run htesq-count error

Question

[yhui_qiu]

My htseq-count command is:

htseq-count -s no -o homo_con_samout ../04_align/homo_con.sam $gtf  >con_read_count.log  2>error

The error message is:

Error occured when processing SAM input (line 464 of file ../04_align/homo_con.sam):my_showwarning() takes from 3 to 5 positiona arguments but 6 were given 
[Exception type :TypeError ,raised in warnings.py:99]

How can I fix this error?

[Devon Ryan]

Can you show us line 464 of the SAM file?

[Tm]

Request you to check the version of python you are using as it can be a probable reason for this error. Please check HTSeq documentation, mentioning its Prequisites and installation.

Similar HTSeq issue is been discussed in one of chinese blog

Answer 1

[yhui_qiu]

I had check the line 464 of the SAM file ,nothing different with other line. When I chang my python version ,it has another wrong message,like this: Error occured when processing SAM input (record #2 in file ../05_sorted_bam/homo_con.bam):my_showwarning() takes from 3 to 5 positional arguments but 6 were given [Exception type : TypeError, raised in warning.py:99]