metatranscriptomic errors

[LiZhihua1982]

(METABOLIC-v4) lizhihua@lizhihua-T640:/media/lizhihua/software/METABOLIC-v4/METABOLIC$ perl METABOLIC-C.pl -t 40 -rt metaT -in GJ_RNA/ -r GJ_RNA_path.txt -o GJ_METABOLIC_RNA_out -tax genus
[2024-06-20 17:38:57] The hmmsearch is running with 40 cpu threads...
[2024-06-20 18:45:09] The hmmsearch is finished
[2024-06-20 18:47:04] Generating each hmm faa collection...
[2024-06-20 18:47:07] Each hmm faa collection has been made
[2024-06-20 18:47:07] The KEGG module result is calculating...
[2024-06-20 22:48:44] The KEGG identifier (KO id) result is calculating...
[2024-06-20 22:48:55] The KEGG identifier (KO id) seaching result is finished
[2024-06-20 22:48:55] Searching CAZymes by dbCAN2...
[2024-06-20 22:59:03] dbCAN2 searching is done
[2024-06-20 22:59:03] Searching MEROPS peptidase...
[2024-06-20 23:11:36] MEROPS peptidase searching is done
[2024-06-20 23:11:45] METABOLIC table has been generated
[2024-06-20 23:11:45] Drawing element cycling diagrams...
Use of uninitialized value $folder in concatenation (.) or string at METABOLIC-C.pl line 1929.
ls: cannot access '/.gene': No such file or directory
Warning: Empty fasta file: 'GJ_METABOLIC_RNA_out/All_gene_collections.gene'
Warning: All fasta inputs were empty
Error: Encountered internal Bowtie 2 exception (#1)
Command: /home/lizhihua/miniconda3/envs/METABOLIC-v4/bin/bowtie2-build-s --wrapper basic-0 --quiet GJ_METABOLIC_RNA_out/All_gene_collections.gene GJ_METABOLIC_RNA_out/All_gene_collections.gene.scaffold
(ERR): "GJ_METABOLIC_RNA_out/All_gene_collections.gene.scaffold" does not exist or is not a Bowtie 2 index
Exiting now ...
(ERR): "GJ_METABOLIC_RNA_out/All_gene_collections.gene.scaffold" does not exist or is not a Bowtie 2 index
Exiting now ...
(ERR): "GJ_METABOLIC_RNA_out/All_gene_collections.gene.scaffold" does not exist or is not a Bowtie 2 index
Exiting now ...
(ERR): "GJ_METABOLIC_RNA_out/All_gene_collections.gene.scaffold" does not exist or is not a Bowtie 2 index
Exiting now ...
(ERR): "GJ_METABOLIC_RNA_out/All_gene_collections.gene.scaffold" does not exist or is not a Bowtie 2 index
Exiting now ...
rm: rm: cannot remove 'GJ_METABOLIC_RNA_out/All_gene_collections_mapped.8.sam'cannot remove 'GJ_METABOLIC_RNA_out/All_gene_collections_mapped.5.sam': No such file or directory
: No such file or directory
rm: cannot remove 'GJ_METABOLIC_RNA_out/All_gene_collections_mapped.7.sam': No such file or directoryrm:
cannot remove 'GJ_METABOLIC_RNA_out/All_gene_collections_mapped.6.sam': No such file or directory
rm: cannot remove 'GJ_METABOLIC_RNA_out/All_gene_collections_mapped.1.sam': No such file or directory
(ERR): "GJ_METABOLIC_RNA_out/All_gene_collections.gene.scaffold" does not exist or is not a Bowtie 2 index
Exiting now ...
rm: cannot remove 'GJ_METABOLIC_RNA_out/All_gene_collections_mapped.2.sam': No such file or directory
(ERR): "GJ_METABOLIC_RNA_out/All_gene_collections.gene.scaffold" does not exist or is not a Bowtie 2 index
Exiting now ...
rm: cannot remove 'GJ_METABOLIC_RNA_out/All_gene_collections_mapped.3.sam': No such file or directory
(ERR): "GJ_METABOLIC_RNA_out/All_gene_collections.gene.scaffold" does not exist or is not a Bowtie 2 index
Exiting now ...
rm: cannot remove 'GJ_METABOLIC_RNA_out/All_gene_collections_mapped.4.sam': No such file or directory
rm: cannot remove 'GJ_METABOLIC_RNA_out/.bt2': No such file or directory
rm: cannot remove 'GJ_METABOLIC_RNA_out/.bam': No such file or directory
rm: cannot remove 'GJ_METABOLIC_RNA_out/.bai': No such file or directory
[2024-06-20 23:13:55] Drawing element cycling diagrams finished
[2024-06-20 23:13:55] Drawing metabolic handoff diagrams...
[2024-06-20 23:14:05] Drawing metabolic handoff diagrams finished
[2024-06-20 23:14:05] Drawing energy flow chart...
Use of uninitialized value $input_genome_folder in concatenation (.) or string at METABOLIC-C.pl line 1365.
mv: cannot stat 'GJ_METABOLIC_RNA_out/Output_energy_flow/Energy_plot/network.plot.pdf': No such file or directory
[2024-06-20 23:14:11] Drawing energy flow chart finished
[2024-06-20 23:14:11] Calculating MW-score ...
[2024-06-20 23:14:17] Calculating MW-score is done
METABOLIC-C was done, the total running time: 05:36:11 (hh:mm:ss)
Use of uninitialized value $input_genome_folder in concatenation (.) or string at METABOLIC-C.pl line 1779.