Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Error in running the tool #16

Open
ap1438 opened this issue Oct 20, 2023 · 7 comments
Open

Error in running the tool #16

ap1438 opened this issue Oct 20, 2023 · 7 comments

Comments

@ap1438
Copy link

ap1438 commented Oct 20, 2023

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
Copy link

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
Copy link

HeQSun commented Feb 2, 2024

same problem observed. not solved yet.

@vlothec
Copy link
Owner

vlothec commented Feb 2, 2024

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
Copy link

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

This was referenced Jun 6, 2024
Open
Open
@adharafardhin
Copy link

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
Copy link
Author

ap1438 commented Jul 18, 2024

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
Copy link

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 .

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
7 participants
@pgonzale60 @HeQSun @vlothec @ap1438 @adharafardhin @CongyangY @GooLey1025