Closed zdk427 closed 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.
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?
@zdk427: did you manage to solve this issue? How?
I ran the example data with ont datatype and same error happened. Anyone solved this ?
@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: