pgonzale60
commented
2 months ago Hi, this was fixed in latest version (don't use the tar.gz) https://github.com/vlothec/TRASH/issues/16#issuecomment-1923237159
Open Gon1976 opened 1 year ago
pgonzale60
commented
2 months ago Hi, this was fixed in latest version (don't use the tar.gz) https://github.com/vlothec/TRASH/issues/16#issuecomment-1923237159
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