dzolier
commented
2 years ago Adding the duplicate absolute path seems to have worked, but a new problem has arisen:
Now, I'm getting a key error from sourmash_checkm_parser:
[metawrap_50_10_bin_1, /home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.1.fa]
executor > local (8)
[f1/4841c4] process > checkm (5) [ 62%] 5 of 8, cached: 5
[ac/99d26b] process > sourmash_bins (3) [100%] 8 of 8, cached: 8 ✔
[31/17d875] process > sourmash_checkm_parser (2) [ 0%] 0 of 5
[40/fa5550] process > eggnog_bin (4) [100%] 8 of 8, cached: 8 ✔
[c1/b09ccc] process > parser_bin (1) [ 75%] 6 of 8
[63/b9925d] process > readme_output [100%] 1 of 1, cached: 1 ✔
Error executing process > 'sourmash_checkm_parser (2)'
Caused by:
executor > local (8)
[f1/4841c4] process > checkm (5) [ 62%] 5 of 8, cached: 5
[ac/99d26b] process > sourmash_bins (3) [100%] 8 of 8, cached: 8 ✔
[31/17d875] process > sourmash_checkm_parser (2) [ 20%] 1 of 5, failed: 1
[40/fa5550] process > eggnog_bin (4) [100%] 8 of 8, cached: 8 ✔
[c1/b09ccc] process > parser_bin (1) [ 85%] 6 of 7
[63/b9925d] process > readme_output [100%] 1 of 1, cached: 1 ✔
Error executing process > 'sourmash_checkm_parser (2)'
Caused by:
Process `sourmash_checkm_parser (2)` terminated with an error exit status (1)
Command executed:
grep -v "] INFO: " summary.txt | grep -v "\-\-\-\-\-\-\-" | grep -v "Bin Id" | sed -e 's/^[ \t]*//'|sed 's/[ \t]*$//' |sed -r 's/ +/,/g'|sed '/^$/d' >checkm.csv
for file in $(ls bin*.txt); do tail -n 1 $file | sed -e 's/.fa//' >>sourmash.csv; done
checkm_sourmash_parser.py -c checkm.csv -s sourmash.csv
Command exit status:
1
Command output:
(empty)
Command error:
Traceback (most recent call last):
File "/home/ubuntu/.nextflow/assets/RVanDamme/MUFFIN/bin/checkm_sourmash_parser.py", line 93, in <module>
main()
File "/home/ubuntu/.nextflow/assets/RVanDamme/MUFFIN/bin/checkm_sourmash_parser.py", line 85, in main
parse(args)
File "/home/ubuntu/.nextflow/assets/RVanDamme/MUFFIN/bin/checkm_sourmash_parser.py", line 53, in parse
dict_checkm_sourmash = sourmash_parser(dict_checkm_sourmash, sourmash)
File "/home/ubuntu/.nextflow/assets/RVanDamme/MUFFIN/bin/checkm_sourmash_parser.py", line 25, in sourmash_parser
dict_checkm_sourmash[row[0]].extend( row[1:] )
KeyError: 'bin.1'
Work dir:
/home/ubuntu/work/31/17d875cdcccd85bc7c2328d25dbe8b
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command lineI'm afraid I have no idea what the problem is on this one. I know that Python returns a KeyError when the key doesn't exist in a dictionary, but I'm a little confused about where exactly this key doesn't exist.
Any ideas you might have are greatly appreciated.
replikation
Hello,
I'm trying to run MUFFIN's class-annot steps and running into some trouble. It seems like I'm not structuring the .csv properly.
My command is as follows:
nextflow -log /home/ubuntu/MUFFIN_skip_assembly/assembly_skipped.log run RVanDamme/MUFFIN/main.nf --output /home/ubuntu/MUFFIN_skip_assembly/ --ont /home/ubuntu/TFQAB/zip_out/filtlong/filtlong_out.fastq --illumina /home/ubuntu/TFQAB/zip_out/intermediary/*.fastq --bin_classify /home/ubuntu/assembled_bins.csv --bin_assemble /home/ubuntu/assembled_bins.csv --cpus 120 --memory 490g --check_db /home/ubuntu/nextflow-autodownload-databases/checkm/db/ --eggnog_db /home/ubuntu/nextflow-autodownload-databases/eggnogdb_5.0.1 --sourmash_db /home/ubuntu/nextflow-autodownload-databases/sourmash/genbank-k31.lca.json.gz --modular class-annot -profile local,condaAnd my .csv is structured as follows:
which is giving me the result
For the record, I also tried a one-line format for the .csv:
which worked, but: : the
bin_annotationfolder only showsbin.2.annotations.tsv&bin.2.seed_orthologs.tsv:parser_resultonly seems to provide results forbin.2as well (MUFFIN_bin.2_result.html&MUFFIN_sample_result.html) :classifyonly looks to have results related tobin.1The MUFFIN readme seems to say that each
/ngoes with sample name followed by absolute path of sample, which the former version has. I'm going to try just listing the sample path twice per row and seeing if that works, but in case that doesn't work, I thought you might have some thoughts.