MUFFIN
MUFFIN copied to clipboard
RVanDamme
MUFFIN class-annot feedback: no such file: /home/ubuntu/null
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,conda
And my .csv is structured as follows:
metawrap_50_10_bin_1,/home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.1.fa
metawrap_50_10_bin_2,/home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.2.fa
metawrap_50_10_bin_3,/home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.3.fa
metawrap_50_10_bin_4,/home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.4.fa
metawrap_50_10_bin_5,/home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.5.fa
metawrap_50_10_bin_6,/home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.6.fa
metawrap_50_10_bin_7,/home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.7.fa
metawrap_50_10_bin_8,/home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.8.fa
which is giving me the result
N E X T F L O W ~ version 21.10.5
Launching `RVanDamme/MUFFIN` [mad_bhabha] - revision: 939ff8ca71 [master]
[- ] process > checkm -
[- ] process > sourmash_bins -
[- ] process > sourmash_checkm_parser -
[- ] process > eggnog_bin -
[- ] process > parser_bin -
[- ] process > readme_output -
*********Start running MUFFIN*********
[- ] process > checkm -
[- ] process > sourmash_bins -
[- ] process > sourmash_checkm_parser -
[- ] process > eggnog_bin -
[- ] process > parser_bin -
[- ] process > readme_output -
*********Start running MUFFIN*********
MUFFIN is a hybrid assembly and differential binning workflow for metagenomics, transcriptomics and pathway analysis.
If you use MUFFIN for your research pleace cite:
https://www.biorxiv.org/content/10.1101/2020.02.08.939843v1
[- ] process > checkm -
[- ] process > sourmash_bins [ 0%] 0 of 8
[- ] process > sourmash_checkm_parser -
[- ] process > eggnog_bin -
[- ] process > parser_bin -
[- ] process > readme_output [ 0%] 0 of 1
*********Start running MUFFIN*********
MUFFIN is a hybrid assembly and differential binning workflow for metagenomics, transcriptomics and pathway analysis.
If you use MUFFIN for your research pleace cite:
https://www.biorxiv.org/content/10.1101/2020.02.08.939843v1
or
Van Damme R., Hölzer M., Viehweger A., Müller B., Bongcam-Rudloff E., Brandt C., 2020
"Metagenomics workflow for hybrid assembly, differential coverage binning, transcriptomics and pathway analysis (MUFFIN)",
doi: https://doi.org/10.1101/2020.02.08.939843
**************************************
[metawrap_50_10_bin_1, /home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.1.fa]
[metawrap_50_10_bin_2, /home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.2.fa]
[metawrap_50_10_bin_3, /home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.3.fa]
[metawrap_50_10_bin_4, /home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.4.fa]
[metawrap_50_10_bin_5, /home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.5.fa]
[metawrap_50_10_bin_6, /home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.6.fa]
[metawrap_50_10_bin_7, /home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.7.fa]
[metawrap_50_10_bin_8, /home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.8.fa]
No such file: /home/ubuntu/null
-- Check script '.nextflow/assets/RVanDamme/MUFFIN/main.nf' at line: 571 or see '/home/ubuntu/MUFFIN_skip_assembly/assembly_skipped.log' file for more details
For the record, I also tried a one-line format for the .csv:
metawrap_50_10,/home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.1.fa,/home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.2.fa,/home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.3.fa,/home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.4.fa,/home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.5.fa,/home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.6.fa,/home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.7.fa,/home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.8.fa
which worked, but:
: the bin_annotation folder only shows bin.2.annotations.tsv & bin.2.seed_orthologs.tsv
: parser_result only seems to provide results for bin.2 as well (MUFFIN_bin.2_result.html & MUFFIN_sample_result.html)
: classify only looks to have results related to bin.1
The MUFFIN readme seems to say that each /n goes 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.
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 line
I'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.
I have found a few more pieces of information, in case they help.
My checkm.csv file reads as follows:
bin.2,o__Sphingomonadales,(UID3310),26,569,293,2,561,5,1,0,0,99.64,1.48,12.50
Whereas my sourmash.csv file reads thus:
bin.1,found,Bacteria,Firmicutes,Bacilli,Bacillales,Paenibacillaceae,Paenibacillus,,
bin.2,disagree,Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Sphingopyxis,,
bin.3,found,Bacteria,Bacteroidetes,Chitinophagia,Chitinophagales,Chitinophagaceae,Niastella,Niastella populi,
bin.4,disagree,Bacteria,Proteobacteria,Betaproteobacteria,Burkholderiales,Comamonadaceae,Variovorax,,
bin.5,disagree,Bacteria,Firmicutes,Bacilli,Bacillales,Bacillaceae,Bacillus,,
bin.6,nomatch,,,,,,,,
bin.7,disagree,Bacteria,Firmicutes,Bacilli,Bacillales,Paenibacillaceae,Paenibacillus,,
bin.8,found,Bacteria,Firmicutes,Bacilli,Bacillales,Bacillaceae,Bacillus,Bacillus subtilis,
As far as checkm.nf outputs go, I see 5 taxonomy.txt files and 8 summary.txt files lying around:
(base) ubuntu@ip-172-31-7-4:~$ find /home/ubuntu/work -iname summary.txt
/home/ubuntu/work/f1/4841c4157cbe44123caa270ba08ffc/summary.txt
/home/ubuntu/work/51/b568c4feaa2a9a5bb42bf7e8d67d7c/summary.txt
/home/ubuntu/work/7b/9010596449084d52a2fe3a04252e14/summary.txt
/home/ubuntu/work/31/17d875cdcccd85bc7c2328d25dbe8b/summary.txt
/home/ubuntu/work/87/76e144c7a4c5db64adf692149f9df5/summary.txt
/home/ubuntu/work/a0/309ad21707099f74d21a95573fde70/summary.txt
/home/ubuntu/work/06/4eac7efcaf8693be5ba4562973f392/summary.txt
/home/ubuntu/work/80/ce5c7c9eef078e6f9efc5f4904abdb/summary.txt
and
(base) ubuntu@ip-172-31-7-4:~$ find /home/ubuntu/work -iname taxonomy.txt
/home/ubuntu/work/f1/4841c4157cbe44123caa270ba08ffc/taxonomy.txt
/home/ubuntu/work/7b/9010596449084d52a2fe3a04252e14/taxonomy.txt
/home/ubuntu/work/87/76e144c7a4c5db64adf692149f9df5/taxonomy.txt
/home/ubuntu/work/06/4eac7efcaf8693be5ba4562973f392/taxonomy.txt
/home/ubuntu/work/80/ce5c7c9eef078e6f9efc5f4904abdb/taxonomy.txt
(edit: having read through the summary.txt files, it looks as if the files for bins 1 through 5 finished properly, whereas the files for bins 6 and 7 were interrupted at slightly different stages of constructing the summary.txt file. I do not see a file for bin 8; the final summary.txt file is in the folder which contains all of the bin.*.txt files in it, although that particular summary.txt file (the one with all 8 bins in the same folder) only has in it a row for bin.2
So from what I have seen, I would assume this is an error I made and not one with the code, and I'm not sure what to change about the way I entered the command and/or the way I referenced/structured the .csv file(s). )
I'm not sure how helpful all this is, but I am not exactly having an easy time understanding the issue so I'm grateful for any insights.
I found a way to do it. My guess had something to do with the program reading the file a certain way, but I used two alterations to the script to get it past the part I've been having trouble with.
So first, I gave them all the same first column name, so all of them are in metawrap_50_10 instead of in metawrap_50_10_bin_* like they were. And second is the thing in the previous comment where I added a duplicate path. My current assembled_bins.csv looks like this:
metawrap_50_10,/ABS_PATH_TO/metawrap_50_10_bins/bin.1.fa,/ABS_PATH_TO/metawrap_50_10_bins/bin.1.fa
metawrap_50_10,/ABS_PATH_TO/metawrap_50_10_bins/bin.2.fa,/ABS_PATH_TO/metawrap_50_10_bins/bin.2.fa
... and so on, which takes me through eggnog but now it's pankegg_bin.py that isn't working; it's outputted a single bin_6.result file instead of the eight I was expecting, and the _result files are filled with unknow by KEGG DB entries.
Unfortunately, there were no errors this time. I have a guess it has something to do with the fact that I cut it off after it seemed to have stalled either in or before the parser_bin step in the penultimate run. The final -resume took less than five minutes.
cut it off at the bottom of this part:
Van Damme R., Hölzer M., Viehweger A., Müller B., Bongcam-Rudloff E., Brandt C.,executor > local (3)
[ce/5afe22] process > checkm (1) [100%] 1 of 1, cached: 1 ✔
[1f/bd615b] process > sourmash_bins (4) [100%] 8 of 8, cached: 8 ✔
[b8/9b19b1] process > sourmash_checkm_parser (1) [100%] 1 of 1 ✔
[81/0064e9] process > eggnog_bin (6) [100%] 8 of 8, cached: 7 ✔
[5f/10b431] process > parser_bin (1) [ 0%] 0 of 1
[ce/7fc4a1] process > readme_output [100%] 1 of 1, cached: 1 ✔
executor > local (3)
[ce/5afe22] process > checkm (1) [100%] 1 of 1, cached: 1 ✔
[1f/bd615b] process > sourmash_bins (4) [100%] 8 of 8, cached: 8 ✔
[b8/9b19b1] process > sourmash_checkm_parser (1) [100%] 1 of 1 ✔
[81/0064e9] process > eggnog_bin (6) [100%] 8 of 8, cached: 7 ✔
[5f/10b431] process > parser_bin (1) [ 0%] 0 of 1
[ce/7fc4a1] process > readme_output [100%] 1 of 1, cached: 1 ✔
[metawrap_50_10, [/home/ubuntu/work/fc/3964aefc155eb93a112e7996e507ea/bin.6.annotations.tsv, /home/ubuntu/work/dd/97c8b92b5405b9e3a1928282f7efbe/bin.3.annotations.tsv, /home/ubuntu/work/9b/bfa547a61fff7c6cfd340d5727316f/bin.2.annotations.tsv, /home/ubuntu/work/43/0d537f672418326d28bd328d6c1f1c/bin.4.annotations.tsv, /home/ubuntu/work/1f/65f376470cb6df587bd859f25ce0c1/bin.5.annotations.tsv, /home/ubuntu/work/94/cae3df3ddc54e14c445b88720e8832/bin.8.annotations.tsv, /home/ubuntu/work/5b/d18d10ea3964c3ab5bd134894840ca/bin.1.annotations.tsv, /home/ubuntu/work/81/0064e99019e2e49b72674a9f1726e5/bin.7.annotations.tsv]]
And resumed afterward:
(base) ubuntu@ip-172-31-13-21:~$ nextflow -log /home/ubuntu/MUFFIN_skip_assembly/assembly_skipped_resume_001.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,conda -resume
N E X T F L O W ~ version 21.10.5
Launching `RVanDamme/MUFFIN` [gloomy_lichterman] - revision: 939ff8ca71 [master]
[- ] process > checkm -
[- ] process > sourmash_bins -
[- ] process > sourmash_checkm_parser -
[- ] process > eggnog_bin -
[- ] process > parser_bin -
[- ] process > readme_output -
*********Start running MUFFIN*********
MUFFIN is a hybrid assembly and differential binning workflow for metagenomics, transcriptomics and pathway analysis.
If you use MUFFIN for your research pleace cite:
[- ] process > checkm -
[- ] process > sourmash_bins -
[- ] process > sourmash_checkm_parser -
[- ] process > eggnog_bin -
[- ] process > parser_bin -
[- ] process > readme_output -
*********Start running MUFFIN*********
MUFFIN is a hybrid assembly and differential binning workflow for metagenomics, transcriptomics and pathway analysis.
If you use MUFFIN for your research pleace cite:
https://www.biorxiv.org/content/10.1101/2020.02.08.939843v1
or
Van Damme R., Hölzer M., Viehweger A., Müller B., Bongcam-Rudloff E., Brandt C., 2020
[ce/5afe22] process > checkm (1) [100%] 1 of 1, cached: 1 ✔
[64/408ca5] process > sourmash_bins (3) [100%] 8 of 8, cached: 8 ✔
[b8/9b19b1] process > sourmash_checkm_parser (1) [100%] 1 of 1, cached: 1 ✔
[43/0d537f] process > eggnog_bin (5) [100%] 8 of 8, cached: 8 ✔
[5f/10b431] process > parser_bin (1) [100%] 1 of 1, cached: 1 ✔
[ce/7fc4a1] process > readme_output [100%] 1 of 1, cached: 1 ✔
*********Start running MUFFIN*********
MUFFIN is a hybrid assembly and differential binning workflow for metagenomics, transcriptomics and pathway analysis.
If you use MUFFIN for your research pleace cite:
https://www.biorxiv.org/content/10.1101/2020.02.08.939843v1
or
Van Damme R., Hölzer M., Viehweger A., Müller B., Bongcam-Rudloff E., Brandt C., 2020
"Metagenomics workflow for hybrid assembly, differential coverage binning, transcriptomics and pathway analysis (MUFFIN)",
doi: https://doi.org/10.1101/2020.02.08.939843
**************************************
[metawrap_50_10, /home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.1.fa]
[metawrap_50_10, /home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin[ce/5afe22] process > checkm (1) [100%] 1 of 1, cached: 1 ✔
[64/408ca5] process > sourmash_bins (3) [100%] 8 of 8, cached: 8 ✔
[b8/9b19b1] process > sourmash_checkm_parser (1) [100%] 1 of 1, cached: 1 ✔
[43/0d537f] process > eggnog_bin (5) [100%] 8 of 8, cached: 8 ✔
[5f/10b431] process > parser_bin (1) [100%] 1 of 1, cached: 1 ✔
[ce/7fc4a1] process > readme_output [100%] 1 of 1, cached: 1 ✔
*********Start running MUFFIN*********
MUFFIN is a hybrid assembly and differential binning workflow for metagenomics, transcriptomics and pathway analysis.
If you use MUFFIN for your research pleace cite:
https://www.biorxiv.org/content/10.1101/2020.02.08.939843v1
or
Van Damme R., Hölzer M., Viehweger A., Müller B., Bongcam-Rudloff E., Brandt C., 2020
"Metagenomics workflow for hybrid assembly, differential coverage binning, transcriptomics and pathway analysis (MUFFIN)",
doi: https://doi.org/10.1101/2020.02.08.939843
**************************************
[metawrap_50_10, /home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.1.fa]
[metawrap_50_10, /home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.2.fa]
[metawrap_50_10, /home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.3.fa]
[metawrap_50_10, /home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.4.fa]
[metawrap_50_10, /home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.1.fa]
[metawrap_50_10, /home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.5.fa]
[metawrap_50_10, /home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.6.fa]
[metawrap_50_10, /home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.7.fa]
[metawrap_50_10, /home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.8.fa]
[metawrap_50_10, /home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.2.fa]
[metawrap_50_10, /home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.3.fa]
[metawrap_50_10, /home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.4.fa]
[metawrap_50_10, /home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.5.fa]
[metawrap_50_10, /home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.6.fa]
[metawrap_50_10, /home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.7.fa]
[metawrap_50_10, /home/ubuntu/TFQAB/zip_out/metaWRAP_out/metawrap_50_10_bins/bin.8.fa]
[metawrap_50_10, [/home/ubuntu/work/dd/97c8b92b5405b9e3a1928282f7efbe/bin.3.annotations.tsv, /home/ubuntu/work/9b/bfa547a61fff7c6cfd340d5727316f/bin.2.annotations.tsv, /home/ubuntu/work/1f/65f376470cb6df587bd859f25ce0c1/bin.5.annotations.tsv, /home/ubuntu/work/94/cae3df3ddc54e14c445b88720e8832/bin.8.annotations.tsv, /home/ubuntu/work/fc/3964aefc155eb93a112e7996e507ea/bin.6.annotations.tsv, /home/ubuntu/work/81/0064e99019e2e49b72674a9f1726e5/bin.7.annotations.tsv, /home/ubuntu/work/43/0d537f672418326d28bd328d6c1f1c/bin.4.annotations.tsv, /home/ubuntu/work/5b/d18d10ea3964c3ab5bd134894840ca/bin.1.annotations.tsv]]
Done! Results are stored here --> /home/ubuntu/MUFFIN_skip_assembly/
The Readme file in /home/ubuntu/MUFFIN_skip_assembly/ describe the structure of the results directories.
But as I said, there's just bin.6_result.html and the sample result in the parser_result folder, and I'm not sure why.