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JialiUMassWengLab / TEMP

TEMP is a software package for detecting transposable elements (TEs) insertions and excisions from pooled high-throughput sequencing data
GNU General Public License v2.0
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Error on the test data #11

Closed jychoilab closed 7 years ago

jychoilab commented 7 years ago

Hello

I was trying to run the test data using the Absence script and ran into the following error:

Testing required softwares/scripts: "echo" is using: /usr/bin/echo "rm" is using: /usr/bin/rm "mkdir" is using: /usr/bin/mkdir "date" is using: /usr/bin/date "mv" is using: /usr/bin/mv "sort" is using: /usr/bin/sort "touch" is using: /usr/bin/touch "awk" is using: /usr/bin/awk "grep" is using: /usr/bin/grep "twoBitToFa" is using: /storage/jae.youngchoi/PROGRAMS_AND_SCRIPTS/PROGRAMS/kentUtils/bin/twoBitToFa "bwa" is using: /storage/jae.youngchoi/miniconda2/bin/bwa "samtools" is using: /storage/jae.youngchoi/miniconda2/bin/samtools Done with testing required softwares/scripts, starting pipeline... test_chromosome.sorted.bam test_chromosome Error: Type checker found wrong number of fields while tokenizing data line.

I ran with command:

bash /storage/jae.youngchoi/PROGRAMS_AND_SCRIPTS/PROGRAMS/TEMP/scripts/TEMP_Absence.sh \ -i /storage/jae.youngchoi/PROGRAMS_AND_SCRIPTS/PROGRAMS/TEMP/test_dataset/test_chromosome.sorted.bam \ -s /storage/jae.youngchoi/PROGRAMS_AND_SCRIPTS/PROGRAMS/TEMP/scripts/ \ -o /storage/jae.youngchoi/PROGRAMS_AND_SCRIPTS/PROGRAMS/TEMP/test_dataset/TMP/ \ -r /storage/jae.youngchoi/PROGRAMS_AND_SCRIPTS/PROGRAMS/TEMP/test_dataset/test_TE_annotation.bed \ -t /storage/jae.youngchoi/PROGRAMS_AND_SCRIPTS/PROGRAMS/TEMP/test_dataset/dm3_chr2L.2bit \ -x 10

I'm using samtools v1.4.1; bwa 0.7.15-r1140; bedtools v2.26.0. Quick google search indicates that error is from bedtools and I'm wondering if there's any suggestion for the error?

Many thanks!

Best

Jae

JialiUMassWengLab commented 7 years ago

Hi Jae,

Is there any way you can share the intermediate files? It's hard for me to diagnose with current information.

Jiali

yfu commented 7 years ago

It appears that bedtools v2.26.0 is having problems dealing with bedtools intersect -a test_TE_annotation.bed -b test_chromosome.unproper.uniq.interval.bed. I tried bedtools v2.25.0 and it worked here.

Best! Yu

jychoilab commented 7 years ago

Yes it was a version issue and its work with bedtools v2.25.0 for me as well. Thanks yfu!