Not able to generate the final circ.gtf output

[eltonjrv]

Dear CIRIquant developers,

After over 1 hour running CIRIquant, I'm getting stuck with following error(s): ######################################################### [Tue 2021-03-09 03:24:07] [INFO ] Input reads: KH1W_S1318_L004_R1-trimmed_paired.fq.gz,KH1W_S1318_L004_R2-trimmed_paired.fq.gz [Tue 2021-03-09 03:24:07] [INFO ] Library type: TAKARA SMARTer [Tue 2021-03-09 03:24:07] [INFO ] Output directory: /nobackup/fbsev/LeedsOmics/Kathy-circRNAs/CIRIquant-run/02-CIRIquant/R_normal_1, Output prefix: R_normal_1 [Tue 2021-03-09 03:24:07] [INFO ] Config: config.yml Loaded [Tue 2021-03-09 03:24:07] [INFO ] 40 CPU cores availble, using 40 [Tue 2021-03-09 03:24:07] [INFO ] Align RNA-seq reads to reference genome .. [Tue 2021-03-09 04:02:06] [INFO ] Estimate gene abundance .. [Tue 2021-03-09 04:08:02] [INFO ] No circRNA information provided, run CIRI2 for junction site prediction .. [Tue 2021-03-09 04:08:02] [INFO ] Running BWA-mem mapping candidate reads .. [Tue 2021-03-09 04:16:52] [INFO ] Running CIRI2 for circRNA detection .. [Tue 2021-03-09 04:30:41] [INFO ] Extract circular sequence ^M[Tue 2021-03-09 04:30:41] [0% ] [..................................................]Traceback (most recent call last): File "/nobackup/fbsev/bioinformatics-tools/CIRIquant/venv/bin/CIRIquant", line 33, in sys.exit(load_entry_point('CIRIquant==1.1.1', 'console_scripts', 'CIRIquant')()) File "/nobackup/fbsev/bioinformatics-tools/CIRIquant/venv/lib/python3.7/site-packages/CIRIquant-1.1.1-py3.7.egg/CIRIquant/main.py", line 183, in main out_file = circ.proc(log_file, thread, bed_file, hisat_bam, rnaser_file, reads, outdir, prefix, anchor, lib_type) File "/nobackup/fbsev/bioinformatics-tools/CIRIquant/venv/lib/python3.7/site-packages/circ/init.py", line 644, in proc generate_index(log_file, circ_info, circ_fasta) File "/nobackup/fbsev/bioinformatics-tools/CIRIquant/venv/lib/python3.7/site-packages/circ/init.py", line 189, in generate_index chrom_seq = extract_seq(utils.FASTA, chrom_start, chrom_length) File "/nobackup/fbsev/bioinformatics-tools/CIRIquant/venv/lib/python3.7/site-packages/circ/init.py", line 141, in extract_seq seq = f.read(length) TypeError: argument should be integer or None, not 'float' #########################################################

I'm afraid there are uninitialized variables in the code (e.g. length). Could anyone share a light on how to better solve this?

Thanks very much, Best, Elton PS: I installed the program through your "virtualenv" recommended way (https://ciriquant-cookbook.readthedocs.io/en/latest/installation.html#install-ciriquant-from-source-code). I needed to fix a couple of issues, such as filling up empty init.py files from both "CIRIquant/venv/lib/python3.7/site-packages/circ" and "CIRIquant/venv/lib/python3.7/site-packages/pipeline" with the content from circ.py and pipeline.py, respectively (pulled from "CIRIquant/venv/lib/python3.7/site-packages/CIRIquant-1.1.1-py3.7.egg/CIRIquant/" dir). Also, I needed to replace "izip_longest" occurrences to "zip_longest" within circ.py. I'm now a bit concerned on keep handling your code several times which may probably mess everything up in a certain point. Hope you can help. Thanks again!

[Kevinzjy]

Hi Elton,

CIRIquant only support python 2, please try reinstalling CIRIquant with py2 environments.

Best,

Jinyang

[eltonjrv]

Ok, thanks. I'll give it a try under python 2, which is no longer installed in our servers' default system. Best, Elton

Em ter., 9 de mar. de 2021 às 15:09, Jinyang Zhang notifications@github.com escreveu:

Hi Elton,

CIRIquant only support python 2, please try reinstalling CIRIquant with py2 environments.

Best,

Jinyang

Jinyang Zhang PhD Student Computational Genomics Lab Beijing Institutes of Life Science, CAS Tel: +86-18810504758 Email: zhangjinyang@biols.ac.cn

From: Elton Vasconcelos Date: 2021-03-09 22:54 To: bioinfo-biols/CIRIquant CC: Subscribed Subject: [bioinfo-biols/CIRIquant] Not able to generate the final circ.gtf output (#24) Dear CIRIquant developers, After over 1 hour running CIRIquant, I'm getting stuck with following error(s): ######################################################### [Tue 2021-03-09 03:24:07] [INFO ] Input reads: KH1W_S1318_L004_R1-trimmed_paired.fq.gz,KH1W_S1318_L004_R2-trimmed_paired.fq.gz

[Tue 2021-03-09 03:24:07] [INFO ] Library type: TAKARA SMARTer [Tue 2021-03-09 03:24:07] [INFO ] Output directory: /nobackup/fbsev/LeedsOmics/Kathy-circRNAs/CIRIquant-run/02-CIRIquant/R_normal_1, Output prefix: R_normal_1 [Tue 2021-03-09 03:24:07] [INFO ] Config: config.yml Loaded [Tue 2021-03-09 03:24:07] [INFO ] 40 CPU cores availble, using 40 [Tue 2021-03-09 03:24:07] [INFO ] Align RNA-seq reads to reference genome .. [Tue 2021-03-09 04:02:06] [INFO ] Estimate gene abundance .. [Tue 2021-03-09 04:08:02] [INFO ] No circRNA information provided, run CIRI2 for junction site prediction .. [Tue 2021-03-09 04:08:02] [INFO ] Running BWA-mem mapping candidate reads .. [Tue 2021-03-09 04:16:52] [INFO ] Running CIRI2 for circRNA detection .. [Tue 2021-03-09 04:30:41] [INFO ] Extract circular sequence ^M[Tue 2021-03-09 04:30:41] [0% ] [..................................................]Traceback (most recent call last): File "/nobackup/fbsev/bioinformatics-tools/CIRIquant/venv/bin/CIRIquant", line 33, in sys.exit(load_entry_point('CIRIquant==1.1.1', 'console_scripts', 'CIRIquant')()) File "/nobackup/fbsev/bioinformatics-tools/CIRIquant/venv/lib/python3.7/site-packages/CIRIquant-1.1.1-py3.7.egg/CIRIquant/main.py", line 183, in main out_file = circ.proc(log_file, thread, bed_file, hisat_bam, rnaser_file, reads, outdir, prefix, anchor, lib_type) File "/nobackup/fbsev/bioinformatics-tools/CIRIquant/venv/lib/python3.7/site-packages/circ/init.py", line 644, in proc generate_index(log_file, circ_info, circ_fasta) File "/nobackup/fbsev/bioinformatics-tools/CIRIquant/venv/lib/python3.7/site-packages/circ/init.py", line 189, in generate_index chrom_seq = extract_seq(utils.FASTA, chrom_start, chrom_length) File "/nobackup/fbsev/bioinformatics-tools/CIRIquant/venv/lib/python3.7/site-packages/circ/init.py", line 141, in extract_seq seq = f.read(length) TypeError: argument should be integer or None, not 'float' ######################################################### I'm afraid there are uninitialized variables in the code (e.g. length). Could anyone share a light on how to better solve this? Thanks very much, Best, Elton PS: I installed the program through your "virtualenv" recommended way ( https://ciriquant-cookbook.readthedocs.io/en/latest/installation.html#install-ciriquant-from-source-code). I needed to fix a couple of issues, such as filling up empty init.py files from both "CIRIquant/venv/lib/python3.7/site-packages/circ" and "CIRIquant/venv/lib/python3.7/site-packages/pipeline" with the content from circ.py and pipeline.py, respectively (pulled from "CIRIquant/venv/lib/python3.7/site-packages/CIRIquant-1.1.1-py3.7.egg/CIRIquant/" dir). Also, I needed to replace "izip_longest" occurrences to "zip_longest" within circ.py. I'm now a bit concerned on keep handling your code several times which may probably mess everything up in a certain point. Hope you can help. Thanks again! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.

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-- Elton J. R. Vasconcelos DVM, PhD

[eltonjrv]

Hi Jyniang, The program is working smoothly under python 2.7. Thanks again! I'm just encountering an R error (duplicated rows) in the very final step (CIRI_DE_replicate), which I'll post in a new issue. Still on this current issue, would you mind if I suggest you to fix the following command from your installation tutorial at https://ciri-cookbook.readthedocs.io/en/latest/CIRIquant_1_installation.html#install-ciriquant-from-source-code $ virtualenv -p /path/to/your/python2/executable venv I believe this would prevent others to fall in the same mistake as I did. Thanks, Cheers, Elton

[Kevinzjy]

Thanks for the useful advice! I've updated the installation commands accordingly.