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AnantharamanLab / METABOLIC

A scalable high-throughput metabolic and biogeochemical functional trait profiler
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When I used “METABOLIC-C.pl” module, it appeared "readline() on closed filehandle _IN at METABOLIC-C.pl line 1905."/"rm: cannot remove ‘/home/ecopub/yeyonglian/metabolic_mr01-1/*.bam’: No such file or directory" and "mv: cannot stat ‘/home/ecopub/yeyonglian/metabolic_mr01-1/Output_energy_flow/Energy_plot/network.plot.pdf’: No such file or directory" #113

Open Ye-Yonglian opened 1 year ago

Ye-Yonglian commented 1 year ago

Describe the bug When I used METABOLIC-C.pl , I met some bugs：

This is the METABOLIC_log.log： [2022-10-30 19:50:08] The Prodigal annotation is running... [2022-10-30 19:50:34] The Prodigal annotation is finished readline() on closed filehandle _IN at METABOLIC-C.pl line 1905. readline() on closed filehandle _IN at METABOLIC-C.pl line 1905. readline() on closed filehandle _IN at METABOLIC-C.pl line 1905. readline() on closed filehandle _IN at METABOLIC-C.pl line 1905. readline() on closed filehandle _IN at METABOLIC-C.pl line 1905. readline() on closed filehandle _IN at METABOLIC-C.pl line 1905. readline() on closed filehandle _IN at METABOLIC-C.pl line 1905. readline() on closed filehandle _IN at METABOLIC-C.pl line 1905. readline() on closed filehandle _IN at METABOLIC-C.pl line 1905. readline() on closed filehandle _IN at METABOLIC-C.pl line 1905. readline() on closed filehandle _IN at METABOLIC-C.pl line 1905. readline() on closed filehandle _IN at METABOLIC-C.pl line 1905. readline() on closed filehandle _IN at METABOLIC-C.pl line 1905. readline() on closed filehandle _IN at METABOLIC-C.pl line 1905. readline() on closed filehandle _IN at METABOLIC-C.pl line 1905. readline() on closed filehandle _IN at METABOLIC-C.pl line 1905. readline() on closed filehandle _IN at METABOLIC-C.pl line 1905. readline() on closed filehandle _IN at METABOLIC-C.pl line 1905. readline() on closed filehandle _IN at METABOLIC-C.pl line 1905. readline() on closed filehandle _IN at METABOLIC-C.pl line 1905. [2022-10-30 19:50:36] The hmmsearch is running with 20 cpu threads... [2022-10-30 20:06:15] The hmmsearch is finished [2022-10-30 20:06:22] Generating each hmm faa collection... [2022-10-30 20:06:23] Each hmm faa collection has been made [2022-10-30 20:06:23] The KEGG module result is calculating... [2022-10-30 20:16:55] The KEGG identifier (KO id) result is calculating... [2022-10-30 20:16:56] The KEGG identifier (KO id) seaching result is finished [2022-10-30 20:16:56] Searching CAZymes by dbCAN2... [2022-10-30 20:22:46] dbCAN2 searching is done [2022-10-30 20:22:46] Searching MEROPS peptidase... [2022-10-30 20:24:14] MEROPS peptidase searching is done [2022-10-30 20:24:15] METABOLIC table has been generated [2022-10-30 20:24:15] Drawing element cycling diagrams... readline() on closed filehandle IN at METABOLIC-C.pl line 1965. readline() on closed filehandle IN at METABOLIC-C.pl line 1965. rm: cannot remove ‘/home/ecopub/yeyonglian/metabolic_mr01-1/.bam’: No such file or directory rm: cannot remove ‘/home/ecopub/yeyonglian/metabolic_mr01-1/.bam’: No such file or directory rm: cannot remove ‘/home/ecopub/yeyonglian/metabolic_mr01-1/.sorted.stat’: No such file or directory rm: cannot remove ‘/home/ecopub/yeyonglian/metabolic_mr01-1/.sorted.stat’: No such file or directory rm: cannot remove ‘/home/ecopub/yeyonglian/metabolic_mr01-1/.bai’: No such file or directory rm: cannot remove ‘/home/ecopub/yeyonglian/metabolic_mr01-1/.bai’: No such file or directory [2022-10-30 20:24:30] Drawing element cycling diagrams finished [2022-10-30 20:24:30] Drawing metabolic handoff diagrams... [2022-10-30 20:24:34] Drawing metabolic handoff diagrams finished [2022-10-30 20:24:34] Drawing energy flow chart... [2022-10-30 20:24:34] INFO: GTDB-Tk v1.6.0 [2022-10-30 20:24:34] INFO: gtdbtk classify_wf --cpus 20 -x fasta --genome_dir /home/ecopub/yeyonglian/metagenome/YYL-2022/MR01-bin --out_dir /home/ecopub/yeyonglian/metabolic_mr01-1/intermediate_files/gtdbtk_Genome_files [2022-10-30 20:24:34] INFO: Using GTDB-Tk reference data version r202: /home/renyanhu/software/Miniconda3/envs/metabolic/share/gtdbtk-1.6.0/db/release202 [2022-10-30 20:24:34] INFO: Identifying markers in 10 genomes with 20 threads. [2022-10-30 20:24:34] TASK: Running Prodigal V2.6.3 to identify genes. [2022-10-30 20:24:56] INFO: Completed 10 genomes in 21.58 seconds (2.16 seconds/genome). [2022-10-30 20:24:56] TASK: Identifying TIGRFAM protein families. [2022-10-30 20:25:04] INFO: Completed 10 genomes in 8.24 seconds (1.21 genomes/second). [2022-10-30 20:25:04] TASK: Identifying Pfam protein families. [2022-10-30 20:25:06] INFO: Completed 10 genomes in 1.33 seconds (7.53 genomes/second). [2022-10-30 20:25:06] INFO: Annotations done using HMMER 3.1b2 (February 2015). [2022-10-30 20:25:06] TASK: Summarising identified marker genes. [2022-10-30 20:25:06] INFO: Completed 10 genomes in 0.37 seconds (26.89 genomes/second). [2022-10-30 20:25:06] INFO: Done. [2022-10-30 20:25:06] INFO: Aligning markers in 10 genomes with 20 CPUs. [2022-10-30 20:25:06] INFO: Processing 10 genomes identified as bacterial. [2022-10-30 20:25:11] INFO: Read concatenated alignment for 45,555 GTDB genomes. [2022-10-30 20:25:11] TASK: Generating concatenated alignment for each marker. [2022-10-30 20:25:14] INFO: Completed 10 genomes in 0.07 seconds (134.07 genomes/second). [2022-10-30 20:25:15] TASK: Aligning 120 identified markers using hmmalign 3.1b2 (February 2015). [2022-10-30 20:25:19] INFO: Completed 120 markers in 0.81 seconds (148.89 markers/second). [2022-10-30 20:25:19] TASK: Masking columns of bacterial multiple sequence alignment using canonical mask. [2022-10-30 20:26:23] INFO: Completed 45,565 sequences in 1.07 minutes (42,472.70 sequences/minute). [2022-10-30 20:26:23] INFO: Masked bacterial alignment from 41,084 to 5,037 AAs. [2022-10-30 20:26:23] INFO: 0 bacterial user genomes have amino acids in <10.0% of columns in filtered MSA. [2022-10-30 20:26:23] INFO: Creating concatenated alignment for 45,565 bacterial GTDB and user genomes. [2022-10-30 20:26:24] INFO: Creating concatenated alignment for 10 bacterial user genomes. [2022-10-30 20:26:24] INFO: Done. [2022-10-30 20:26:24] TASK: Placing 10 bacterial genomes into reference tree with pplacer using 20 CPUs (be patient). [2022-10-30 20:26:25] INFO: pplacer version: v1.1.alpha19-0-g807f6f3 [2022-10-30 21:04:09] INFO: Calculating RED values based on reference tree. [2022-10-30 21:04:19] TASK: Traversing tree to determine classification method. [2022-10-30 21:04:19] INFO: Completed 10 genomes in 0.01 seconds (1,222.40 genomes/second). [2022-10-30 21:04:19] TASK: Calculating average nucleotide identity using FastANI (v1.32). [2022-10-30 21:04:43] INFO: Completed 396 comparisons in 22.94 seconds (17.26 comparisons/second). [2022-10-30 21:04:43] INFO: 1 genome(s) have been classified using FastANI and pplacer. [2022-10-30 21:04:43] INFO: Done. mv: cannot stat ‘/home/ecopub/yeyonglian/metabolic_mr01-1/Output_energy_flow/Energy_plot/network.plot.pdf’: No such file or directory mv: cannot stat ‘/home/ecopub/yeyonglian/metabolic_mr01-1/Output_energy_flow/Energy_plot/network.plot.pdf’: No such file or directory [2022-10-30 21:04:48] Drawing energy flow chart finished [2022-10-30 21:04:48] Calculating MW-score ... [2022-10-30 21:04:49] Calculating MW-score is done METABOLIC-C was done, the total running time: 01:14:41 (hh:mm:ss)

and this is the METABOLIC_run.log: METABOLIC-C.pl v4.0 Run Start: 2022-10-30 19:50:08 Run End: 2022-10-30 21:04:49 Total running time: 01:14:41 (hh:mm:ss) Input Reads: /home/ecopub/yeyonglian/clean_data/MR01/MR01_350.1.fq,/home/ecopub/yeyonglian/clean_data/MR01/MR01_350.2.fq Reads type: metaG Sequencing type: illumina Input Genome directory (nucleotides): /home/ecopub/yeyonglian/metagenome/YYL-2022/MR01-bin Number of Threads: 20 Prodigal Method: meta KOfam DB: full Module Cutoff Value: 0.75 Taxonomic level to calculate MW-score table: phylum Output directory: /home/ecopub/yeyonglian/metabolic_mr01-1

can you help me solve these problems?

ChaoLab commented 1 year ago

It seems that "gene" files in "/home/ecopub/yeyonglian/metagenome/YYL-2022/MR01-bin" were not properly generated

Ye-Yonglian commented 1 year ago

Yes, I solved the problem. It has worked successfully. And I want to know if I can merge different samples of the same type and run "METABOLIC-C.pl"

ChaoLab commented 1 year ago

METABOLIC-C can allow you to provide multiple sets of reads to run for a microbial community. The input MAGs should be all the MAGs that are reconstructed from this microbial community. I am not sure whether you are referring to this or can you explain your situation a little bit clearer?

qikongwanli commented 1 year ago

Yes, I solved the problem. It has worked successfully. And I want to know if I can merge different samples of the same type and run "METABOLIC-C.pl"

How can you solve this problem? Thanks!

Sharifah89 commented 1 year ago

How did you solve the problem. What reads did you use here -r . Was it reverse and forward files of clean metagenomic reads? or contigs? please advice,

Ye-Yonglian commented 1 year ago

Yes, I solved the problem. It has worked successfully. And I want to know if I can merge different samples of the same type and run "METABOLIC-C.pl"

How can you solve this problem? Thanks!

I changed the name of MAG and used the default parameters, and then it worked.

Ye-Yonglian commented 1 year ago

How did you solve the problem. What reads did you use here -r . Was it reverse and forward files of clean metagenomic reads? or contigs? please advice,

I changed the name of MAG and used the default parameters. I used the reverse and forward files of clean metagenomic reads in the parameter "-r"