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vlothec / TRASH

RepeatIdentifier
MIT License
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Running TRASH #13

Closed Gon1976 closed 1 year ago

Gon1976 commented 1 year ago

Hi Finally I launch trash with this command to detect repeats in my assembly with 481 contigs: grep -c '>' JJ_R2Pilon.fasta 481

I use this command line: ./TRASH/TRASH_run.sh JoseJulio/JJ_R2Pilon.fasta --o JJTR/ And this is the output in the screen:

/home/ggreif/TRASH TRASH will be run with JoseJulio/JJ_R2Pilon.fasta --o JJTR/ arguments [1] "start" [1] "2023-08-22 09:27:53 -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/JoseJulio/JJ_R2Pilon.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 JJ_R2Pilon.fasta tig00000057_pilon_pilon 3 JJ_R2Pilon.fasta tig00000075_pilon_pilon 4 JJ_R2Pilon.fasta tig00000104_pilon_pilon 5 JJ_R2Pilon.fasta tig00000127_pilon_pilon 6 JJ_R2Pilon.fasta tig00000138_pilon_pilon 7 JJ_R2Pilon.fasta tig00000151_pilon_pilon 8 JJ_R2Pilon.fasta tig00000156_pilon_pilon 9 JJ_R2Pilon.fasta tig00000195_pilon_pilon 10 JJ_R2Pilon.fasta tig00000197_pilon_pilon 11 JJ_R2Pilon.fasta tig00000200_pilon_pilon 12 JJ_R2Pilon.fasta tig00000208_pilon_pilon 13 JJ_R2Pilon.fasta tig00000218_pilon_pilon 14 JJ_R2Pilon.fasta tig00000220_pilon_pilon 15 JJ_R2Pilon.fasta tig00000221_pilon_pilon 16 JJ_R2Pilon.fasta tig00000284_pilon_pilon 17 JJ_R2Pilon.fasta tig00000289_pilon_pilon 18 JJ_R2Pilon.fasta tig00000293_pilon_pilon 19 JJ_R2Pilon.fasta tig00000305_pilon_pilon 20 JJ_R2Pilon.fasta tig00000331_pilon_pilon 21 JJ_R2Pilon.fasta tig00000345_pilon_pilon 22 JJ_R2Pilon.fasta tig00000348_pilon_pilon 23 JJ_R2Pilon.fasta tig00000350_pilon_pilon 24 JJ_R2Pilon.fasta tig00000361_pilon_pilon 25 JJ_R2Pilon.fasta tig00000363_pilon_pilon 26 JJ_R2Pilon.fasta tig00000374_pilon_pilon 27 JJ_R2Pilon.fasta tig00000375_pilon_pilon 28 JJ_R2Pilon.fasta tig00000380_pilon_pilon 29 JJ_R2Pilon.fasta tig00000381_pilon_pilon 30 JJ_R2Pilon.fasta tig00000388_pilon_pilon 31 JJ_R2Pilon.fasta tig00000398_pilon_pilon 32 JJ_R2Pilon.fasta tig00000400_pilon_pilon 33 JJ_R2Pilon.fasta tig00000401_pilon_pilon 34 JJ_R2Pilon.fasta tig00000410_pilon_pilon 35 JJ_R2Pilon.fasta tig00000420_pilon_pilon 36 JJ_R2Pilon.fasta tig00000424_pilon_pilon 37 JJ_R2Pilon.fasta tig00000427_pilon_pilon 38 JJ_R2Pilon.fasta tig00000438_pilon_pilon 39 JJ_R2Pilon.fasta tig00000448_pilon_pilon 40 JJ_R2Pilon.fasta tig00000457_pilon_pilon 41 JJ_R2Pilon.fasta tig00000459_pilon_pilon 42 JJ_R2Pilon.fasta tig00000460_pilon_pilon 43 JJ_R2Pilon.fasta tig00000462_pilon_pilon 44 JJ_R2Pilon.fasta tig00000464_pilon_pilon 45 JJ_R2Pilon.fasta tig00000472_pilon_pilon 46 JJ_R2Pilon.fasta tig00000481_pilon_pilon 47 JJ_R2Pilon.fasta tig00000513_pilon_pilon 48 JJ_R2Pilon.fasta tig00000514_pilon_pilon 49 JJ_R2Pilon.fasta tig00000517_pilon_pilon [1] "2023-08-22 09:28:00 -03" [1] "Working on sequence 1" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 2" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 3" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 4" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 5" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 6" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 7" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 8" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 9" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 10" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 11" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 12" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 13" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 14" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 15" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 16" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 17" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 18" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 19" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 20" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 21" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 22" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 23" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 24" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 25" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 26" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 27" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 28" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 29" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 30" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 31" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 32" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 33" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 34" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 35" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 36" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 37" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 38" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 39" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 40" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 41" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 42" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 43" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 44" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 45" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 46" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 47" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" [1] "2023-08-22 09:29:06 -03" [1] "Working on sequence 48" [1] "Repeat Identification new" [1] "JJTR/" [1] "JJ_R2Pilon.fasta" Error in { : task 1 failed - "cannot open the connection" Calls: %dopar% -> In addition: Warning messages: 1: In dir.create(paste(temp.folder, "/", paste(assemblyName, "_out", : cannot create dir 'JJTR//JJ_R2Pilon.fasta_out/temp1', reason 'No such file or directory' 2: In file(file, ifelse(append, "a", "w")) : cannot open file 'JJ_R2Pilon.fasta_out/temp1/Pre_Primary_regions_JJ_R2Pilon.fasta_tig00000057_pilon_pilon.csv': No such file or directory Execution halted

The output directory result in two files (empty debug file and out txt only for one contig: more tig00000057_pilon_pilon.out.txt starting the main function JJ_R2Pilon.fasta tig00000057_pilon_pilon Checking windows of sequence tig00000057_pilon_pilon, window 100/2011 Checking windows of sequence tig00000057_pilon_pilon, window 200/2011 Checking windows of sequence tig00000057_pilon_pilon, window 300/2011 Checking windows of sequence tig00000057_pilon_pilon, window 400/2011 Checking windows of sequence tig00000057_pilon_pilon, window 500/2011 Checking windows of sequence tig00000057_pilon_pilon, window 600/2011 Checking windows of sequence tig00000057_pilon_pilon, window 700/2011 Checking windows of sequence tig00000057_pilon_pilon, window 800/2011 Checking windows of sequence tig00000057_pilon_pilon, window 900/2011 Checking windows of sequence tig00000057_pilon_pilon, window 1000/2011 Checking windows of sequence tig00000057_pilon_pilon, window 1100/2011 Checking windows of sequence tig00000057_pilon_pilon, window 1200/2011 Checking windows of sequence tig00000057_pilon_pilon, window 1300/2011 Checking windows of sequence tig00000057_pilon_pilon, window 1400/2011 Checking windows of sequence tig00000057_pilon_pilon, window 1500/2011 Checking windows of sequence tig00000057_pilon_pilon, window 1600/2011 Checking windows of sequence tig00000057_pilon_pilon, window 1700/2011 Checking windows of sequence tig00000057_pilon_pilon, window 1800/2011 Checking windows of sequence tig00000057_pilon_pilon, window 1900/2011 Checking windows of sequence tig00000057_pilon_pilon, window 2000/2011 sequence tig00000057_pilon_pilon, window 2011/2011 sequence tig00000057_pilon_pilon finished scoring windows sequence tig00000057_pilon_pilon finished calculating regions Step 1 (identify windows) done calculating distances on region 1/5 region size: 10000 calculating distances on region 2/5 region size: 39000 calculating distances on region 3/5 region size: 4000 calculating distances on region 4/5 region size: 63000 calculating distances on region 5/5 region size: 7000 sequence tig00000057_pilon_pilon: finished calculating main distances

Can you help me to understand what is happen?

Gon1976 commented 1 year ago

I miss to use complete path to the output directory, now I think is running ok thanks