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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
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Getting error in running Squeezemeta #628

Closed vmevada102 closed 1 year ago

vmevada102 commented 1 year ago

As i am trying to run the squeezemeta, i am receiving error for 

Try 'perl prinseq-lite.pl -h' for more information.
Exit program.
Error running command:    /home/user/miniconda3/envs/squeezemeta/SqueezeMeta/bin/prinseq-lite.pl -fasta /home/user/Desktop/squeezemetarun/saline1/results/01.saline1.fasta -min_len 200 -out_good /home/user/Desktop/squeezemetarun/saline1/results/prinseq; mv /home/user/Desktop/squeezemetarun/saline1/results/prinseq.fasta /home/user/Desktop/squeezemetarun/saline1/results/01.saline1.fasta > /dev/null 2>&1 at /home/user/miniconda3/envs/squeezemeta/SqueezeMeta/scripts/01.run_all_assemblies.pl line 242.
Stopping in STEP1 -> 01.run_all_assemblies.pl. Program finished abnormally

  If you don't know what went wrong or want further advice, please look for similar issues in https://github.com/jtamames/SqueezeMeta/issues
  Feel free to open a new issue if you don't find the answer there. Please add a brief description of the problem and upload the /home/user/Desktop/squeezemetarun/saline1/syslog file (zip it first)

Sys.log is as follows

Run started Sat Feb 18 21:48:47 2023 in coassembly mode

SqueezeMeta v1.6.0, September 2022 - (c) J. Tamames, F. Puente-Sánchez CNB-CSIC, Madrid, SPAIN

Please cite: Tamames & Puente-Sanchez, Frontiers in Microbiology 10.3389 (2019). doi: https://doi.org/10.3389/fmicb.2018.03349

Run started for saline1, Sat Feb 18 21:48:47 2023 Project: saline1 Map file: /home/user/Desktop/squeezemetarun/saline.samples Fastq directory: /home/user/Desktop/squeezemetarun/raw/ Command: /home/user/miniconda3/envs/squeezemeta/bin/SqueezeMeta.pl -m coassembly -p saline1 -s /home/user/Desktop/squeezemetarun/saline.samples -f /home/user/Desktop/squeezemetarun/raw/ -t 24 -miniden 50 [0 seconds]: STEP0 -> SqueezeMeta.pl COGS; KEGG; PFAM;

[0 seconds]: STEP1 -> 01.run_all_assemblies.pl (megahit) Stopping in STEP1 -> 01.run_all_assemblies.pl. Program finished abnormally

System information:

Tree for the project: .fastq.gz /home/user/Desktop/squeezemetarun/raw//SRR953534_1.fastq.gz /home/user/Desktop/squeezemetarun/raw//SRR953542_1.fastq.gz /home/user/Desktop/squeezemetarun/raw//SRR953559_1.fastq.gz /home/user/Desktop/squeezemetarun/raw//SRR975526_1.fastq.gz /home/user/Desktop/squeezemetarun/raw//SRR975528_1.fastq.gz /home/user/Desktop/squeezemetarun/raw//SRR975530_1.fastq.gz /home/user/Desktop/squeezemetarun/raw//SRR975533_1.fastq.gz /home/user/Desktop/squeezemetarun/raw//SRR975534_1.fastq.gz > /home/user/Desktop/squeezemetarun/saline1/data/raw_fastq/par1.fastq.gz Preparing files for pair2: cat /home/user/Desktop/squeezemetarun/raw//SRR953534_2.fastq.gz /home/user/Desktop/squeezemetarun/raw//SRR953533_2.fastq.gz /home/user/Desktop/squeezemetarun/raw//SRR953534_2.fastq.gz /home/user/Desktop/squeezemetarun/raw//SRR953542_2.fastq.gz /home/user/Desktop/squeezemetarun/raw//SRR953559_2.fastq.gz /home/user/Desktop/squeezemetarun/raw//SRR975526_2.fastq.gz /home/user/Desktop/squeezemetarun/raw//SRR975528_2.fastq.gz /home/user/Desktop/squeezemetarun/raw//SRR975530_2.fastq.gz /home/user/Desktop/squeezemetarun/raw//SRR975533_2.fastq.gz /home/user/Desktop/squeezemetarun/raw//SRR975534_2.fastq.gz > /home/user/Desktop/squeezemetarun/saline1/data/raw_fastq/par2.fastq.gz Running assembly with megahit: perl /home/user/miniconda3/envs/squeezemeta/SqueezeMeta/lib/SqueezeMeta/assembly_megahit.pl /home/user/Desktop/squeezemetarun/saline1 saline1 /home/user/Desktop/squeezemetarun/saline1/data/raw_fastq/par1.fastq.gz /home/user/Desktop/squeezemetarun/saline1/data/raw_fastq/par2.fastq.gz 2023-02-18 21:48:48 - MEGAHIT v1.2.9 2023-02-18 21:48:48 - Using megahit_core with POPCNT and BMI2 support 2023-02-18 21:48:48 - Convert reads to binary library 2023-02-18 21:49:05 - b'INFO sequence/io/sequence_lib.cpp : 77 - Lib 0 (/home/user/Desktop/squeezemetarun/saline1/data/raw_fastq/par1.fastq.gz,/home/user/Desktop/squeezemetarun/saline1/data/raw_fastq/par2.fastq.gz): pe, 14507212 reads, 151 max length' 2023-02-18 21:49:05 - b'INFO utils/utils.h : 152 - Real: 16.9887\tuser: 11.9544\tsys: 1.9591\tmaxrss: 252436' 2023-02-18 21:49:05 - Error occurs when reading inputs Running prinseq for selecting contigs longer than 200: /home/user/miniconda3/envs/squeezemeta/SqueezeMeta/bin/prinseq-lite.pl -fasta /home/user/Desktop/squeezemetarun/saline1/results/01.saline1.fasta -min_len 200 -out_good /home/user/Desktop/squeezemetarun/saline1/results/prinseq; mv /home/user/Desktop/squeezemetarun/saline1/results/prinseq.fasta /home/user/Desktop/squeezemetarun/saline1/results/01.saline1.fasta > /dev/null 2>&1 Linux vnsgu 3.10.0-1160.81.1.el7.x86_64 #1 SMP Fri Dec 16 17:29:43 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux [ 224 Feb 18 21:48] /home/user/Desktop/squeezemetarun/saline1 ├── [ 80 Feb 18 21:48] data │   ├── [ 740 Feb 18 21:48] 00.saline1.samples │   ├── [ 123 Feb 18 21:48] megahit │   │   ├── [ 7 Feb 18 21:48] checkpoints.txt │   │   ├── [ 6 Feb 18 21:48] intermediate_contigs │   │   ├── [ 863 Feb 18 21:49] log │   │   ├── [ 997 Feb 18 21:48] options.json │   │   └── [ 70 Feb 18 21:49] tmp │   │   ├── [ 297 Feb 18 21:48] reads.lib │   │   ├── [606M Feb 18 21:49] reads.lib.bin │   │   └── [ 183 Feb 18 21:49] reads.lib.lib_info │   └── [ 60 Feb 18 21:48] raw_fastq │   ├── [508M Feb 18 21:48] par1.fastq.gz │   └── [518M Feb 18 21:48] par2.fastq.gz ├── [ 10 Feb 18 21:48] ext_tables ├── [ 29 Feb 18 21:48] intermediate │   └── [ 6 Feb 18 21:48] binners ├── [ 121 Feb 18 21:48] methods.txt ├── [3.2K Feb 18 21:48] parameters.pl ├── [ 37 Feb 18 21:48] progress ├── [ 10 Feb 18 21:48] results ├── [8.2K Feb 18 21:48] SqueezeMeta_conf.pl ├── [3.6K Feb 18 21:49] syslog └── [ 10 Feb 18 21:48] temp

10 directories, 14 files

jtamames commented 1 year ago

Hello Looks like you put a unequal number of pair1 and pair2 sampled (8 and
10). You must put the same number for both Best, J

vmevada102 @.***> escribió:

As i am trying to run the squeezemeta, i am receiving error for

Try 'perl prinseq-lite.pl -h' for more information.
Exit program.
Error running command:     
/home/user/miniconda3/envs/squeezemeta/SqueezeMeta/bin/prinseq-lite.pl  
-fasta  
/home/user/Desktop/squeezemetarun/saline1/results/01.saline1.fasta  
-min_len 200 -out_good  
/home/user/Desktop/squeezemetarun/saline1/results/prinseq; mv  
/home/user/Desktop/squeezemetarun/saline1/results/prinseq.fasta  
/home/user/Desktop/squeezemetarun/saline1/results/01.saline1.fasta >  
/dev/null 2>&1 at  
/home/user/miniconda3/envs/squeezemeta/SqueezeMeta/scripts/01.run_all_assemblies.pl line  
242.
Stopping in STEP1 -> 01.run_all_assemblies.pl. Program finished abnormally

  If you don't know what went wrong or want further advice, please  
look for similar issues in  
https://github.com/jtamames/SqueezeMeta/issues
  Feel free to open a new issue if you don't find the answer there.  
Please add a brief description of the problem and upload the  
/home/user/Desktop/squeezemetarun/saline1/syslog file (zip it first)

Sys.log is as follows

Run started Sat Feb 18 21:48:47 2023 in coassembly mode

SqueezeMeta v1.6.0, September 2022 - (c) J. Tamames, F.
Puente-Sánchez CNB-CSIC, Madrid, SPAIN

Please cite: Tamames & Puente-Sanchez, Frontiers in Microbiology
10.3389 (2019). doi: https://doi.org/10.3389/fmicb.2018.03349

Run started for saline1, Sat Feb 18 21:48:47 2023 Project: saline1 Map file: /home/user/Desktop/squeezemetarun/saline.samples Fastq directory: /home/user/Desktop/squeezemetarun/raw/ Command: /home/user/miniconda3/envs/squeezemeta/bin/SqueezeMeta.pl
-m coassembly -p saline1 -s
/home/user/Desktop/squeezemetarun/saline.samples -f
/home/user/Desktop/squeezemetarun/raw/ -t 24 -miniden 50 [0 seconds]: STEP0 -> SqueezeMeta.pl COGS; KEGG; PFAM;

[0 seconds]: STEP1 -> 01.run_all_assemblies.pl (megahit) Stopping in STEP1 -> 01.run_all_assemblies.pl. Program finished abnormally

System information:

Tree for the project: .fastq.gz
/home/user/Desktop/squeezemetarun/raw//SRR953534_1.fastq.gz
/home/user/Desktop/squeezemetarun/raw//SRR953542_1.fastq.gz
/home/user/Desktop/squeezemetarun/raw//SRR953559_1.fastq.gz
/home/user/Desktop/squeezemetarun/raw//SRR975526_1.fastq.gz
/home/user/Desktop/squeezemetarun/raw//SRR975528_1.fastq.gz
/home/user/Desktop/squeezemetarun/raw//SRR975530_1.fastq.gz
/home/user/Desktop/squeezemetarun/raw//SRR975533_1.fastq.gz
/home/user/Desktop/squeezemetarun/raw//SRR975534_1.fastq.gz >
/home/user/Desktop/squeezemetarun/saline1/data/raw_fastq/par1.fastq.gz Preparing files for pair2: cat
/home/user/Desktop/squeezemetarun/raw//SRR953534_2.fastq.gz
/home/user/Desktop/squeezemetarun/raw//SRR953533_2.fastq.gz
/home/user/Desktop/squeezemetarun/raw//SRR953534_2.fastq.gz
/home/user/Desktop/squeezemetarun/raw//SRR953542_2.fastq.gz
/home/user/Desktop/squeezemetarun/raw//SRR953559_2.fastq.gz
/home/user/Desktop/squeezemetarun/raw//SRR975526_2.fastq.gz
/home/user/Desktop/squeezemetarun/raw//SRR975528_2.fastq.gz
/home/user/Desktop/squeezemetarun/raw//SRR975530_2.fastq.gz
/home/user/Desktop/squeezemetarun/raw//SRR975533_2.fastq.gz
/home/user/Desktop/squeezemetarun/raw//SRR975534_2.fastq.gz >
/home/user/Desktop/squeezemetarun/saline1/data/raw_fastq/par2.fastq.gz Running assembly with megahit: perl
/home/user/miniconda3/envs/squeezemeta/SqueezeMeta/lib/SqueezeMeta/assembly_megahit.pl /home/user/Desktop/squeezemetarun/saline1 saline1 /home/user/Desktop/squeezemetarun/saline1/data/raw_fastq/par1.fastq.gz
/home/user/Desktop/squeezemetarun/saline1/data/raw_fastq/par2.fastq.gz 2023-02-18 21:48:48 - MEGAHIT v1.2.9 2023-02-18 21:48:48 - Using megahit_core with POPCNT and BMI2 support 2023-02-18 21:48:48 - Convert reads to binary library 2023-02-18 21:49:05 - b'INFO sequence/io/sequence_lib.cpp : 77 -
Lib 0
(/home/user/Desktop/squeezemetarun/saline1/data/raw_fastq/par1.fastq.gz,/home/user/Desktop/squeezemetarun/saline1/data/raw_fastq/par2.fastq.gz): pe, 14507212 reads, 151 max
length' 2023-02-18 21:49:05 - b'INFO utils/utils.h : 152 -
Real: 16.9887\tuser: 11.9544\tsys: 1.9591\tmaxrss: 252436' 2023-02-18 21:49:05 - Error occurs when reading inputs Running prinseq for selecting contigs longer than 200:
/home/user/miniconda3/envs/squeezemeta/SqueezeMeta/bin/prinseq-lite.pl
-fasta
/home/user/Desktop/squeezemetarun/saline1/results/01.saline1.fasta
-min_len 200 -out_good
/home/user/Desktop/squeezemetarun/saline1/results/prinseq; mv
/home/user/Desktop/squeezemetarun/saline1/results/prinseq.fasta
/home/user/Desktop/squeezemetarun/saline1/results/01.saline1.fasta >
/dev/null 2>&1 Linux vnsgu 3.10.0-1160.81.1.el7.x86_64 #1 SMP Fri Dec 16 17:29:43
UTC 2022 x86_64 x86_64 x86_64 GNU/Linux [ 224 Feb 18 21:48] /home/user/Desktop/squeezemetarun/saline1 ├── [ 80 Feb 18 21:48] data │   ├── [ 740 Feb 18 21:48] 00.saline1.samples │   ├── [ 123 Feb 18 21:48] megahit │   │   ├── [ 7 Feb 18 21:48] checkpoints.txt │   │   ├── [ 6 Feb 18 21:48] intermediate_contigs │   │   ├── [ 863 Feb 18 21:49] log │   │   ├── [ 997 Feb 18 21:48] options.json │   │   └── [ 70 Feb 18 21:49] tmp │   │   ├── [ 297 Feb 18 21:48] reads.lib │   │   ├── [606M Feb 18 21:49] reads.lib.bin │   │   └── [ 183 Feb 18 21:49] reads.lib.lib_info │   └── [ 60 Feb 18 21:48] raw_fastq │   ├── [508M Feb 18 21:48] par1.fastq.gz │   └── [518M Feb 18 21:48] par2.fastq.gz ├── [ 10 Feb 18 21:48] ext_tables ├── [ 29 Feb 18 21:48] intermediate │   └── [ 6 Feb 18 21:48] binners ├── [ 121 Feb 18 21:48] methods.txt ├── [3.2K Feb 18 21:48] parameters.pl ├── [ 37 Feb 18 21:48] progress ├── [ 10 Feb 18 21:48] results ├── [8.2K Feb 18 21:48] SqueezeMeta_conf.pl ├── [3.6K Feb 18 21:49] syslog └── [ 10 Feb 18 21:48] temp

10 directories, 14 files

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vmevada102 commented 1 year ago

This way, we might not able use this tool for analysing the single-end sequences.

fpusan commented 1 year ago

You can analize single end sequences, but you can't combine paired and single end libraries. You can however manually assemble your sequences with SPAdes, I think they support this. Then you can analize your contigs with SqueezeMeta.pl -m coassembly -s samples.file -p project_name -f raw_fastq_dir -extassembly your.spades.assembly.fasta

fpusan commented 1 year ago

Closing due to lack of activity, feel free to reopen!