rvalieris
commented
1 year ago these variant files missing are because the respective sequences were not found on the fasta.
double check your variant_groups file and make sure the variants in the second column are present in the fasta. from the error logs I can see there might be some typos, stray double quotes, extra spaces, etc.
MissingOutputException in line 6 of /data/Student_Data/Vinay/LCS-master/rules/pango-matrix-pipe.py: Job Missing files after 5 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait: outputs/fasta_lineages/Alpha.fa.gz outputs/fasta_lineages/BA.1.X.fa.gz outputs/fasta_lineages/BA.2.10.fa.gz outputs/fasta_lineages/BA.2.12.fa.gz outputs/fasta_lineages/BA.2.38.fa.gz Error1.txt outputs/fasta_lineages/BA.2.75.fa.gz outputs/fasta_lineages/BA.2.X.fa.gz outputs/fasta_lineages/BA.4.fa.gz outputs/fasta_lineages/BA.5.fa.gz outputs/fasta_lineages/Beta.fa.gz outputs/fasta_lineages/Delta.fa.gz outputs/fasta_lineages/Gamma.fa.gz outputs/fasta_lineages/Omicron.fa.gz outputs/fasta_lineages/Other.fa.gz outputs/fasta_lineages/XBB.fa.gz completed successfully, but some output files are missing. 6 Removing output files of failed job split_fasta_lineages since they might be corrupted: outputs/fasta_lineages/BA.1.fa.gz, outputs/fasta_lineages/BA.2.fa.gz, outputs/fasta_lineages/BA.3.fa.gz, outputs/fasta_lineages/Epsilon.fa.gz, outputs/fasta_lineages/Eta.fa.gz, outputs/fasta_lineages/Iota.fa.gz, outputs/fasta_lineages/Kappa.fa.gz, outputs/fasta_lineages/Zeta.fa.gz Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2022-11-18T102225.028837.snakemake.log