FileNotFoundError at the FST step

[MalickNdiye]

Hi @metaGmetapop! The pipeline fails during the Fst calculation step. I get the following error message

Error in eval(jsub, SDenv, parent.frame()) : object 'V1' not found Calls: [ -> [.data.table -> eval -> eval Execution halted Traceback (most recent call last): File "/work/FAC/FBM/DMF/pengel/beemicrophage/mndiaye1/PHOSTER/workflow/.snakemake/conda/451345fbc2f73c6d7e98f3f6feffea2d/bin/metapop", line 10, in sys.exit(main()) File "/work/FAC/FBM/DMF/pengel/beemicrophage/mndiaye1/PHOSTER/workflow/.snakemake/conda/451345fbc2f73c6d7e98f3f6feffea2d/lib/python3.7/site-packages/metapop/metapop_main.py", line 351, in main metapop.metapop_fst.perform_fst(microdiv_file, lengths_file, output_directorybase, threads) File "/work/FAC/FBM/DMF/pengel/beemicrophage/mndiaye1/PHOSTER/workflow/.snakemake/conda/451345fbc2f73c6d7e98f3f6feffea2d/lib/python3.7/site-packages/metapop/metapop_fst.py", line 267, in perform_fst ct_lens = contig_lengths(lengthsfile) File "/work/FAC/FBM/DMF/pengel/beemicrophage/mndiaye1/PHOSTER/workflow/.snakemake/conda/451345fbc2f73c6d7e98f3f6feffea2d/lib/python3.7/site-packages/metapop/metapop_fst.py", line 22, in contig_lengths fh = open(file) FileNotFoundError: [Errno 2] No such file or directory: '../results/metapop/B_test/MetaPop/10.Microdiversity/global_contig_microdiversity.tsv'

Looks like the global_contig_microdiversity.tsv doesn't get created. Do you have any idea on what may be causing this issue.

Thanks in advance!

[marina-vn]

Hi, I'm dealing with this same error, did you managed to solve it?

Best,

[MalickNdiye]

Unfortunately not, I decided to change tool

[marina-vn]

Which program did you change to? Any recommendations?

[MalickNdiye]

I switched to InStrain (https://instrain.readthedocs.io/en/latest/). Conceptually, it is very similar to Metapop. I highly recommend it.