Error in running the tool

[ap1438]

I tried istalling it with conda and stand alone but still it didnot work .

TRASH_run.sh: 3: Bad substitution /vol/pac/Software/TRASH TRASH will be run with /vol/pac/New/old_TRASH_results/TRASH/Ragtag_PW/P_ragtag.scaffold.fasta --o /vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/ --simpleplot --par 22 arguments [1] "start" [1] "2023-10-18 16:04:01 UTC" [1] "attaching function from: /vol/pac/Software/TRASH/src/fn_circos.R" [1] "attaching function from: /vol/pac/Software/TRASH/src/fn_consensus_N.R" [1] "attaching function from: /vol/pac/Software/TRASH/src/fn_draw_scaffold_repeat_plots.R" [1] "attaching function from: /vol/pac/Software/TRASH/src/fn_edit_distance.R" [1] "attaching function from: /vol/pac/Software/TRASH/src/fn_export_gff.R" [1] "attaching function from: /vol/pac/Software/TRASH/src/fn_extract_all_repeats.R" [1] "attaching function from: /vol/pac/Software/TRASH/src/fn_extract_kmers.R" [1] "attaching function from: /vol/pac/Software/TRASH/src/fn_hash_and_reverse.R" [1] "attaching function from: /vol/pac/Software/TRASH/src/fn_HOR_wrapper.R" [1] "attaching function from: /vol/pac/Software/TRASH/src/fn_kmer_compare.R" [1] "attaching function from: /vol/pac/Software/TRASH/src/fn_movav.R" [1] "attaching function from: /vol/pac/Software/TRASH/src/fn_new_distance_N.R" [1] "attaching function from: /vol/pac/Software/TRASH/src/fn_plot_edit.R" [1] "attaching function from: /vol/pac/Software/TRASH/src/fn_plot_rep.R" [1] "attaching function from: /vol/pac/Software/TRASH/src/fn_repeat_identifier.R" [1] "attaching function from: /vol/pac/Software/TRASH/src/fn_repetitiveness.R" [1] "attaching function from: /vol/pac/Software/TRASH/src/fn_rev_comp_string.R" [1] "/vol/pac/Software/TRASH/libs" [1] "/vol/pac/New/old_TRASH_results/TRASH/Ragtag_PW/P_ragtag.scaffold.fasta" [1] "Currently registered parallel backend name, version and cores" [1] "doParallelMC" [1] "1.0.17" [1] 22 [1] "Sequences to analyse:" file.name fasta.name 2 P_ragtag.scaffold.fasta D111_tig00000762_RagTag 3 P_ragtag.scaffold.fasta D111_tig00000774_RagTag 4 P_ragtag.scaffold.fasta D111_tig00000814_RagTag 5 P_ragtag.scaffold.fasta D111_tig00000860_RagTag 6 P_ragtag.scaffold.fasta D111_tig00000934_RagTag 7 P_ragtag.scaffold.fasta D111_tig00001076_RagTag 8 P_ragtag.scaffold.fasta D111_tig00105668_RagTag 9 P_ragtag.scaffold.fasta D111_tig00105671_RagTag 10 P_ragtag.scaffold.fasta D111_tig00105674_RagTag 11 P_ragtag.scaffold.fasta chrL.1_RagTag 12 P_ragtag.scaffold.fasta chrL.2_RagTag 13 P_ragtag.scaffold.fasta chrL.3_RagTag 14 P_ragtag.scaffold.fasta chrL.4_RagTag 15 P_ragtag.scaffold.fasta chrL.5_RagTag 16 P_ragtag.scaffold.fasta chrL.6_RagTag 17 P_ragtag.scaffold.fasta chrL.7_RagTag 18 P_ragtag.scaffold.fasta chrL.8_RagTag 19 P_ragtag.scaffold.fasta h2tg000028l 20 P_ragtag.scaffold.fasta h2tg000039l 21 P_ragtag.scaffold.fasta h2tg000041l 22 P_ragtag.scaffold.fasta h2tg000075l 23 P_ragtag.scaffold.fasta h2tg000080l 24 P_ragtag.scaffold.fasta h2tg000083l 25 P_ragtag.scaffold.fasta h2tg000141l 26 P_ragtag.scaffold.fasta h2tg000143l 27 P_ragtag.scaffold.fasta h2tg000146l 28 P_ragtag.scaffold.fasta h2tg000157l 29 P_ragtag.scaffold.fasta h2tg000168l 30 P_ragtag.scaffold.fasta h2tg000170l 31 P_ragtag.scaffold.fasta h2tg000188l 32 P_ragtag.scaffold.fasta h2tg000202l 33 P_ragtag.scaffold.fasta h2tg000221l 34 P_ragtag.scaffold.fasta h2tg000236l 35 P_ragtag.scaffold.fasta h2tg000258l 36 P_ragtag.scaffold.fasta h2tg000287c 37 P_ragtag.scaffold.fasta h2tg000342l 38 P_ragtag.scaffold.fasta h2tg000355l 39 P_ragtag.scaffold.fasta h2tg000450l 40 P_ragtag.scaffold.fasta h2tg000457l 41 P_ragtag.scaffold.fasta h2tg000480l 42 P_ragtag.scaffold.fasta h2tg000505l 43 P_ragtag.scaffold.fasta h2tg000538l 44 P_ragtag.scaffold.fasta h2tg000613l 45 P_ragtag.scaffold.fasta h2tg000622l 46 P_ragtag.scaffold.fasta h2tg000669l 47 P_ragtag.scaffold.fasta h2tg000841l 48 P_ragtag.scaffold.fasta h2tg000857l 49 P_ragtag.scaffold.fasta h2tg001043l [1] "2023-10-18 16:04:21 UTC" [1] "Working on sequence 1" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:04:22 UTC" [1] "Working on sequence 2" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:04:22 UTC" [1] "Working on sequence 3" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:04:22 UTC" [1] "Working on sequence 4" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:04:22 UTC" [1] "2023-10-18 16:04:22 UTC" [1] "Working on sequence 6" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "Working on sequence 5" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:04:22 UTC" [1] "Working on sequence 7" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:04:22 UTC" [1] "Working on sequence 8" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:04:22 UTC" [1] "Working on sequence 9" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:04:22 UTC" [1] "Working on sequence 10" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:04:22 UTC" [1] "Working on sequence 11" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:04:22 UTC" [1] "Working on sequence 12" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:04:22 UTC" [1] "Working on sequence 13" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:04:22 UTC" [1] "Working on sequence 14" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:04:22 UTC" [1] "Working on sequence 15" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:04:22 UTC" [1] "Working on sequence 16" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:04:22 UTC" [1] "Working on sequence 17" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:04:22 UTC" [1] "Working on sequence 18" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:04:22 UTC" [1] "Working on sequence 19" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:04:22 UTC" [1] "Working on sequence 20" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:04:22 UTC" [1] "Working on sequence 21" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:04:22 UTC" [1] "Working on sequence 22" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:04:27 UTC" [1] "Working on sequence 41" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:04:28 UTC" [1] "Working on sequence 44" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:04:30 UTC" [1] "Working on sequence 42" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:04:31 UTC" [1] "Working on sequence 28" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:04:31 UTC" [1] "Working on sequence 27" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:04:32 UTC" [1] "Working on sequence 43" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:04:34 UTC" [1] "Working on sequence 26" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:04:39 UTC" [1] "Working on sequence 48" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:04:42 UTC" [1] "Working on sequence 24" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:04:48 UTC" [1] "Working on sequence 40" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:04:48 UTC" [1] "Working on sequence 46" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:04:52 UTC" [1] "Working on sequence 25" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:04:52 UTC" [1] "Working on sequence 23" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:04:53 UTC" [1] "Working on sequence 30" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:04:56 UTC" [1] "Working on sequence 47" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:04:56 UTC" [1] "Working on sequence 45" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:05:01 UTC" [1] "Working on sequence 29" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:05:21 UTC" [1] "Working on sequence 31" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:34:16 UTC" [1] "Working on sequence 32" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:45:50 UTC" [1] "Working on sequence 34" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:48:13 UTC" [1] "Working on sequence 39" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:52:21 UTC" [1] "Working on sequence 36" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 16:52:43 UTC" [1] "Working on sequence 38" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 17:08:23 UTC" [1] "Working on sequence 33" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 17:08:24 UTC" [1] "Working on sequence 35" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" [1] "2023-10-18 17:20:08 UTC" [1] "Working on sequence 37" [1] "Repeat Identification new" [1] "/vol/pac/New/old_TRASH_results/TRASH/Pais_09_Hifiasm_assemblie_scafolded/" [1] "P_ragtag.scaffold.fasta" Error in { : task 3 failed - "'length = 1855' in coercion to 'logical(1)'" Calls: %dopar% -> Execution halted

[CongyangY]

Hi, have you solved the problem? I encounted the same issued with you. I re-produced the problems even when I used the examle data.

[HeQSun]

same problem observed. not solved yet.

[vlothec]

There was an update to the base R that changed a warning to an error on a logical comparison with making the program crash on an up-to-date R. I am close to finishing a new release that addresses this and all other raised issues, that will be ready next week. I'll drop a line here when that's available

[pgonzale60]

Hi @vlothec ,

I can verify that the latest version available from github fixed this issue for me. @vlothec, I would recommend updating the README to point to a new tar.gz if possible instead of https://github.com/vlothec/TRASH/raw/main/TRASH.v1.2.tar.gz

Thank you for sharing your work!

Pablo

[adharafardhin]

Hello, I have cloned this repository but facing similar issue. Is there a new link to the fixed version of the tar.gz file?

Thank you.

[ap1438]

I will suggest give a try with conda create -n name -c conda-forge zlib. by removing the r base version specification, it will use the latest r base. It might work. Let me know if it works.

[GooLey1025]

错误于{: task 1 failed - "'length = 3840' in coercion to 'logical(1)'" Calls: %dopar% -> 停止执行

Did anyone meet the same error , although I have reinstalled ? At the first time I ran this program , nothing wrong happen , but the second day I encountered this problem and then I have tried reinstalled or reconda create , but all of this did not work .