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bioinfo-ut / StrainSeeker

A bacterial identification program for fast identification of bacterial strains from raw sequencing reads
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Error: No list files specified #2

Open ryjohnson09 opened 7 years ago

ryjohnson09 commented 7 years ago

Hello,

I've been trying to get builder.pl to work on a custom set of 23 assembled bacterial genomes. Here is the command I'm running: perl builder.pl -t $SLURM_CPUS_PER_TASK -n skoreensis_tree.nwk -d genomes -w 32 -b ss_blacklist_w32.list -o skoreensis_ss_db

The program runs up until right after the "Eliminate multiple occurring" step. Here is the last few bits of stdout that I get.

Eliminate multiple occurring: 48 of 51 Eliminate multiple occurring: 50 of 51 Eliminate multiple occurring: all remaining GET INITAL K-MER COUNT IN LISTS... REMOVING UNUSED LISTS... REDUCING LISTS... Reduce lists: 23 of 51 Error: No list files specified! Usage: glistcompare [OPTIONS] Options: -v, --version - print version information and exit -h, --help - print this usage screen and exit -u, --union - union of input lists -i, --intersection - intersection of input lists -d, --difference - difference of input lists -dd, --double_difference - double difference of input lists -du, --diff_union - subtract first list from the second and finds difference -mm, --mismatch NUMBER - specify number of mismatches (default 0, can be used with -diff and -ddiff) -c, --cutoff NUMBER - specify frequency cut-off (default 1) -o, --outputname STRING - specify output name (default "out") -r, --rule STRING - specify rule how final frequencies are calculated (default, add, subtract, min, max, first, second) NOTE: rules min, subtract, first and second can only be used with finding the intersection. --count_only - output count of k-mers instead of k-mers themself -D - increase debug level Error: No list files specified! Usage: glistcompare [OPTIONS] Options: -v, --version - print version information and exit -h, --help - print this usage screen and exit -u, --union - union of input lists -i, --intersection - intersection of input lists -d, --difference - difference of input lists -dd, --double_difference - double difference of input lists -du, --diff_union - subtract first list from the second and finds difference -mm, --mismatch NUMBER - specify number of mismatches (default 0, can be used with -diff and -ddiff) -c, --cutoff NUMBER - specify frequency cut-off (default 1) -o, --outputname STRING - specify output name (default "out") -r, --rule STRING - specify rule how final frequencies are calculated (default, add, subtract, min, max, first, second) NOTE: rules min, subtract, first and second can only be used with finding the intersection. --count_only - output count of k-mers instead of k-mers themself -D - increase debug level Reduce lists: 38 of 51 Error: No list files specified! Usage: glistcompare [OPTIONS] Options: -v, --version - print version information and exit -h, --help - print this usage screen and exit -u, --union - union of input lists -i, --intersection - intersection of input lists -d, --difference - difference of input lists -dd, --double_difference - double difference of input lists -du, --diff_union - subtract first list from the second and finds difference -mm, --mismatch NUMBER - specify number of mismatches (default 0, can be used with -diff and -ddiff) -c, --cutoff NUMBER - specify frequency cut-off (default 1) -o, --outputname STRING - specify output name (default "out") -r, --rule STRING - specify rule how final frequencies are calculated (default, add, subtract, min, max, first, second) NOTE: rules min, subtract, first and second can only be used with finding the intersection. --count_only - output count of k-mers instead of k-mers themself -D - increase debug level Error: No list files specified! Usage: glistcompare [OPTIONS] Options: -v, --version - print version information and exit -h, --help - print this usage screen and exit -u, --union - union of input lists -i, --intersection - intersection of input lists -d, --difference - difference of input lists -dd, --double_difference - double difference of input lists -du, --diff_union - subtract first list from the second and finds difference -mm, --mismatch NUMBER - specify number of mismatches (default 0, can be used with -diff and -ddiff) -c, --cutoff NUMBER - specify frequency cut-off (default 1) -o, --outputname STRING - specify output name (default "out") -r, --rule STRING - specify rule how final frequencies are calculated (default, add, subtract, min, max, first, second) NOTE: rules min, subtract, first and second can only be used with finding the intersection. --count_only - output count of k-mers instead of k-mers themself -D - increase debug level Renaming all subset files and get new counts mv: cannot stat `skoreensis_ss_db/Sphing_MMR69_060112_subset_32.list': No such file or directory Problem in reduceLists command: mv skoreensis_ss_db/Sphing_MMR69_060112_subset_32.list skoreensis_ss_db/Sphing_MMR69_060112_32.list at builder.pl line 663.

I cannot figure out why it keeps killing the program. Any help would be appreciated.

bioinfo-ut commented 5 years ago

Hi!

This could be caused by an old version of glistcompare, which is missing some options. Can you please try downloading glistcompare binary again from github and see if it fixes the problem?