Syri failed to run. Procedure

schneebergerlab / syri

Synteny and Rearrangement Identifier

https://schneebergerlab.github.io/syri/

MIT License

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Syri failed to run. Procedure #138

Closed hgz2021 closed 2 years ago

hgz2021 commented 2 years ago

Hello, I made a mistake running syir and need your help. I installed Syri using Conda, and here is my command Conda create -n syri conda activate syri cd syri conda install -c bioconda syri But I had a problem running the sample。 I ran the command syri minimap2 -ax asm5 -t 4 --eqx A.fa B.fa \ | samtools sort -O BAM - > A_B.bam syri -c A_B.bam -r A.fa -q B.fa -F B --prefix A_B finally,the picture below is an error 1d64e52c8ff33d013d88a3c56fcf24b

mnshgl0110 commented 2 years ago

The last line in the pic says that it is trying to access file "/home/....//home/../A_Bmapids.txt". Based on other paths, I assume that this is wrong. Though it is not clear why this is happening. A would suggest that you retry in an empty folder containing only the genomes and the alignment file.

hgz2021 commented 2 years ago

They were in a folder.

mnshgl0110 commented 2 years ago

I meant that the issue is most probably happening because of incorrect path. So, to test it please run in a different path. Also, please share the folder name in which you are running syri and in which all the files are there.

hgz2021 commented 2 years ago

Hello, the last problem was solved when I changed the chromosomes of 'ref' and 'qry' to 'chr1,chr2.....chr '. But when I run it with my own data, a new error occurs. The corresponding error message is reported.

syri.log

hgz2021 commented 2 years ago

Hello, I have solved the problem, which is entirely my problem. Thank you and your SYri for your help. I will close this comment. I didn't notice --prefix prefix prefix to add before the output file Names (default:).