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xiezhq / ISEScan

A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome
Apache License 2.0
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Problems with FragGeneScan #11

Closed giuliodimaria92 closed 5 years ago

giuliodimaria92 commented 5 years ago

Good evening...I can't find this programme. How can I solve the problem? Thank you!

isPredict begins at Fri May 3 17:39:37 2019

Begin to translate genome into proteome. /bin/sh: 1: /u/zhiqxie/informatics/inst/FragGeneScan1.30/run_FragGeneScan.pl: not found Translating genome into proteome for /home/usuario/anaconda3/envs/IScan/ISEScan-master/NC_012624.fna , return error!

Finish translating genome into proteome. Fri May 3 17:39:37 2019 No such file or Empty file prueba/ISEScan-master/NC_012624.fna.faa No such file or Empty file prueba/ISEScan-master/NC_012624.fna.faa No hit was returned by HMM search against protein database. Fri May 3 17:39:37 2019 isPredict ends at Fri May 3 17:39:37 2019 (IScan) usuario@pra-dpt-62660:~/anaconda3/envs/IScan/ISEScan-master$ python3 isescan.py ~/anaconda3/envs/IScan/ISEScan-master/NC_012624.fna prueba hmm isPredict begins at Fri May 3 17:40:56 2019

xiezhq commented 5 years ago

You need to configure ISEScan before you run it because the paths of the required pakcages installed on your computer might be different from those on my computer.

Please go to https://github.com/xiezhq/ISEScan, and find 'Configure ISEScan' and follow the instructions there to configure your isescan environment. For example, in your case, the error showed the path pointing to the installed FragGeneScan on my computer, /u/zhiqxie/informatics/inst/FragGeneScan1.30/run_FragGeneScan.pl. You need to change it to the path pointing to the FragGeneScan installed on your computer at line 10 in constants.py. You may also need to change other paths in constants.py to match the correct paths where the required packages are installed on your computer.

Hope it is helpful.

giuliodimaria92 commented 5 years ago

Good morning! FragGeneScan now works and I've changed all the paths but... It generated only 5 files (the first four have content) with format problems: NC_012624.fna.faa NC_012624.fna.ffn NC_012624.fna.gff NC_012624.fna.out clusters.faa.hmm.NC_012624.fna.faa (it is empty)

Begin to translate genome into proteome. /home/usuario/anaconda3/envs/IScan/FragGeneScan1.30/FragGeneScan -s /home/usuario/anaconda3/envs/IScan/ISEScan-master/NC_012624.fna -o prueba/ISEScan-master/NC_012624.fna -w 0 -t illumina_5 -p 4 Using 4 threads. no. of seqs: 1 Clock time used (by 4 threads) = 0.01 mins prepare gff file.. Time elapsed: 0 hours 0 minutes and 1 seconds. Translating genome into proteome for /home/usuario/anaconda3/envs/IScan/ISEScan-master/NC_012624.fna , return 0

Finish translating genome into proteome. Mon May 13 12:32:35 2019

Begin to phmmer search against proteome database. Mon May 13 12:32:35 2019

Error: Sequence file /home/usuario/anaconda3/envs/IScan/ISEScan-master/pHMMs/clusters.faa.hmm is empty or misformatted

Traceback (most recent call last): File "isescan.py", line 57, in isPredictSingle(args4isPredictSingle) File "isescan.py", line 22, in isPredictSingle isPredict.isPredict(filelist, path2proteome, path2hmm) File "/home/usuario/anaconda3/envs/IScan/ISEScan-master/isPredict.py", line 263, in isPredict phmmerSearch(args2concurrent4phmmer) File "/home/usuario/anaconda3/envs/IScan/ISEScan-master/isPredict.py", line 176, in phmmerSearch raise RuntimeError(e) RuntimeError: phmmer searching /home/usuario/anaconda3/envs/IScan/ISEScan-master/pHMMs/clusters.faa.hmm against prueba/ISEScan-master/NC_012624.fna.faa, return error!

Thank you for the help!

xiezhq commented 5 years ago

Please go to your work directory, and then run two commands:

pwd ls -lh /home/usuario/anaconda3/envs/IScan/ISEScan-master/pHMMs/

and show me the outputs of these commands.

By the way, how did you run isescan.py on your computer?

giuliodimaria92 commented 5 years ago

Good evening... (base) usuario@pra-dpt-62660:~$ source deactivate DeprecationWarning: 'source deactivate' is deprecated. Use 'conda deactivate'. usuario@pra-dpt-62660:~$ pwd /home/usuario usuario@pra-dpt-62660:~$ ls -lh /home/usuario/anaconda3/envs/IScan/ISEScan-master/pHMMs/ total 39M -rw-rw-r-- 1 usuario usuario 39M abr 7 10:55 clusters.faa.hmm -rw-rw-r-- 1 usuario usuario 98K abr 7 10:55 clusters.single.faa usuario@pra-dpt-62660:~$ ^C usuario@pra-dpt-62660:~$ I'm working with my PC in the environment of Anaconda Thank you!

giuliodimaria92 commented 5 years ago

usuario@pra-dpt-62660:~$ pwd /home/usuario usuario@pra-dpt-62660:~$ ls -lh /home/usuario/anaconda3/envs/IScan/ISEScan-master/pHMMs/ total 39M -rw-rw-r-- 1 usuario usuario 39M abr 7 10:55 clusters.faa.hmm -rw-rw-r-- 1 usuario usuario 98K abr 7 10:55 clusters.single.faa

xiezhq commented 5 years ago

The problem might be caused by the path pointing to the profile HMM files (clusters.single.faa and clusters.faa.hmm). Please download two updated files, constants.py and isPredict.py from https://github.com/xiezhq/ISEScan, and then try running isescan again. Please let me know if it solves your problem or not. Thank you!

giuliodimaria92 commented 5 years ago

Good evening...how to access to update Aclame database? Thank you! :)

xiezhq commented 5 years ago

You can download ACLAME database from http://aclame.ulb.ac.be/ but it has not been updated since version 0.4 (2009).