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Magdoll / Cogent

Coding Genome Reconstruction using Iso-Seq data
BSD 3-Clause Clear License
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Error when running get_abundance_post_collapse.py #68

Closed stanikae closed 5 years ago

stanikae commented 5 years ago

Hi,

I keep getting the following error: get_abundance_post_collapse.py", line 148, in output_read_count_IsoSeq_csv raise Exception, "cluster_id {0} is not a valid cluster ID!".format(cid) Exception: cluster_id transcript/18747 is not a valid cluster ID! after running get_abundance_post_collapse.py after generating hq_isoforms using iso-seq3

My cluster_report.csv looks like this: cluster_id,read_id,read_type transcript/18747,m54271_190729_134054/56361333/ccs,FL transcript/18747,m54271_190729_134054/67109755/ccs,FL transcript/18748,m54271_190729_134054/61277171/ccs,FL transcript/18748,m54271_190729_134054/36438258/ccs,FL

hq_isoforms.fasta.no5merge.collapsed.group.txt looks like the following: PB.1.1 Cell_1__Raksha_Bcab443__Iso-Seq__HQ_transcript/6659,Cell_1__Raksha_Bcab443__Iso-Seq__HQ_transcript/6944 PB.1.2 Cell_1__Raksha_Bcab443__Iso-Seq__HQ_transcript/6312 PB.1.3 Cell_1__Raksha_Bcab443__Iso-Seq__HQ_transcript/6626

Three months ago when i ran into the same issue i resolved it by following your tutorial about using isoseq3_make isoseq3_make_classify_report.py, but nothing seems to work this time.

stanikae commented 5 years ago

It turned out I still had the old Cupcake scripts in my bin. Everything is working smoothly now after updating my bin with the new Cupcake ToFU scripts