TEMP_Insertion.sh produces empty output

[davidecarlson]

Hi Jiali, I'm having some trouble getting TEMP to work properly. Most of the output files that are produced are empty (or empty except for the headers). No error messages are produced. Everything seems to work fine when I run TEMP on the test data, so I don't think it's an issue with the installation or my environment. In addition, I suspect based on results from other methods that my fastq data should have non-reference TE insertions in them.

Here are the commands I'm running:

bash /path/to/TEMP/scripts/TEMP_Insertion.sh
-i path/to/biennis_merged_nopipe.bam
-s /path/to/TEMP/scripts
-o /path/to/TEMP_test_out
-r /path/to/allRepeats.lib
-c 16 > TEMP_log 2>&1

Here are the contents of the output directory:

-rw------- 1 decarlson decarlson 17M Jul 13 16:24 allRepeats.lib -rw------- 1 decarlson decarlson 304K Jul 13 17:08 allRepeats.lib.amb -rw------- 1 decarlson decarlson 238K Jul 13 17:08 allRepeats.lib.ann -rw------- 1 decarlson decarlson 16M Jul 13 17:08 allRepeats.lib.bwt -rw------- 1 decarlson decarlson 4.0M Jul 13 17:08 allRepeats.lib.pac -rw------- 1 decarlson decarlson 7.9M Jul 13 17:08 allRepeats.lib.sa -rw------- 1 decarlson decarlson 36G Jul 13 16:26 biennis_merged_nopipe.bam -rw------- 1 decarlson decarlson 3.2M Jul 13 16:26 biennis_merged_nopipe.bam.bai -rw------- 1 decarlson decarlson 0 Jul 13 17:08 biennis_merged_nopipe.bam.clipped.reads.aln -rw------- 1 decarlson decarlson 0 Jul 13 17:08 biennis_merged_nopipe.bam.insertion.bp.bed -rw------- 1 decarlson decarlson 0 Jul 13 17:08 biennis_merged_nopipe.bam.insertion.refined.bp -rw------- 1 decarlson decarlson 156 Jul 13 17:08 biennis_merged_nopipe.bam.insertion.refined.bp.summary -rw------- 1 decarlson decarlson 160 Jul 13 17:08 biennis_merged_nopipe.bam.uniq.transposons.filtered.wGap.class.bed -rw------- 1 decarlson decarlson 0 Jul 13 17:08 biennis_merged_nopipe.bam.unpair.uniq.transposons.bed -rw------- 1 decarlson decarlson 0 Jul 13 17:08 biennis_merged_nopipe.bam.unpair.uniq.transposons.filtered.bed

Do you have any idea what could be causing this or what I might try to fix it?
Thanks for any suggestions! Dave

[Anwica]

I am facing the same problem. Were you able to resolve it? FYI: it works on test data.

[cphillips3]

I too have this same issue. Would love to hear if you were able to resolve it!

[davidecarlson]

I never resolved it, unfortunately.

[Anwica]

I set the the x argument to 30 and then it worked.

Here is the command I used: $script -i $bamfile -s $script_dir -o $out_dir -r $te_file -t $te_annotation -x 30 -m 30 -f 285 -c 8

[CGNAT]

I too am having the same problem. I get no input returned. Has this been solved??

Thank you