Execution #14
Description
Hi, I can resolve the first two issues, but I can't continue with the pipeline now:
I am trying with one particular contig of the assembly:
./../TRASH/TRASH_run.sh tig00000057_pilon_pilon.fasta --o /home/ggreif/JJTR/57
/home/ggreif/TRASH
TRASH will be run with tig00000057_pilon_pilon.fasta --o /home/ggreif/JJTR/57 arguments
[1] "start"
[1] "2023-08-22 13:23:03 -03"
[1] "attaching function from: /home/ggreif/TRASH/src/fn_circos.R"
[1] "attaching function from: /home/ggreif/TRASH/src/fn_consensus_N.R"
[1] "attaching function from: /home/ggreif/TRASH/src/fn_draw_scaffold_repeat_plots.R"
[1] "attaching function from: /home/ggreif/TRASH/src/fn_edit_distance.R"
[1] "attaching function from: /home/ggreif/TRASH/src/fn_export_gff.R"
[1] "attaching function from: /home/ggreif/TRASH/src/fn_extract_all_repeats.R"
[1] "attaching function from: /home/ggreif/TRASH/src/fn_extract_kmers.R"
[1] "attaching function from: /home/ggreif/TRASH/src/fn_hash_and_reverse.R"
[1] "attaching function from: /home/ggreif/TRASH/src/fn_HOR_wrapper.R"
[1] "attaching function from: /home/ggreif/TRASH/src/fn_kmer_compare.R"
[1] "attaching function from: /home/ggreif/TRASH/src/fn_movav.R"
[1] "attaching function from: /home/ggreif/TRASH/src/fn_new_distance_N.R"
[1] "attaching function from: /home/ggreif/TRASH/src/fn_plot_edit.R"
[1] "attaching function from: /home/ggreif/TRASH/src/fn_plot_rep.R"
[1] "attaching function from: /home/ggreif/TRASH/src/fn_repeat_identifier.R"
[1] "attaching function from: /home/ggreif/TRASH/src/fn_repetitiveness.R"
[1] "attaching function from: /home/ggreif/TRASH/src/fn_rev_comp_string.R"
[1] "/home/ggreif/TRASH/libs"
[1] "/home/ggreif/JJTR/tig00000057_pilon_pilon.fasta"
[1] "Currently registered parallel backend name, version and cores"
[1] "doParallelMC"
[1] "1.0.17"
[1] 1
[1] "Sequences to analyse:"
file.name fasta.name
2 tig00000057_pilon_pilon.fasta tig00000057_pilon_pilon
[1] "2023-08-22 13:23:05 -03"
[1] "Working on sequence 1"
[1] "Repeat Identification new"
[1] "/home/ggreif/JJTR/57"
[1] "tig00000057_pilon_pilon.fasta"
Error in { : task 1 failed - "'length = 245' in coercion to 'logical(1)'"
Calls: %dopar% ->
Execution halted
The output have two temp folders:
ggreif@UBM12:~/JJTR$ ls 57/tig00000057_pilon_pilon.fasta_out/
temp1 temp2 tig00000057_pilon_pilon.debug.txt tig00000057_pilon_pilon.out.txt