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nh13 / DWGSIM

Whole Genome Simulator for Next-Generation Sequencing
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Contig not found error when using the -x option with multiple bed lines #72

Closed gtollefson closed 2 years ago

gtollefson commented 2 years ago

Hi,

I receive the following error when running dwgsim with the -x option with a 5 region bed file. When I run the same command with a modified version of the bed file containing only 1 region line for each run, each run completed successfully. This looks like a bug with the -x functionality.

Command: dwgsim -e 0.000 -E 0.000 -C 30 -1 150 -2 150 -r 0.00000 -F 0.000 -R 0.0 -x some_directory/5_sim_samples/regions_of_interest_5_samples.bed -q F some_directory/5_sim_samples/sample_1_mutations.fasta some_directory/5_sim_samples/sample_1_sim_reads

Error:

Error: contig not found [chr17]

The bed file contents (tab delimited):

chr3 179148523 179240093 chr17 7668402 7687538 chr16 68737225 68835548 chr10 8058551 8058551 chr2 178525989 178807423 chr7 55019101 55211628

Can you help me to troubleshoot?

Thank you, George

nh13 commented 2 years ago

What is the order of your contigs in your FASTA? The BED file should have entries in the same order.

nh13 commented 2 years ago

Error message improved in #75