object 'new.regions.starts' not found"

[kavonrtep]

Hi, I was running your program on fasta sequence available here: https://data.narodni-repozitar.cz/general/datasets/8t29q-nfr77

getting thy following error:

./TRASH_run.sh ../../CEN6_ver_220406.fasta
/mnt/raid/454_data/MinION/analysis/centromere_assembly_Cameor/220329_CEN6_assembly_correction/scripts/TRASH_v1.0_rdy
TRASH will be run with ../../CEN6_ver_220406.fasta arguments
[1] "start"
[1] "2022-12-16 14:10:45 UTC"
[1] "attaching function from: /mnt/ceph/454_data/MinION/analysis/centromere_assembly_Cameor/220329_CEN6_assembly_correction/scripts/TRASH_v1.0_rdy/src/fn_circos.R"
[1] "attaching function from: /mnt/ceph/454_data/MinION/analysis/centromere_assembly_Cameor/220329_CEN6_assembly_correction/scripts/TRASH_v1.0_rdy/src/fn_consensus_N.R"
[1] "attaching function from: /mnt/ceph/454_data/MinION/analysis/centromere_assembly_Cameor/220329_CEN6_assembly_correction/scripts/TRASH_v1.0_rdy/src/fn_draw_scaffold_repeat_plots.R"
[1] "attaching function from: /mnt/ceph/454_data/MinION/analysis/centromere_assembly_Cameor/220329_CEN6_assembly_correction/scripts/TRASH_v1.0_rdy/src/fn_export_gff.R"
[1] "attaching function from: /mnt/ceph/454_data/MinION/analysis/centromere_assembly_Cameor/220329_CEN6_assembly_correction/scripts/TRASH_v1.0_rdy/src/fn_extract_all_repeats.R"
[1] "attaching function from: /mnt/ceph/454_data/MinION/analysis/centromere_assembly_Cameor/220329_CEN6_assembly_correction/scripts/TRASH_v1.0_rdy/src/fn_extract_kmers.R"
[1] "attaching function from: /mnt/ceph/454_data/MinION/analysis/centromere_assembly_Cameor/220329_CEN6_assembly_correction/scripts/TRASH_v1.0_rdy/src/fn_hash_and_reverse.R"
[1] "attaching function from: /mnt/ceph/454_data/MinION/analysis/centromere_assembly_Cameor/220329_CEN6_assembly_correction/scripts/TRASH_v1.0_rdy/src/fn_HOR_wrapper.R"
[1] "attaching function from: /mnt/ceph/454_data/MinION/analysis/centromere_assembly_Cameor/220329_CEN6_assembly_correction/scripts/TRASH_v1.0_rdy/src/fn_kmer_compare.R"
[1] "attaching function from: /mnt/ceph/454_data/MinION/analysis/centromere_assembly_Cameor/220329_CEN6_assembly_correction/scripts/TRASH_v1.0_rdy/src/fn_repeat_identifier.R"
[1] "attaching function from: /mnt/ceph/454_data/MinION/analysis/centromere_assembly_Cameor/220329_CEN6_assembly_correction/scripts/TRASH_v1.0_rdy/src/fn_rev_comp_string.R"
[1] "/mnt/ceph/454_data/MinION/analysis/centromere_assembly_Cameor/220329_CEN6_assembly_correction/scripts/TRASH_v1.0_rdy/libs"
[1] "/mnt/ceph/454_data/MinION/analysis/centromere_assembly_Cameor/220329_CEN6_assembly_correction/scripts/TRASH_v1.0_rdy/../../CEN6_ver_220406.fasta"
[1] "Currently registered parallel backend name, version and cores"
[1] "doParallelMC"
[1] "1.0.17"
[1] 1
[1] "2022-12-16 14:11:12 UTC"
[1] "Working on sequence 1"
[1] "Repeat Identification new"
[1] "/mnt/ceph/454_data/MinION/analysis/centromere_assembly_Cameor/220329_CEN6_assembly_correction/scripts/TRASH_v1.0_rdy"
[1] "CEN6_ver_220406.fasta"
Error in { : task 1 failed - "object 'new.regions.starts' not found"
Calls: %dopar% -> <Anonymous>
Execution halted

[MntElo]

Hello, I've got the same error "object 'new.regions.starts' not found". Have you found the source of the error and its solution since? Thanks

[vlothec]

Hi, thanks for trying out TRASH. I've looked into it and couldn't replicate the issue. The "new.regions.starts" is now initialised and checked for when in use. Could you please upload the "fasta.file.name.out,txt" file created during the run in the "/assembly_out" directory?

[MntElo]

Hi, Initially the fasta file I'd like to analyze contains 11 sequences and in the "/assembly_out" directory 11 "fasta.file.name.out.txt" have been created. There is also 9 "Regions_fasta.file.name_seq.csv" file created. Here a .csv file and its .out.txt : Regions_Col-CEN_PC.fasta_LeftPC2.csv LeftPC2.out.txt

And here a .out.txt file for which I have no .csv file corresponding : LeftPC3.out.txt

Thanks for the help

[fjruizruano]

Hi, I have got a similar error:

Error in { : task 3 failed - "cannot open the connection"
Calls: %dopar% -> <Anonymous>
Execution halted

Any idea about how to solve it? Thanks in advance.

[vlothec]

Hi, I have got a similar error:

Error in { : task 3 failed - "cannot open the connection"
Calls: %dopar% -> <Anonymous>
Execution halted

Any idea about how to solve it? Thanks in advance.

Hi, this error throws when one of the processes is interrupted and doesn't provide enough information for me to troubleshoot. Could you send the files generated by TRASH by the time this error occured? Other than the output visible in the console/log file, there are additional log files in the fasta_name.out folder generated by TRASH.

Please also indicate the command you are using, as it seems TRASH cannot access an output file / fasta file.

[konczal]

Hi, I have got a similar error:

Error in { : task 3 failed - "cannot open the connection"
Calls: %dopar% -> <Anonymous>
Execution halted

Any idea about how to solve it? Thanks in advance.

In my case, this issue disappeared after providing an absolute path to output directory (instead of a relative path)

[vlothec]

Thank you @konczal. Yes, at this point the output directory needs to be an absolute path or no path at all. I've made this point in the manual.

[fjruizruano]

It worked for me. Thanks a lot!