It runs successfully, but always shows some error messages
Closed this issue · 6 comments
samtools: failed to open "test.transposon.bam" for reading: No such file or directory
[E::hts_open] fail to open file 'test.transposon.bam'
but at the end, it showed : Done, Congras!!!🍺🍺🍺
can I have a sample test.out file to make sure I am good with the result?
Non-fetal errors wouldn't stop the pipeline from running, but the final output is usually screwed. Below is an output example for file "XXX.insertion.bed". If you didn't get the final results, then I suggest check for the installation of samtools (≥v1.9), bedtools, and bwa.
#Chr Start End Transposon:Start:End:Strand Frequency Strand Type SupportReads UnspportReads 5primeSupportReads 3primeSupportReads TSD ConfidenceForSomaticInsertion 5splicSiteSupportReads 3spiceSiteSupportReads
chr2L 27 28 FBgn0063503_G6:92:216:- 1 - singleton 1 0 1 0 unknown 4.71 1 0
chr2L 5484 5868 FBgn0063919_Max-element:8433:8556:+ 0.00869565 + singleton 1 57 0 1 unknown 25.17 0 0
chr2L 76283 76667 FBgn0003519_Stalker:6780:6904:+,FBgn0063897_Stalker4:6887:7011:+ 0.00934579 + singleton 1 53 0 1 unknown 24.98 0 0
chr2L 77351 77735 FBgn0000349_copia:4869:4969:+ 0.00854701 + singleton 1 58 0 1 unknown 70.47 0 0
chr2L 199886 200270 FBgn0063917_McClintock:215:340:+ 0.0114943 + singleton 1 43 1 0 unknown 45.92 0 0
chr2L 205126 205510 FBgn0000481_Doc:534:577:- 0.00787402 - singleton 1 63 1 0 unknown 28.36 0 0
chr2L 451704 452088 FBgn0000652_F-element:4227:4351:+ 0.0120482 + singleton 1 41 1 0 unknown 11.88 0 0
chr2L 512270 512654 FBgn0000349_copia:4891:5015:+ 0.0136986 + singleton 1 36 0 1 unknown 70.47 0 0
chr2L 532328 532712 FBgn0002745_micropia:5026:5149:+ 0.00662252 + singleton 1 75 0 1 unknown 33.47 0 0
chr2L 561178 561562 FBgn0000481_Doc:269:368:+ 0.0126582 + singleton 1 39 1 0 unknown 28.36 0 0
Dear Tianxiong, thanks for you replying, I think I got all those software down on my centos 7. I can get some results in my test.soma.summary.txt file but get nothing for test.insertion.bed.
Here is the error showed in the program:
Traceback (most recent call last):
File "/root/Document/TEMP2_PROJECT/TEMP2/bin/processMergedBed.py", line 108, in
main()
File "/root/Document/TEMP2_PROJECT/TEMP2/bin/processMergedBed.py", line 19, in main
transStrand = transRec[0].split(",")[3]
IndexError: list index out of range
and it repeats again and again in the terminal window. Do you have any idea for this problem? Any suggestion or idea would be great for me!
Hi iserafiml, can you check the content in tmpTEMP2/test.supportReads/FBgn0000005_297.+.merged.bed? It should be a tab-delimited file that the 5th column contains the transposon alignment information of supporting reads.
chr2L 1469447 1469547 1 FBgn0000005_297,49,148,-,0,1 + 1469447 1469547
chr2L 9653203 9653303 1 FBgn0000005_297,6901,6995,+,0,1 - 9653203 9653303
If things go well, please refer to the final test results here.
the content in my FBgn0000005_297.+.merged.bed are
chr2L 1469447 1469547 + 1 FBgn0000005_297,49,148,-,0,1 + 1469447 1469547
chr2L 9653203 9653303 - 1 FBgn0000005_297,6901,6995,+,0,1 - 9653203 9653303
I think the 4th column are different than yours. Any idea?
If the content of tmpTEMP2/test.supportReads/FBgn0000005_297.+.bed is:
chr2L 1469447 1469547 1 FBgn0000005_297,49,148,-,0 +
chr2L 9653203 9653303 1 FBgn0000005_297,6901,6995,+,0 -
Then it is mostly likely that "bedtools merge" is doing something different. I think "bedtools merge" by default outputs 3 columns and TEMP2 added additional information to it. In your version "bedtools merge" outputted 4 columns, including strand information in the 4th column, and makes the output file format different.
If this is true, you can update bedtools to a newer version (>v2.0.0 should work but I suggest taking it to the newest version v2.30.0).
Thanks for your patience, I did it sucessfully.