Argument list too long

[xuechunxu]

When I run python ~/software/Cenote-Taker2/Cenote-Taker2/run_cenote-taker2.py -c AsianEle01.fa -r AsianEle01_ct.out -m 32 -t 32 -p True -db virion --minimum_length_linear 3000 --lin_minimum_hallmark_genes 2
It called:
~/software/Cenote-Taker2/Cenote-Taker2/cenote-taker2.1.3.sh: line 228: /usr/bin/rm: Argument list too long

Is that ok?

[Aveglia]

Hi, I ran into a similar problem, must be an issue when your input fasta has a lot of sequences(?).

To try to fix this error, I made an edit to the cenote-taker2.1.3.sh script at line 228, commented out the rm command and replaced using the find command below:

find . -maxdepth 1 -name "apc_aln*" -print0 | xargs -0 rm

When testing the command in the directory cenote was trying to remove the apc_aln* files, this command removed the apc_aln* files succesfullly. I am testing if this will fix the issue in my Cenote run now.

I will send an update when it finishes but I thought I should share in the case that you are in a hurry to get the run going again.

@mtisza1 I hope this helps/is correct, thank you for the awesome tool!!

-Alex Veglia

[mtisza1]

Thank you, Xuechunxu and Alex for bringing attention to this issue.

First, let me apologize for the delay in replying. I've been extremely busy lately, and I've had to decide to not reply to Cenote-Taker 2 issues temporarily. I will be "back" to quick responses and updates(!) at the end of February.

Alex, I believe your assessment and fix are spot on. These changes will be incorporated to the next update. Much appreciated!

Best,

Mike

[mtisza1]

Hi all,

I believe this issue should be fixed in the new release, v2.1.5. You can update Cenote-Taker 2 via the instructions on the main repo page.

Best,

Mike