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HaploKit / Strainline

Full-length de novo viral haplotype reconstruction from noisy long reads
GNU General Public License v3.0
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ValueError: not enough values to unpack(expected 2, got1) #11

Closed zdk427 closed 1 year ago

zdk427 commented 1 year ago

@HaploKit

I have tried running the given example (reads.fa) file for haplotype calling, it works perfectly fine for me.

Currently trying to run my ONT obtained reads from GridIon Run to identify haplotypes. Every time, I am getting a specific error enlisted below in bold: ......read overlaps filtering finished. processing the 34 seed read... processing the 34 seed read... Traceback (most recent call last): File "/home/ngs/Downloads/Strainline-master/src/clustering.py", line 172, in cluster_list = get_clusters(in_fa, outdir, int(topk), platform, int(threads), int(min_ovlp_len), File "/home/ngs/Downloads/Strainline-master/src/clustering.py", line 92, in get_clusters header, seq = id2fa[id].strip().split('\n') ValueError: not enough values to unpack (expected 2, got 1) (strainline) ngs@ngs-ThinkCentre-M93p:~/Desktop/trialstrainline/example$

Is there any modification that is to be done specifically for ONT reads in Strainline.sh file or do i need to modify my input file obtained from ONT run?

Please find the attached snapshot for your reference:

image

HadrienRegue commented 1 year ago

@zdk427 : Did you solve this issue? I have the same error with my ONT data, and no problems with the testing dataset. Thanks.

LaraFuhrmann commented 8 months ago

Hi, I am running into the same issue when executing Strainline on the example data following the instruction in the README, for both ONT and PacBio: strainline.sh -i reads.fa -o out -p pb -k 20 -t 32 strainline.sh -i reads.fa -o out -p ont -t 32

Did you manage to fix this issue?

npdungca commented 1 month ago

@zdk427: did you manage to solve this issue? How?

linvei commented 3 days ago

I ran the example data with ont datatype and same error happened. Anyone solved this ?