Use of uninitialized value $cat in concatenation (.) or string at /services/tools/metabolic/4.0/METABOLIC/METABOLIC-C.pl line 1648.

[B-1991-ing]

Dear METABOLIC support team,

I now don't have the problem with the conda environment, indicated from the error and log file. For the reason, I don't know, as I didn't change anything with the module loading part yet.

But another new question occurred, the I still got the blank "CommunityPlot.PDF" and "Metabolic_Sankey_diagram.pdf". I read the similar question - Perl error #15. Then, checked my five input fasta files by cat bin_29.fasta|grep ".", no "." there. Firstly, I thought it was the problem of my fasta file names - "bin.29.fasta", so I changed the name from "bin.29.fasta" to "bin_29.fasta". But, that's not the case maybe.

My genome fasta files bin_20.fasta.txt bin_22.fasta.txt bin_27.fasta.txt bin_28.fasta.txt bin_29.fasta.txt

The submitted shell script metabolic_c_test.sh.txt

The METABOLIC_run.log METABOLIC_run.log.txt

The metabolic_c_test2.err metabolic_c_test2.err.txt

The metabolic_c_test2.log metabolic_c_test2.log.txt

Best,

Bing

[B-1991-ing]

Dear METABOLIC support team,

Update For the EXCEPTION: FileNotFoundError MESSAGE: [Errno 2] No such file or directory: '/home/databases/gtdbtk/current/markers/pfam/individual_hmms/PF01868.17.hmm', the dependency of METABOLIC is GTDB-Tk v1.6.0, but I am loading the latest version GTDB-Tk v2.0.0.

Best,

Bing

[B-1991-ing]

Dear METABOLIC support team,

Update It's so strange that I actually loaded "module load gtdbtk/1.7.0" but I always got "EXCEPTION: FileNotFoundError" as shown in screenshot, that the METABOLIC/4.0 used the gtdbtk/2.0.0. I didn't load gtdbtk/2.0.0 actually.

Best,

Bing

[B-1991-ing]

Dear METABOLIC support team,

Update I just checked the reference databases of old versions of gtdbtk - gtdbtk/1.7.0, gtdbtk/1.6.0, gtdbtk/1.4.1 on our HPC cluster. Under the path - "/home/databases/gtdbtk/release95(or 207)/markers/pfam/individual_hmms" of the three versions, none of directories has "PF01868.17.hmm" file. Only the release202 has this file. But, none of gtdbtk versions uses this release 202 version. So, I may need to use the existed gtdbtk annotation files as the input of METABOLIC-C.

Plan to try additional parameters

$output/intermediate_files/gtdbtk_Genome_files/gtdbtk.ar122.summary.tsv

$output/intermediate_files/gtdbtk_Genome_files/gtdbtk.ar122.summary.tsv

gtdbtk/1.7.0

gtdbtk/1.6.0

gtdbtk/1.4.1

Best,

Bing

[B-1991-ing]

Dear METABOLIC support team,

Update

After directly added the gtdbtk classify_wf result tsv table into the subfolder of the output folder, it woked finally. But, maybe one error due to the gtdbtk classify_wf didn't directly ran during the process.

The gtdbtk classify_wf result tsv table gtdbtk.bac120.summary.tsv

Self premade folder $output/intermediate_files/gtdbtk_Genome_files/

Error file only due to gtdbtk classify_wf metabolic_c_drep95_comp70_con5_3.log

Best,

Bing