Open ehsansari1234 opened 1 year ago
Hi Ehsan, Thanks for reaching out. Have you managed to run through "searchNumtCluster_fromDiscordantReads.py"?
Wei
Hi Wei,
Thanks for the quick reply.
I get some warning when the scripts reaches to searchNumtCluster_fromDiscordantReads.py but I believe it worked as 159a1srt.mt.disc.sam.breakpointINPUT.tsv is generated in the output folder. Here are a few lines of breakpointINPUT.tsv file { 159a1srt 2 ./output/159a1srt.mt.disc.sam ./output/159a1srt.mt.split.sam ./159a1srt.bam chr1 1005205 1006728 159a1srt 2 ./output/159a1srt.mt.disc.sam ./output/159a1srt.mt.split.sam ./159a1srt.bam chr1 10057554 10059006 159a1srt 2 ./output/159a1srt.mt.disc.sam ./output/159a1srt.mt.split.sam ./159a1srt.bam chr1 10059036 10060651 159a1srt 2 ./output/159a1srt.mt.disc.sam ./output/159a1srt.mt.split.sam ./159a1srt.bam chr1 1015885 1017220 159a1srt 2 ./output/159a1srt.mt.disc.sam ./output/159a1srt.mt.split.sam ./159a1srt.bam chr1 10174241 10175740 159a1srt 2 ./output/159a1srt.mt.disc.sam ./output/159a1srt.mt.split.sam ./159a1srt.bam chr1 10186464 10187796 159a1srt 2 ./output/159a1srt.mt.disc.sam ./output/159a1srt.mt.split.sam ./159a1srt.bam chr1 10244730 10246102 }
Please let me know should you need further info.
Thanks Ehsan
Hi Ehsan, It looks samtools can't find input. You may need to double check your input files.
Wei
Hi Wei,
Thanks. Your clue helped to me find the issue. The breakpointINPUT.tsv file is a tab limited but a comma separated input in expected for breakpint detection part. No I am off the error loop but I get numerous complains from Pandas. May I know the version of Pandas and Python on your system: here is a returned error message{ File "/globalhome/ehs220/HPC/.local/lib/python2.7/site-packages/pandas/core/frame.py", line 3426, in _ensure_valid_index raise ValueError('Cannot set a frame with no defined index ' ValueError: Cannot set a frame with no defined index and a value that cannot be converted to a Series}
Best Ehsan
Hi, I also encountered the error same as you. but the python version I used was python3.6. Did you successfully resolve this issue in the end?
Hi.
Thanks for sharing very interesting scripts. I have two questions which will help me to resolve errors I am getting with the script:
1) In NUMTs_detection.sh, I have difficult time to understand ${OUTPUT_wgs} variable. This is not define in the script, so when I run the script on my bam file, the split file won't be generated. When I change it to ${OUTPUT} I get 159a1srt.mt.split.sam in the output folder as expected. 2) The pipeline then progress until I reach to searchBreakpoint_fromblatoutputs.py script. I get following errors { look for cluster's done, move to look for breakpoints 159a1srt [E::hts_open_format] Failed to open file "159a1srt" : No such file or directory samtools view: failed to open "159a1srt" for reading: No such file or directory End of file reading 4 bytes Traceback (most recent call last):}
I am not sure the source of issue. Could you please help out? I am concerned, there must be some reservation for naming files etc. Note that I am using non-human genome and here are my chromsome naming { chr1, chr2, chr3, chr4, chr_mt} To accommodate difference between the chromosome names, I changed the grep part of NUMTs_detection.sh scripts as follow { grep -e @ -e MT -e chr_mt }
please let me know if you need any other information.
Best Ehsan