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jgurtowski / ectools

tools for error correction and working with long read data
BSD 3-Clause "New" or "Revised" License
44 stars 11 forks source link

cp: cannot stat ‘/mouse/Mya/ectools/0001/p0000’: No such file or directory #2

Closed macmanes closed 9 years ago

macmanes commented 9 years ago

Trying to run the correction: 

python /share/ectools/partition.py 20 500 /mouse/Mya/pacbio/fasta/mya.pacbio.fasta
...
/mouse/Mya/ectools/0001$ ../correct.sh
+ set -e
+ source /home/macmanes/.bashrc
++ '[' -z '' ']'
++ return
+ CORRECT_SCRIPT=/share/ectools/pb_correct.py
+ PRE_DELTA_FILTER_SCRIPT=/share/ectools/pre_delta_filter.py
+ MIN_ALIGNMENT_LEN=200
+ WIGGLE_PCT=0.05
+ CONTAINED_PCT_ID=0.80
+ UNITIG_FILE=/mouse/Mya/ectools/organism_correct/clam67-long-scaffs.fa
+ CLR_PCT_ID=0.96
+ MIN_READ_LEN=3000
+ NUCMER_BREAK_LEN=2000
+ PRE_DELTA_FILTER=true
++ printf %04d
+ suffix=0000
+ FILE=p0000
++ pwd
+ ORIGINAL_DIR=/mouse/Mya/ectools/0001
+ [[ -n '' ]]
+ cp /mouse/Mya/ectools/0001/p0000 .
cp: cannot stat ‘/mouse/Mya/ectools/0001/p0000’: No such file or directory

In folder 0001 and all others, there is no p0000, it starts with p0001

Please advise.

jgurtowski commented 9 years ago

correct.sh is meant to be run under sge. If you are not using SGE take a look at optional step 11 in the README. The following should work:

SGE_TASK_ID=1 TMPDIR=/tmp ../correct.sh