/ubuntu/temp/example/output/mapped/sam/example_2.mapping.log 2>&1 ERROR:root:Please check log files for more information: /home/ubuntu/temp/example/output/mapped/sam ERROR:root:Mapping unsuccessful ERROR:root:Pipeline broke.