Open andreluizherpeto opened 1 year ago
Hi Andre,
Change the —workflow
to phasing
- it looks like there is a typo in the documentation.
-b
Of course! I knew the problem would be something small but critical. Thank you very much Dr. Faircloth for catching that mistake. That solved the problem. I really appreciate it. Best, A.
this one’s on me! i’ll get that typo fixed shortly 👍
bams: Eurolophosaurus_amathites_MTR11349: /media/digitalstorm/Storage2/andre/andre_uce_jan_2023/phase-tropiduridae/mapping-results/mapped_reads/Eurolophosaurus_amathites_MTR11349.fxm.sorted.md.bam
contigs: Eurolophosaurus_amathites_MTR11349: /media/digitalstorm/Storage2/andre/andre_uce_jan_2023/phase-tropiduridae/spades-assemblies/contigs/Eurolophosaurus_amathites_MTR11349.contigs.fasta
(phyluce-1.7.1) digitalstorm@Velox-XXXXX:/media/digitalstorm/Storage2/andre/andre_uce_jan_2023/phase-tropiduridae/mapping-results/mapped_reads$ phyluce_workflow --config /media/digitalstorm/Storage2/andre/andre_uce_jan_2023/phase-tropiduridae/phasing.conf \
Building DAG of jobs... InputFunctionException in line 48 of /home/digitalstorm/miniconda3/envs/phyluce-1.7.1/phyluce/workflows/mapping/Snakefile: Error: KeyError: 'reads' Wildcards: sample=Eurolophosaurus_amathites_MTR11349 Traceback: File "/home/digitalstorm/miniconda3/envs/phyluce-1.7.1/phyluce/workflows/mapping/Snakefile", line 25, in get_fq1