not enough values to unpack error

Question

not enough values to unpack error

bcpd opened this issue 5 years ago · comments

Dear all,

Thank you for this great tool. After smoothly running 65 fastq files using -a diamond and -db DB_100, I get the following error:

File "/usr/bin/miniconda3/lib/python3.6/site-packages/superfocus_app/superfocus.py", line 342, in main
del_alignments)
ValueError: not enough values to unpack (expected 2, got 0)

This does not appear to be a disk space issue, as I have 430GB of space available, nor is it a memory deficit, as I have 256GB of RAM available. Any help would be greatly appreciated.

Geni Silva · Answer 1 · Fri Dec 06 2019 06:53:54 GMT+0800 (China Standard Time)

Sorry for the late answer. Did you figure it out? Probably one of the FASTQs is too small and did not generate any alignments.

Let me know what you found, so I can fix the bug, if any.

Best

pad · Answer 2 · Fri Dec 13 2019 08:32:01 GMT+0800 (China Standard Time)

Hi Geni,
Thank you for your reply. I cannot say for sure if the size of the alignment is causing the issue, but I just had the same problem with another dataset (the one giving me problems ended up running fine). If what you say is true, then it would be great if superfocus could skip the small files and run to completion.
Thanks very much.

Geni Silva · Answer 3 · Fri Dec 13 2019 14:37:05 GMT+0800 (China Standard Time)

Do you still have the command line you ran? I recently fixed a bug related to this.

Best

pad · Answer 4 · Sat Dec 14 2019 00:55:02 GMT+0800 (China Standard Time)

Hi Geni,

This is the command (excluding or including the -d makes no difference):
superfocus -q /folder/ -dir /folder/ -db DB_100 -a diamond -t 8 -d

Also, a negative control with ~1000 reads ran fine, so size does not appear to be an issue.

Geni Silva · Answer 5 · Sat Dec 21 2019 00:31:23 GMT+0800 (China Standard Time)

I see. Thanks for sharing it.