Execution halted and ERROR: strict merge also failed

[M-Asim-Javed]

Hello, I was trying to use Earl Gray for my genome but at the end the end the execution was halted due to error below:

FileNotFoundError: [Errno 2] No such file or directory: '/home/edelab/pacbio/genome_analysis/earlgray/pb_output/plasmodiophoraBrassicae_EarlGrey/plasmodiophoraBrassicae_mergedRepeats//plasmodiophoraBrassicae.filteredRepeats.bed' mv: cannot stat '/home/edelab/pacbio/genome_analysis/earlgray/pb_output/plasmodiophoraBrassicae_EarlGrey/plasmodiophoraBrassicae_mergedRepeats//plasmodiophoraBrassicae.filteredRepeats.bed.2': No such file or directory ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.2 ── ✔ ggplot2 3.4.4 ✔ purrr 1.0.2 ✔ tibble 3.2.1 ✔ dplyr 1.1.4 ✔ tidyr 1.3.0 ✔ stringr 1.5.1 ✔ readr 2.1.4 ✔ forcats 1.0.0 ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ── ✖ dplyr::filter() masks stats::filter() ✖ dplyr::lag() masks stats::lag() Warning messages: 1: package ‘ggplot2’ was built under R version 4.2.3 2: package ‘tibble’ was built under R version 4.2.3 3: package ‘tidyr’ was built under R version 4.2.3 4: package ‘readr’ was built under R version 4.2.3 5: package ‘purrr’ was built under R version 4.2.3 6: package ‘dplyr’ was built under R version 4.2.3 7: package ‘stringr’ was built under R version 4.2.3 8: package ‘forcats’ was built under R version 4.2.3 [1] "/home/edelab/miniconda3/envs/earlgrey/lib/R/bin/exec/R" [2] "--no-echo" [3] "--no-restore" [4] "--file=/home/edelab/miniconda3/envs/earlgrey/share/earlgrey-4.0-0/scripts//makeGff.R" [5] "--args" [6] "/home/edelab/pacbio/genome_analysis/earlgray/pb_output/plasmodiophoraBrassicae_EarlGrey/plasmodiophoraBrassicae_mergedRepeats//plasmodiophoraBrassicae.filteredRepeats.bed" [7] "/home/edelab/pacbio/genome_analysis/earlgray/pb_output/plasmodiophoraBrassicae_EarlGrey/plasmodiophoraBrassicae_mergedRepeats//plasmodiophoraBrassicae.rmerge.gff.filtered" [8] "/home/edelab/pacbio/genome_analysis/earlgray/pb_output/plasmodiophoraBrassicae_EarlGrey/plasmodiophoraBrassicae_mergedRepeats//plasmodiophoraBrassicae.filteredRepeats.gff" Error in file(file, "rt") : cannot open the connection Calls: read.table -> file In addition: Warning message: In file(file, "rt") : cannot open file '/home/edelab/pacbio/genome_analysis/earlgray/pb_output/plasmodiophoraBrassicae_EarlGrey/plasmodiophoraBrassicae_mergedRepeats//plasmodiophoraBrassicae.filteredRepeats.bed': No such file or directory Execution halted

          )  (
         (   ) )
         ) ( (
       _______)_
    .-'---------|
   ( C|/\/\/\/\/|
    '-./\/\/\/\/|
     '_________'
      '-------'
    <<< Done! >>>

ERROR: strict merge also failed, check /home/edelab/pacbio/genome_analysis/earlgray/pb_output/plasmodiophoraBrassicae_EarlGrey/plasmodiophoraBrassicae_RepeatMasker_Against_Custom_Library/pb3A_assembly.fasta.prep.out looks as expected

Can you help me in this regard!

Thanks

[TobyBaril]

Hi, can you upload the log file from the EarlGrey directory? The issue might be further up in the pipeline - I’m happy to take a look!

[M-Asim-Javed]

plasmodiophoraBrassicaeEarlGrey.log

Thanks for the response. Here's the log file!

[ammarabdalrahem]

Hello, I have the same error,

[6] "/Commun/ammar/TE/ref_v2._EarlGrey/ref_v2._mergedRepeats//ref_v2..filteredRepeats.bed"
[7] "/Commun/ammar/TE/ref_v2._EarlGrey/ref_v2._mergedRepeats//ref_v2..rmerge.gff.filtered"
[8] "/Commun/ammar/TE/ref_v2._EarlGrey/ref_v2._mergedRepeats//ref_v2..filteredRepeats.gff"
Error in file(file, "rt") : cannot open the connection Calls: read.table -> file In addition: Warning message: In file(file, "rt") : cannot open file '/Commun/ammar/TE/ref_v2._EarlGrey/ref_v2._mergedRepeats//ref_v2..filteredRepeats.bed': No such file or directory Execution halted

          )  (
         (   ) )
         ) ( (
       _______)_
    .-'---------|  
   ( C|/\/\/\/\/|
    '-./\/\/\/\/|
     '_________'
      '-------'
    <<< Done! >>>

I believe the issue is due to the double forward slashes: [6] "/Commun/ammar/TE/ref_v2._EarlGrey/ref_v2._mergedRepeats//ref_v2..filteredRepeats.bed"
[7] "/Commun/ammar/TE/ref_v2._EarlGrey/ref_v2._mergedRepeats//ref_v2..rmerge.gff.filtered"
[8] "/Commun/ammar/TE/ref_v2._EarlGrey/ref_v2._mergedRepeats//ref_v2..filteredRepeats.gff"

[TobyBaril]

This was an issue with argument parsing in the new update. I have patched this and merged for version 4.0.2. This might take a while to show up in conda, but should be fixed after this.

If you want to update before that, find your conda environment install: which earlGrey | sed 's|bin.*|share/earlgrey*/|g'. Then replace the earlGrey main script with the one in this github repo. Then also replace rcMergeRepeatsLoose and rcMergeRepeats in the scripts directory within this. Otherwise, the new version should be pushed to bioconda sometime today.

@ammarabdalrahem note in bash a double slash doesn't change file paths. This issue was due to an argument not being parsed properly by a subscript.

NOTE: If you choose to edit the scripts before the update is available, you will also need to change the variable SCRIPT_DIR= in several subscripts. I would recommend waiting for the update to hit bioconda if you are not totally sure how to do this

[TobyBaril]

Pushed to bioconda, closing as fixed