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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
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RESTART SEQUENTIAL MODE #853

Open EorgeKit opened 2 weeks ago

EorgeKit commented 2 weeks ago

Hi @fpusan @jtamames @ggnatalia I am using squeezemeta to analyse my samples individually using the sequential mode. Thing is I am using a cluster that uses PBS job sceduler. I request a lot of nodes for each sample and they are assigned to me. However despite all that, almost everytime a job is killed during a diamond process despite me playing with different -b values.

Each node has about 120GB of RAM and I request 6 nodes. That makes 720GB of RAM to be available per sample run. Dividing by 8 that makes -b value of about 90. What I discovered is that only one node is utilized during the diamond process for some reasons and all the others are left free. So I tried the automatic choice of block size by not specifying the block size and it manage to calculate that the node it works on has about 109GB of RAM so it assigns about -b 11 and this makes diamond to run until step6 which involves the LCA algorithm and then it dies again. At this point I don't know what the problem is.

All attempts to restart the run with --restart option have proven futile as I keep getting the error despite the fact that the file is in the project directory with read permissions:

SqueezeMeta.pl /home/maloo/SW_sample --restart -step 4
***
Can't open samples file (-s) in /data/00..samples. Please check that it is the correct file

File availability:

pwd
/home/maloo/SW_sample

 ls -lhtr data/
total 4.0K
-rw-rw-r-- 1 maloo maloo 37 Jun 14 13:50 00.SW_sample.samples
drwxrwxr-x 2 maloo maloo 26 Jun 14 13:50 raw_fastq
drwxrwxr-x 3 maloo maloo 95 Jun 14 17:23 megahit

My original code is :

#!/bin/bash
#PBS -l select=6:ncpus=24:mpiprocs=24:mem=120gb
#PBS -N squeezemeta_water_sample
#PBS -l walltime=48:00:00

##DATA LOCATIONS
RAW_DATA_DIR=/mnt/lustre/users/maloo/euMwanza/George/marwahsab/raw_data
OUTPUT_DIR=/mnt/lustre/users/maloo/euMwanza/George/marwahsab/analysis
SAMPLE_FILES=/mnt/lustre/users/maloo/euMwanza/George/marwahsab/sqm_prerequisites_files

SqueezeMeta.pl \
-m sequential \
-s $SAMPLE_FILES/SW.samples \
-f $RAW_DATA_DIR/SW \
-a megahit \
--assembly_options \
"--presets meta-large --k-min 27 --kmin-1pass --k-step 10" \
-binners maxbin,metabat2,concoct \
-taxbinmode s+c \
-D -t 138

Here is the syslog output:

Run started Fri Jun 14 13:50:47 2024 in sequential mode

SqueezeMeta v1.6.3, September 2023 - (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 maloo, Fri Jun 14 13:50:47 2024
Project: SW_sample
Map file: /mnt/lustre/users/maloo/euMwanza/George/marwahsab/sqm_prerequisites_files/SW.samples
Fastq directory: /mnt/lustre/users/maloo/euMwanza/George/marwahsab/raw_data/SW
Command: /apps/chpc/bio/anaconda3-2020.02/envs/SqueezeMeta-1.6.3/bin/SqueezeMeta.pl -m sequential -s /mnt/lustre/users/maloo/euMwanza/George/marwahsab/sqm_prerequisites_files/SW.samples -f /mnt/lustre/users/maloo/euMwanza/George/marwahsab/raw_data/SW -a megahit --assembly_options --presets meta-large --k-min 27 --kmin-1pass --k-step 10 -binners maxbin,metabat2,concoct -taxbinmode s+c -D -t 138
[0 seconds]: STEP0 -> SqueezeMeta.pl
 COGS; KEGG; PFAM; DOUBLEPASS;

[0 seconds]: STEP1 -> 01.run_all_assemblies.pl (megahit)
  Preparing files for pair1: cat /mnt/lustre/users/maloo/euMwanza/George/marwahsab/raw_data/SW/SW_clean_data1.fq.gz > /home/maloo/SW_sample/data/raw_fastq/par1.fastq.gz
Running assembly with megahit: perl /apps/chpc/bio/anaconda3-2020.02/envs/SqueezeMeta-1.6.3/SqueezeMeta/lib/SqueezeMeta/assembly_megahit.pl /home/maloo/SW_sample SW_sample /home/maloo/SW_sample/data/raw_fastq/par1.fastq.gz 
2024-06-14 13:50:55 - MEGAHIT v1.2.9
2024-06-14 13:50:55 - Maximum number of available CPU thread is 24.
2024-06-14 13:50:55 - Number of thread is reset to the 24.
2024-06-14 13:50:55 - Using megahit_core with POPCNT and BMI2 support
2024-06-14 13:50:55 - Convert reads to binary library
2024-06-14 13:52:23 - b'INFO  sequence/io/sequence_lib.cpp  :   77 - Lib 0 (/home/maloo/SW_sample/data/raw_fastq/par1.fastq.gz): se, 41421475 reads, 150 max length'
2024-06-14 13:52:24 - b'INFO  utils/utils.h                 :  152 - Real: 88.5761\tuser: 33.8813\tsys: 3.5171\tmaxrss: 244560'
2024-06-14 13:52:24 - k-max reset to: 127 
2024-06-14 13:52:24 - Start assembly. Number of CPU threads 24 
2024-06-14 13:52:24 - k list: 27,37,47,57,67,77,87,97,107,117,127 
2024-06-14 13:52:24 - Memory used: 121575835238
2024-06-14 13:52:24 - Extracting solid (k+1)-mers and building sdbg for k = 27
2024-06-14 13:55:00 - Assemble contigs from SdBG for k = 27
2024-06-14 14:20:17 - Local assembly for k = 27
2024-06-14 14:29:19 - Extract iterative edges from k = 27 to 37 
2024-06-14 14:31:40 - Build graph for k = 37 
2024-06-14 14:34:40 - Assemble contigs from SdBG for k = 37
2024-06-14 14:57:19 - Local assembly for k = 37
2024-06-14 15:07:23 - Extract iterative edges from k = 37 to 47 
2024-06-14 15:08:10 - Build graph for k = 47 
2024-06-14 15:10:04 - Assemble contigs from SdBG for k = 47
2024-06-14 15:30:25 - Local assembly for k = 47
2024-06-14 15:40:14 - Extract iterative edges from k = 47 to 57 
2024-06-14 15:40:35 - Build graph for k = 57 
2024-06-14 15:41:52 - Assemble contigs from SdBG for k = 57
2024-06-14 15:53:01 - Local assembly for k = 57
2024-06-14 16:03:08 - Extract iterative edges from k = 57 to 67 
2024-06-14 16:03:20 - Build graph for k = 67 
2024-06-14 16:03:51 - Assemble contigs from SdBG for k = 67
2024-06-14 16:08:55 - Local assembly for k = 67
2024-06-14 16:19:06 - Extract iterative edges from k = 67 to 77 
2024-06-14 16:19:19 - Build graph for k = 77 
2024-06-14 16:19:44 - Assemble contigs from SdBG for k = 77
2024-06-14 16:23:50 - Local assembly for k = 77
2024-06-14 16:33:27 - Extract iterative edges from k = 77 to 87 
2024-06-14 16:33:39 - Build graph for k = 87 
2024-06-14 16:34:02 - Assemble contigs from SdBG for k = 87
2024-06-14 16:37:14 - Local assembly for k = 87
2024-06-14 16:45:56 - Extract iterative edges from k = 87 to 97 
2024-06-14 16:46:03 - Build graph for k = 97 
2024-06-14 16:46:19 - Assemble contigs from SdBG for k = 97
2024-06-14 16:48:47 - Local assembly for k = 97
2024-06-14 16:58:18 - Extract iterative edges from k = 97 to 107 
2024-06-14 16:58:25 - Build graph for k = 107 
2024-06-14 16:58:38 - Assemble contigs from SdBG for k = 107
2024-06-14 17:00:46 - Local assembly for k = 107
2024-06-14 17:09:45 - Extract iterative edges from k = 107 to 117 
2024-06-14 17:09:53 - Build graph for k = 117 
2024-06-14 17:10:05 - Assemble contigs from SdBG for k = 117
2024-06-14 17:12:07 - Local assembly for k = 117
2024-06-14 17:21:04 - Extract iterative edges from k = 117 to 127 
2024-06-14 17:21:10 - Build graph for k = 127 
2024-06-14 17:21:24 - Assemble contigs from SdBG for k = 127
2024-06-14 17:23:09 - Merging to output final contigs 
2024-06-14 17:23:10 - 762723 contigs, total 452994294 bp, min 203 bp, max 198925 bp, avg 593 bp, N50 568 bp
2024-06-14 17:23:11 - ALL DONE. Time elapsed: 12736.550011 seconds 
Running prinseq for selecting contigs longer than 200: /apps/chpc/bio/anaconda3-2020.02/envs/SqueezeMeta-1.6.3/SqueezeMeta/bin/prinseq-lite.pl -fasta /home/maloo/SW_sample/results/01.SW_sample.fasta -min_len 200 -out_good /home/maloo/SW_sample/results/prinseq; mv /home/maloo/SW_sample/results/prinseq.fasta /home/maloo/SW_sample/results/01.SW_sample.fasta > /dev/null 2>&1
  Running prinseq for contig statistics: /apps/chpc/bio/anaconda3-2020.02/envs/SqueezeMeta-1.6.3/SqueezeMeta/bin/prinseq-lite.pl -fasta /home/maloo/SW_sample/results/01.SW_sample.fasta -stats_len -stats_info -stats_assembly > /home/maloo/SW_sample/intermediate/01.SW_sample.stats
  Running barrnap for Bacteria: /apps/chpc/bio/anaconda3-2020.02/envs/SqueezeMeta-1.6.3/SqueezeMeta/bin/barrnap --quiet --threads 138 --kingdom bac --reject 0.1 /home/maloo/SW_sample/intermediate/02.SW_sample.maskedrna.fasta --dbdir /mnt/lustre/bsp/DB/SqueezeMeta-1.6.3/db > /home/maloo/SW_sample/temp/bac.gff
Running barrnap for Archaea: /apps/chpc/bio/anaconda3-2020.02/envs/SqueezeMeta-1.6.3/SqueezeMeta/bin/barrnap --quiet --threads 138 --kingdom arc --reject 0.1 /home/maloo/SW_sample/intermediate/02.SW_sample.maskedrna.fasta --dbdir /mnt/lustre/bsp/DB/SqueezeMeta-1.6.3/db > /home/maloo/SW_sample/temp/arc.gff
Running barrnap for Eukaryote: /apps/chpc/bio/anaconda3-2020.02/envs/SqueezeMeta-1.6.3/SqueezeMeta/bin/barrnap --quiet --threads 138 --kingdom euk --reject 0.1 /home/maloo/SW_sample/intermediate/02.SW_sample.maskedrna.fasta --dbdir /mnt/lustre/bsp/DB/SqueezeMeta-1.6.3/db > /home/maloo/SW_sample/temp/euk.gff
Running barrnap for Mitochondrial: /apps/chpc/bio/anaconda3-2020.02/envs/SqueezeMeta-1.6.3/SqueezeMeta/bin/barrnap --quiet --threads 138 --kingdom mito --reject 0.1 /home/maloo/SW_sample/intermediate/02.SW_sample.maskedrna.fasta --dbdir /mnt/lustre/bsp/DB/SqueezeMeta-1.6.3/db > /home/maloo/SW_sample/temp/mito.gff
Running RDP classifier: java -jar /apps/chpc/bio/anaconda3-2020.02/envs/SqueezeMeta-1.6.3/SqueezeMeta/lib/classifier/classifier.jar classify /home/maloo/SW_sample/temp/16S.fasta -o /home/maloo/SW_sample/temp/16S.out -f filterbyconf
Running Aragorn: /apps/chpc/bio/anaconda3-2020.02/envs/SqueezeMeta-1.6.3/SqueezeMeta/bin/aragorn -w /home/maloo/SW_sample/intermediate/02.SW_sample.maskedrna.fasta -o /home/maloo/SW_sample/temp/trnas.aragorn
Creating new gff file: cat /home/maloo/SW_sample/temp/*gff.mod > /home/maloo/SW_sample/temp/02.SW_sample.rna.gff
Running prodigal for predicting ORFs: /apps/chpc/bio/anaconda3-2020.02/envs/SqueezeMeta-1.6.3/SqueezeMeta/bin/prodigal -q -m -p meta -i /home/maloo/SW_sample/intermediate/02.SW_sample.maskedrna.fasta -a /home/maloo/SW_sample/results/03.SW_sample.faa -d /home/maloo/SW_sample/results/03.SW_sample.fna -f gff -o /home/maloo/SW_sample/temp/02.SW_sample.cds.gff.temp
Diamond block size set to 13.7 (Free Mem 109.56 Gb)
  Working with taxonomy database in /mnt/lustre/bsp/DB/SqueezeMeta-1.6.3/db/nr.dmnd
Running Diamond for taxa: /apps/chpc/bio/anaconda3-2020.02/envs/SqueezeMeta-1.6.3/SqueezeMeta/bin/diamond blastp -q /home/maloo/SW_sample/results/03.SW_sample.faa -p 138 -d /mnt/lustre/bsp/DB/SqueezeMeta-1.6.3/db/nr.dmnd -e 0.001 --id 40 -f tab -b 13.7 -o /home/maloo/SW_sample/intermediate/04.SW_sample.nr.diamond > /home/maloo/SW_sample/temp/diamond.nr.log 2>&1
Running Diamond for COGs: /apps/chpc/bio/anaconda3-2020.02/envs/SqueezeMeta-1.6.3/SqueezeMeta/bin/diamond blastp -q /home/maloo/SW_sample/results/03.SW_sample.faa -p 138 -d /mnt/lustre/bsp/DB/SqueezeMeta-1.6.3/db/eggnog -e 0.001 --id 30 --quiet -b 13.7 -f 6 qseqid qlen sseqid slen pident length evalue bitscore qstart qend sstart send -o /home/maloo/SW_sample/intermediate/04.SW_sample.eggnog.diamond
Running Diamond for KEGG: /apps/chpc/bio/anaconda3-2020.02/envs/SqueezeMeta-1.6.3/SqueezeMeta/bin/diamond blastp -q /home/maloo/SW_sample/results/03.SW_sample.faa -p 138 -d /mnt/lustre/bsp/DB/SqueezeMeta-1.6.3/db/keggdb -e 0.001 --id 30 --quiet -b 13.7 -f 6 qseqid qlen sseqid slen pident length evalue bitscore qstart qend sstart send -o /home/maloo/SW_sample/intermediate/04.SW_sample.kegg.diamond
Running HMMER3 for Pfam: /apps/chpc/bio/anaconda3-2020.02/envs/SqueezeMeta-1.6.3/SqueezeMeta/bin/hmmer/hmmsearch --domtblout /home/maloo/SW_sample/intermediate/05.SW_sample.pfam.hmm -E 1e-10 --cpu 138 /mnt/lustre/bsp/DB/SqueezeMeta-1.6.3/db/Pfam-A.hmm /home/maloo/SW_sample/results/03.SW_sample.faa > /dev/null 2>&1
  Splitting Diamond file
  Total lines in Diamond: 18949274; Allocating 177096 in 107 threads
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  Starting multithread LCA in 107 threads
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  Starting thread 103
  Starting thread 95
  Creating /home/maloo/SW_sample/results/06.SW_sample.fun3.tax.wranks file: cat /home/maloo/SW_sample/temp/fun3tax_1.wranks /home/maloo/SW_sample/temp/fun3tax_2.wranks /home/maloo/SW_sample/temp/fun3tax_3.wranks /home/maloo/SW_sample/temp/fun3tax_4.wranks /home/maloo/SW_sample/temp/fun3tax_5.wranks /home/maloo/SW_sample/temp/fun3tax_6.wranks /home/maloo/SW_sample/temp/fun3tax_7.wranks /home/maloo/SW_sample/temp/fun3tax_8.wranks /home/maloo/SW_sample/temp/fun3tax_9.wranks /home/maloo/SW_sample/temp/fun3tax_10.wranks /home/maloo/SW_sample/temp/fun3tax_11.wranks /home/maloo/SW_sample/temp/fun3tax_12.wranks /home/maloo/SW_sample/temp/fun3tax_13.wranks /home/maloo/SW_sample/temp/fun3tax_14.wranks /home/maloo/SW_sample/temp/fun3tax_15.wranks /home/maloo/SW_sample/temp/fun3tax_16.wranks /home/maloo/SW_sample/temp/fun3tax_17.wranks /home/maloo/SW_sample/temp/fun3tax_18.wranks /home/maloo/SW_sample/temp/fun3tax_19.wranks /home/maloo/SW_sample/temp/fun3tax_20.wranks /home/maloo/SW_sample/temp/fun3tax_21.wranks /home/maloo/SW_sample/temp/fun3tax_22.wranks /home/maloo/SW_sample/temp/fun3tax_23.wranks /home/maloo/SW_sample/temp/fun3tax_24.wranks /home/maloo/SW_sample/temp/fun3tax_25.wranks /home/maloo/SW_sample/temp/fun3tax_26.wranks /home/maloo/SW_sample/temp/fun3tax_27.wranks /home/maloo/SW_sample/temp/fun3tax_28.wranks /home/maloo/SW_sample/temp/fun3tax_29.wranks /home/maloo/SW_sample/temp/fun3tax_30.wranks /home/maloo/SW_sample/temp/fun3tax_31.wranks /home/maloo/SW_sample/temp/fun3tax_32.wranks /home/maloo/SW_sample/temp/fun3tax_33.wranks /home/maloo/SW_sample/temp/fun3tax_34.wranks /home/maloo/SW_sample/temp/fun3tax_35.wranks /home/maloo/SW_sample/temp/fun3tax_36.wranks /home/maloo/SW_sample/temp/fun3tax_37.wranks /home/maloo/SW_sample/temp/fun3tax_38.wranks /home/maloo/SW_sample/temp/fun3tax_39.wranks /home/maloo/SW_sample/temp/fun3tax_40.wranks /home/maloo/SW_sample/temp/fun3tax_41.wranks /home/maloo/SW_sample/temp/fun3tax_42.wranks /home/maloo/SW_sample/temp/fun3tax_43.wranks /home/maloo/SW_sample/temp/fun3tax_44.wranks /home/maloo/SW_sample/temp/fun3tax_45.wranks /home/maloo/SW_sample/temp/fun3tax_46.wranks /home/maloo/SW_sample/temp/fun3tax_47.wranks /home/maloo/SW_sample/temp/fun3tax_48.wranks /home/maloo/SW_sample/temp/fun3tax_49.wranks /home/maloo/SW_sample/temp/fun3tax_50.wranks /home/maloo/SW_sample/temp/fun3tax_51.wranks /home/maloo/SW_sample/temp/fun3tax_52.wranks /home/maloo/SW_sample/temp/fun3tax_53.wranks /home/maloo/SW_sample/temp/fun3tax_54.wranks /home/maloo/SW_sample/temp/fun3tax_55.wranks /home/maloo/SW_sample/temp/fun3tax_56.wranks /home/maloo/SW_sample/temp/fun3tax_57.wranks /home/maloo/SW_sample/temp/fun3tax_58.wranks /home/maloo/SW_sample/temp/fun3tax_59.wranks /home/maloo/SW_sample/temp/fun3tax_60.wranks /home/maloo/SW_sample/temp/fun3tax_61.wranks /home/maloo/SW_sample/temp/fun3tax_62.wranks /home/maloo/SW_sample/temp/fun3tax_63.wranks /home/maloo/SW_sample/temp/fun3tax_64.wranks /home/maloo/SW_sample/temp/fun3tax_65.wranks /home/maloo/SW_sample/temp/fun3tax_66.wranks /home/maloo/SW_sample/temp/fun3tax_67.wranks /home/maloo/SW_sample/temp/fun3tax_68.wranks /home/maloo/SW_sample/temp/fun3tax_69.wranks /home/maloo/SW_sample/temp/fun3tax_70.wranks /home/maloo/SW_sample/temp/fun3tax_71.wranks /home/maloo/SW_sample/temp/fun3tax_72.wranks /home/maloo/SW_sample/temp/fun3tax_73.wranks /home/maloo/SW_sample/temp/fun3tax_74.wranks /home/maloo/SW_sample/temp/fun3tax_75.wranks /home/maloo/SW_sample/temp/fun3tax_76.wranks /home/maloo/SW_sample/temp/fun3tax_77.wranks /home/maloo/SW_sample/temp/fun3tax_78.wranks /home/maloo/SW_sample/temp/fun3tax_79.wranks /home/maloo/SW_sample/temp/fun3tax_80.wranks /home/maloo/SW_sample/temp/fun3tax_81.wranks /home/maloo/SW_sample/temp/fun3tax_82.wranks /home/maloo/SW_sample/temp/fun3tax_83.wranks /home/maloo/SW_sample/temp/fun3tax_84.wranks /home/maloo/SW_sample/temp/fun3tax_85.wranks /home/maloo/SW_sample/temp/fun3tax_86.wranks /home/maloo/SW_sample/temp/fun3tax_87.wranks /home/maloo/SW_sample/temp/fun3tax_88.wranks /home/maloo/SW_sample/temp/fun3tax_89.wranks /home/maloo/SW_sample/temp/fun3tax_90.wranks /home/maloo/SW_sample/temp/fun3tax_91.wranks /home/maloo/SW_sample/temp/fun3tax_92.wranks /home/maloo/SW_sample/temp/fun3tax_93.wranks /home/maloo/SW_sample/temp/fun3tax_94.wranks /home/maloo/SW_sample/temp/fun3tax_95.wranks /home/maloo/SW_sample/temp/fun3tax_96.wranks /home/maloo/SW_sample/temp/fun3tax_97.wranks /home/maloo/SW_sample/temp/fun3tax_98.wranks /home/maloo/SW_sample/temp/fun3tax_99.wranks /home/maloo/SW_sample/temp/fun3tax_100.wranks /home/maloo/SW_sample/temp/fun3tax_101.wranks /home/maloo/SW_sample/temp/fun3tax_102.wranks /home/maloo/SW_sample/temp/fun3tax_103.wranks /home/maloo/SW_sample/temp/fun3tax_104.wranks /home/maloo/SW_sample/temp/fun3tax_105.wranks /home/maloo/SW_sample/temp/fun3tax_106.wranks /home/maloo/SW_sample/temp/fun3tax_107.wranks > /home/maloo/SW_sample/results/06.SW_sample.fun3.tax.wranks
  Creating /home/maloo/SW_sample/results/06.SW_sample.fun3.tax.noidfilter.wranks file: cat /home/maloo/SW_sample/temp/fun3tax_1.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_2.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_3.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_4.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_5.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_6.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_7.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_8.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_9.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_10.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_11.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_12.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_13.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_14.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_15.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_16.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_17.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_18.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_19.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_20.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_21.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_22.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_23.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_24.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_25.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_26.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_27.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_28.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_29.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_30.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_31.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_32.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_33.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_34.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_35.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_36.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_37.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_38.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_39.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_40.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_41.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_42.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_43.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_44.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_45.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_46.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_47.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_48.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_49.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_50.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_51.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_52.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_53.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_54.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_55.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_56.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_57.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_58.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_59.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_60.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_61.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_62.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_63.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_64.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_65.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_66.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_67.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_68.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_69.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_70.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_71.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_72.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_73.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_74.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_75.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_76.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_77.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_78.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_79.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_80.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_81.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_82.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_83.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_84.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_85.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_86.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_87.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_88.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_89.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_90.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_91.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_92.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_93.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_94.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_95.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_96.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_97.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_98.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_99.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_100.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_101.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_102.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_103.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_104.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_105.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_106.noidfilter.wranks /home/maloo/SW_sample/temp/fun3tax_107.noidfilter.wranks  > /home/maloo/SW_sample/results/06.SW_sample.fun3.tax.noidfilter.wranks
  Removing temporaty diamond files in /home/maloo/SW_sample/temp
Linux cnode0099 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
[4.0K Jun 14 13:50]  /home/maloo/SW_sample
├── [  35 Jun 14 13:50]  creator.txt
├── [  63 Jun 14 13:50]  data
│   ├── [  37 Jun 14 13:50]  00.SW_sample.samples
│   ├── [  95 Jun 14 17:23]  megahit
│   │   ├── [ 350 Jun 14 17:23]  checkpoints.txt
│   │   ├── [   0 Jun 14 17:23]  done
│   │   ├── [4.0K Jun 14 17:23]  intermediate_contigs
│   │   │   ├── [465K Jun 14 17:00]  k107.addi.fa
│   │   │   ├── [   8 Jun 14 17:00]  k107.addi.fa.info
│   │   │   ├── [3.5M Jun 14 17:00]  k107.bubble_seq.fa
│   │   │   ├── [  12 Jun 14 17:00]  k107.bubble_seq.fa.info
│   │   │   ├── [463M Jun 14 17:00]  k107.contigs.fa
│   │   │   ├── [  16 Jun 14 17:00]  k107.contigs.fa.info
│   │   │   ├── [   0 Jun 14 17:00]  k107.final.contigs.fa
│   │   │   ├── [   4 Jun 14 17:00]  k107.final.contigs.fa.info
│   │   │   ├── [933K Jun 14 17:09]  k107.local.fa
│   │   │   ├── [  12 Jun 14 17:09]  k107.local.fa.info
│   │   │   ├── [232K Jun 14 17:12]  k117.addi.fa
│   │   │   ├── [   7 Jun 14 17:12]  k117.addi.fa.info
│   │   │   ├── [1.8M Jun 14 17:12]  k117.bubble_seq.fa
│   │   │   ├── [  11 Jun 14 17:12]  k117.bubble_seq.fa.info
│   │   │   ├── [463M Jun 14 17:12]  k117.contigs.fa
│   │   │   ├── [  16 Jun 14 17:12]  k117.contigs.fa.info
│   │   │   ├── [   0 Jun 14 17:11]  k117.final.contigs.fa
│   │   │   ├── [   4 Jun 14 17:12]  k117.final.contigs.fa.info
│   │   │   ├── [780K Jun 14 17:21]  k117.local.fa
│   │   │   ├── [  12 Jun 14 17:21]  k117.local.fa.info
│   │   │   ├── [   0 Jun 14 17:22]  k127.addi.fa
│   │   │   ├── [   4 Jun 14 17:23]  k127.addi.fa.info
│   │   │   ├── [   0 Jun 14 17:22]  k127.bubble_seq.fa
│   │   │   ├── [   4 Jun 14 17:23]  k127.bubble_seq.fa.info
│   │   │   ├── [463M Jun 14 17:23]  k127.contigs.fa
│   │   │   ├── [  16 Jun 14 17:23]  k127.contigs.fa.info
│   │   │   ├── [   0 Jun 14 17:22]  k127.final.contigs.fa
│   │   │   ├── [   4 Jun 14 17:23]  k127.final.contigs.fa.info
│   │   │   ├── [ 80M Jun 14 14:20]  k27.addi.fa
│   │   │   ├── [  15 Jun 14 14:20]  k27.addi.fa.info
│   │   │   ├── [742M Jun 14 14:20]  k27.bubble_seq.fa
│   │   │   ├── [  18 Jun 14 14:20]  k27.bubble_seq.fa.info
│   │   │   ├── [4.0G Jun 14 14:20]  k27.contigs.fa
│   │   │   ├── [  19 Jun 14 14:20]  k27.contigs.fa.info
│   │   │   ├── [   0 Jun 14 14:13]  k27.final.contigs.fa
│   │   │   ├── [   4 Jun 14 14:20]  k27.final.contigs.fa.info
│   │   │   ├── [ 57M Jun 14 14:29]  k27.local.fa
│   │   │   ├── [  16 Jun 14 14:29]  k27.local.fa.info
│   │   │   ├── [ 42M Jun 14 14:57]  k37.addi.fa
│   │   │   ├── [  14 Jun 14 14:57]  k37.addi.fa.info
│   │   │   ├── [462M Jun 14 14:57]  k37.bubble_seq.fa
│   │   │   ├── [  17 Jun 14 14:57]  k37.bubble_seq.fa.info
│   │   │   ├── [3.2G Jun 14 14:57]  k37.contigs.fa
│   │   │   ├── [  19 Jun 14 14:57]  k37.contigs.fa.info
│   │   │   ├── [   0 Jun 14 14:52]  k37.final.contigs.fa
│   │   │   ├── [   4 Jun 14 14:57]  k37.final.contigs.fa.info
│   │   │   ├── [ 29M Jun 14 15:07]  k37.local.fa
│   │   │   ├── [  16 Jun 14 15:07]  k37.local.fa.info
│   │   │   ├── [ 11M Jun 14 15:30]  k47.addi.fa
│   │   │   ├── [  12 Jun 14 15:30]  k47.addi.fa.info
│   │   │   ├── [ 93M Jun 14 15:30]  k47.bubble_seq.fa
│   │   │   ├── [  16 Jun 14 15:30]  k47.bubble_seq.fa.info
│   │   │   ├── [2.9G Jun 14 15:30]  k47.contigs.fa
│   │   │   ├── [  19 Jun 14 15:30]  k47.contigs.fa.info
│   │   │   ├── [   0 Jun 14 15:26]  k47.final.contigs.fa
│   │   │   ├── [   4 Jun 14 15:30]  k47.final.contigs.fa.info
│   │   │   ├── [ 12M Jun 14 15:40]  k47.local.fa
│   │   │   ├── [  15 Jun 14 15:40]  k47.local.fa.info
│   │   │   ├── [4.8M Jun 14 15:52]  k57.addi.fa
│   │   │   ├── [  11 Jun 14 15:52]  k57.addi.fa.info
│   │   │   ├── [ 42M Jun 14 15:52]  k57.bubble_seq.fa
│   │   │   ├── [  15 Jun 14 15:52]  k57.bubble_seq.fa.info
│   │   │   ├── [973M Jun 14 15:52]  k57.contigs.fa
│   │   │   ├── [  17 Jun 14 15:52]  k57.contigs.fa.info
│   │   │   ├── [   0 Jun 14 15:51]  k57.final.contigs.fa
│   │   │   ├── [   4 Jun 14 15:52]  k57.final.contigs.fa.info
│   │   │   ├── [5.4M Jun 14 16:03]  k57.local.fa
│   │   │   ├── [  14 Jun 14 16:03]  k57.local.fa.info
│   │   │   ├── [2.2M Jun 14 16:08]  k67.addi.fa
│   │   │   ├── [  10 Jun 14 16:08]  k67.addi.fa.info
│   │   │   ├── [ 20M Jun 14 16:08]  k67.bubble_seq.fa
│   │   │   ├── [  14 Jun 14 16:08]  k67.bubble_seq.fa.info
│   │   │   ├── [843M Jun 14 16:08]  k67.contigs.fa
│   │   │   ├── [  17 Jun 14 16:08]  k67.contigs.fa.info
│   │   │   ├── [   0 Jun 14 16:08]  k67.final.contigs.fa
│   │   │   ├── [   4 Jun 14 16:08]  k67.final.contigs.fa.info
│   │   │   ├── [3.0M Jun 14 16:19]  k67.local.fa
│   │   │   ├── [  14 Jun 14 16:19]  k67.local.fa.info
│   │   │   ├── [1.3M Jun 14 16:23]  k77.addi.fa
│   │   │   ├── [   9 Jun 14 16:23]  k77.addi.fa.info
│   │   │   ├── [ 12M Jun 14 16:23]  k77.bubble_seq.fa
│   │   │   ├── [  13 Jun 14 16:23]  k77.bubble_seq.fa.info
│   │   │   ├── [707M Jun 14 16:23]  k77.contigs.fa
│   │   │   ├── [  17 Jun 14 16:23]  k77.contigs.fa.info
│   │   │   ├── [   0 Jun 14 16:23]  k77.final.contigs.fa
│   │   │   ├── [   4 Jun 14 16:23]  k77.final.contigs.fa.info
│   │   │   ├── [1.9M Jun 14 16:33]  k77.local.fa
│   │   │   ├── [  13 Jun 14 16:33]  k77.local.fa.info
│   │   │   ├── [864K Jun 14 16:37]  k87.addi.fa
│   │   │   ├── [   9 Jun 14 16:37]  k87.addi.fa.info
│   │   │   ├── [8.5M Jun 14 16:37]  k87.bubble_seq.fa
│   │   │   ├── [  13 Jun 14 16:37]  k87.bubble_seq.fa.info
│   │   │   ├── [571M Jun 14 16:37]  k87.contigs.fa
│   │   │   ├── [  17 Jun 14 16:37]  k87.contigs.fa.info
│   │   │   ├── [   0 Jun 14 16:36]  k87.final.contigs.fa
│   │   │   ├── [   4 Jun 14 16:37]  k87.final.contigs.fa.info
│   │   │   ├── [1.4M Jun 14 16:45]  k87.local.fa
│   │   │   ├── [  13 Jun 14 16:45]  k87.local.fa.info
│   │   │   ├── [644K Jun 14 16:48]  k97.addi.fa
│   │   │   ├── [   8 Jun 14 16:48]  k97.addi.fa.info
│   │   │   ├── [5.8M Jun 14 16:48]  k97.bubble_seq.fa
│   │   │   ├── [  13 Jun 14 16:48]  k97.bubble_seq.fa.info
│   │   │   ├── [481M Jun 14 16:48]  k97.contigs.fa
│   │   │   ├── [  16 Jun 14 16:48]  k97.contigs.fa.info
│   │   │   ├── [   0 Jun 14 16:48]  k97.final.contigs.fa
│   │   │   ├── [   4 Jun 14 16:48]  k97.final.contigs.fa.info
│   │   │   ├── [1.1M Jun 14 16:58]  k97.local.fa
│   │   │   └── [  12 Jun 14 16:58]  k97.local.fa.info
│   │   ├── [195K Jun 14 17:23]  log
│   │   └── [ 877 Jun 14 13:50]  options.json
│   └── [  26 Jun 14 13:50]  raw_fastq
│       └── [2.8G Jun 14 13:50]  par1.fastq.gz
├── [   6 Jun 14 13:50]  ext_tables
├── [4.0K Jun 15 02:15]  intermediate
│   ├── [ 14M Jun 14 17:23]  01.SW_sample.lon
│   ├── [ 315 Jun 14 17:23]  01.SW_sample.stats
│   ├── [444M Jun 14 17:29]  02.SW_sample.maskedrna.fasta
│   ├── [1.1G Jun 15 02:09]  04.SW_sample.eggnog.diamond
│   ├── [837M Jun 15 02:15]  04.SW_sample.kegg.diamond
│   ├── [1.3G Jun 15 02:03]  04.SW_sample.nr.diamond
│   ├── [144M Jun 15 09:18]  05.SW_sample.pfam.hmm
│   ├── [   6 Jun 14 13:50]  binners
│   └── [  56 Jun 14 18:10]  DB_BUILD_DATE
├── [1.2K Jun 15 09:18]  methods.txt
├── [3.1K Jun 14 13:50]  parameters.pl
├── [ 120 Jun 15 09:18]  progress
├── [4.0K Jun 14 18:10]  results
│   ├── [451M Jun 14 17:23]  01.SW_sample.fasta
│   ├── [ 20K Jun 14 17:25]  02.SW_sample.16S.txt
│   ├── [389K Jun 14 17:25]  02.SW_sample.rnas
│   ├── [116K Jun 14 17:29]  02.SW_sample.trnas
│   ├── [495K Jun 14 17:29]  02.SW_sample.trnas.fasta
│   ├── [250M Jun 14 18:09]  03.SW_sample.faa
│   ├── [510M Jun 14 18:09]  03.SW_sample.fna
│   └── [382M Jun 14 18:10]  03.SW_sample.gff
├── [8.3K Jun 14 13:50]  SqueezeMeta_conf.pl
├── [ 28K Jun 15 11:11]  syslog
└── [ 12K Jun 15 09:23]  temp
    ├── [381M Jun 14 18:10]  02.SW_sample.cds.gff
    ├── [369M Jun 14 18:09]  02.SW_sample.cds.gff.temp
    ├── [442K Jun 14 17:29]  02.SW_sample.rna.gff
    ├── [ 83K Jun 14 17:25]  16S.fasta
    ├── [ 27K Jun 14 17:25]  16S.out
    ├── [2.9K Jun 14 17:24]  arc.gff
    ├── [3.4K Jun 14 17:24]  arc.gff.mod
    ├── [110K Jun 14 17:24]  bac.gff
    ├── [128K Jun 14 17:24]  bac.gff.mod
    ├── [ 13M Jun 15 09:19]  diamond_lca.100.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.101.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.102.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.103.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.104.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.105.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.106.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.107.m8
    ├── [ 12M Jun 15 09:18]  diamond_lca.10.m8
    ├── [ 12M Jun 15 09:18]  diamond_lca.11.m8
    ├── [ 12M Jun 15 09:18]  diamond_lca.12.m8
    ├── [ 12M Jun 15 09:18]  diamond_lca.13.m8
    ├── [ 12M Jun 15 09:18]  diamond_lca.14.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.15.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.16.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.17.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.18.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.19.m8
    ├── [ 12M Jun 15 09:18]  diamond_lca.1.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.20.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.21.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.22.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.23.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.24.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.25.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.26.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.27.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.28.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.29.m8
    ├── [ 12M Jun 15 09:18]  diamond_lca.2.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.30.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.31.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.32.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.33.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.34.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.35.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.36.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.37.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.38.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.39.m8
    ├── [ 12M Jun 15 09:18]  diamond_lca.3.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.40.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.41.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.42.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.43.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.44.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.45.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.46.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.47.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.48.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.49.m8
    ├── [ 12M Jun 15 09:18]  diamond_lca.4.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.50.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.51.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.52.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.53.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.54.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.55.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.56.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.57.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.58.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.59.m8
    ├── [ 12M Jun 15 09:18]  diamond_lca.5.m8
    ├── [ 13M Jun 15 09:18]  diamond_lca.60.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.61.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.62.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.63.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.64.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.65.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.66.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.67.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.68.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.69.m8
    ├── [ 12M Jun 15 09:18]  diamond_lca.6.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.70.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.71.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.72.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.73.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.74.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.75.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.76.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.77.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.78.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.79.m8
    ├── [ 12M Jun 15 09:18]  diamond_lca.7.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.80.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.81.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.82.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.83.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.84.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.85.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.86.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.87.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.88.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.89.m8
    ├── [ 12M Jun 15 09:18]  diamond_lca.8.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.90.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.91.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.92.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.93.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.94.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.95.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.96.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.97.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.98.m8
    ├── [ 13M Jun 15 09:19]  diamond_lca.99.m8
    ├── [ 12M Jun 15 09:18]  diamond_lca.9.m8
    ├── [ 46K Jun 15 02:03]  diamond.nr.log
    ├── [7.4K Jun 14 17:24]  euk.gff
    ├── [8.6K Jun 14 17:24]  euk.gff.mod
    ├── [732K Jun 15 11:10]  fun3tax_100.noidfilter.wranks
    ├── [659K Jun 15 11:10]  fun3tax_100.wranks
    ├── [749K Jun 15 11:09]  fun3tax_101.noidfilter.wranks
    ├── [671K Jun 15 11:09]  fun3tax_101.wranks
    ├── [749K Jun 15 11:09]  fun3tax_102.noidfilter.wranks
    ├── [668K Jun 15 11:09]  fun3tax_102.wranks
    ├── [735K Jun 15 11:10]  fun3tax_103.noidfilter.wranks
    ├── [662K Jun 15 11:10]  fun3tax_103.wranks
    ├── [725K Jun 15 11:10]  fun3tax_104.noidfilter.wranks
    ├── [650K Jun 15 11:10]  fun3tax_104.wranks
    ├── [728K Jun 15 11:09]  fun3tax_105.noidfilter.wranks
    ├── [652K Jun 15 11:09]  fun3tax_105.wranks
    ├── [737K Jun 15 11:09]  fun3tax_106.noidfilter.wranks
    ├── [661K Jun 15 11:09]  fun3tax_106.wranks
    ├── [732K Jun 15 11:10]  fun3tax_107.noidfilter.wranks
    ├── [657K Jun 15 11:10]  fun3tax_107.wranks
    ├── [722K Jun 15 11:05]  fun3tax_10.noidfilter.wranks
    ├── [653K Jun 15 11:05]  fun3tax_10.wranks
    ├── [729K Jun 15 11:07]  fun3tax_11.noidfilter.wranks
    ├── [655K Jun 15 11:07]  fun3tax_11.wranks
    ├── [725K Jun 15 11:07]  fun3tax_12.noidfilter.wranks
    ├── [649K Jun 15 11:07]  fun3tax_12.wranks
    ├── [729K Jun 15 11:09]  fun3tax_13.noidfilter.wranks
    ├── [653K Jun 15 11:09]  fun3tax_13.wranks
    ├── [739K Jun 15 11:09]  fun3tax_14.noidfilter.wranks
    ├── [662K Jun 15 11:09]  fun3tax_14.wranks
    ├── [737K Jun 15 11:09]  fun3tax_15.noidfilter.wranks
    ├── [660K Jun 15 11:09]  fun3tax_15.wranks
    ├── [733K Jun 15 11:08]  fun3tax_16.noidfilter.wranks
    ├── [660K Jun 15 11:08]  fun3tax_16.wranks
    ├── [734K Jun 15 11:09]  fun3tax_17.noidfilter.wranks
    ├── [659K Jun 15 11:09]  fun3tax_17.wranks
    ├── [731K Jun 15 11:08]  fun3tax_18.noidfilter.wranks
    ├── [654K Jun 15 11:08]  fun3tax_18.wranks
    ├── [734K Jun 15 11:08]  fun3tax_19.noidfilter.wranks
    ├── [659K Jun 15 11:08]  fun3tax_19.wranks
    ├── [709K Jun 15 11:08]  fun3tax_1.noidfilter.wranks
    ├── [635K Jun 15 11:08]  fun3tax_1.wranks
    ├── [737K Jun 15 11:08]  fun3tax_20.noidfilter.wranks
    ├── [659K Jun 15 11:08]  fun3tax_20.wranks
    ├── [729K Jun 15 11:07]  fun3tax_21.noidfilter.wranks
    ├── [657K Jun 15 11:07]  fun3tax_21.wranks
    ├── [736K Jun 15 11:06]  fun3tax_22.noidfilter.wranks
    ├── [661K Jun 15 11:06]  fun3tax_22.wranks
    ├── [720K Jun 15 11:08]  fun3tax_23.noidfilter.wranks
    ├── [647K Jun 15 11:08]  fun3tax_23.wranks
    ├── [731K Jun 15 11:09]  fun3tax_24.noidfilter.wranks
    ├── [658K Jun 15 11:09]  fun3tax_24.wranks
    ├── [723K Jun 15 11:09]  fun3tax_25.noidfilter.wranks
    ├── [651K Jun 15 11:09]  fun3tax_25.wranks
    ├── [731K Jun 15 11:07]  fun3tax_26.noidfilter.wranks
    ├── [659K Jun 15 11:07]  fun3tax_26.wranks
    ├── [734K Jun 15 11:10]  fun3tax_27.noidfilter.wranks
    ├── [656K Jun 15 11:10]  fun3tax_27.wranks
    ├── [748K Jun 15 11:07]  fun3tax_28.noidfilter.wranks
    ├── [670K Jun 15 11:07]  fun3tax_28.wranks
    ├── [729K Jun 15 11:09]  fun3tax_29.noidfilter.wranks
    ├── [654K Jun 15 11:09]  fun3tax_29.wranks
    ├── [716K Jun 15 11:05]  fun3tax_2.noidfilter.wranks
    ├── [642K Jun 15 11:05]  fun3tax_2.wranks
    ├── [723K Jun 15 11:06]  fun3tax_30.noidfilter.wranks
    ├── [651K Jun 15 11:06]  fun3tax_30.wranks
    ├── [734K Jun 15 11:07]  fun3tax_31.noidfilter.wranks
    ├── [659K Jun 15 11:07]  fun3tax_31.wranks
    ├── [736K Jun 15 11:08]  fun3tax_32.noidfilter.wranks
    ├── [661K Jun 15 11:08]  fun3tax_32.wranks
    ├── [735K Jun 15 11:09]  fun3tax_33.noidfilter.wranks
    ├── [661K Jun 15 11:09]  fun3tax_33.wranks
    ├── [729K Jun 15 11:08]  fun3tax_34.noidfilter.wranks
    ├── [654K Jun 15 11:08]  fun3tax_34.wranks
    ├── [731K Jun 15 11:09]  fun3tax_35.noidfilter.wranks
    ├── [656K Jun 15 11:09]  fun3tax_35.wranks
    ├── [727K Jun 15 11:05]  fun3tax_36.noidfilter.wranks
    ├── [655K Jun 15 11:05]  fun3tax_36.wranks
    ├── [728K Jun 15 11:08]  fun3tax_37.noidfilter.wranks
    ├── [653K Jun 15 11:08]  fun3tax_37.wranks
    ├── [741K Jun 15 11:09]  fun3tax_38.noidfilter.wranks
    ├── [665K Jun 15 11:09]  fun3tax_38.wranks
    ├── [738K Jun 15 11:09]  fun3tax_39.noidfilter.wranks
    ├── [661K Jun 15 11:09]  fun3tax_39.wranks
    ├── [730K Jun 15 11:04]  fun3tax_3.noidfilter.wranks
    ├── [656K Jun 15 11:04]  fun3tax_3.wranks
    ├── [745K Jun 15 11:07]  fun3tax_40.noidfilter.wranks
    ├── [668K Jun 15 11:07]  fun3tax_40.wranks
    ├── [737K Jun 15 11:09]  fun3tax_41.noidfilter.wranks
    ├── [660K Jun 15 11:09]  fun3tax_41.wranks
    ├── [733K Jun 15 11:08]  fun3tax_42.noidfilter.wranks
    ├── [658K Jun 15 11:08]  fun3tax_42.wranks
    ├── [731K Jun 15 11:08]  fun3tax_43.noidfilter.wranks
    ├── [656K Jun 15 11:08]  fun3tax_43.wranks
    ├── [733K Jun 15 11:10]  fun3tax_44.noidfilter.wranks
    ├── [663K Jun 15 11:10]  fun3tax_44.wranks
    ├── [733K Jun 15 11:08]  fun3tax_45.noidfilter.wranks
    ├── [658K Jun 15 11:08]  fun3tax_45.wranks
    ├── [734K Jun 15 11:09]  fun3tax_46.noidfilter.wranks
    ├── [662K Jun 15 11:09]  fun3tax_46.wranks
    ├── [737K Jun 15 11:09]  fun3tax_47.noidfilter.wranks
    ├── [660K Jun 15 11:09]  fun3tax_47.wranks
    ├── [732K Jun 15 11:08]  fun3tax_48.noidfilter.wranks
    ├── [656K Jun 15 11:08]  fun3tax_48.wranks
    ├── [743K Jun 15 11:08]  fun3tax_49.noidfilter.wranks
    ├── [666K Jun 15 11:08]  fun3tax_49.wranks
    ├── [730K Jun 15 11:05]  fun3tax_4.noidfilter.wranks
    ├── [652K Jun 15 11:05]  fun3tax_4.wranks
    ├── [733K Jun 15 11:07]  fun3tax_50.noidfilter.wranks
    ├── [657K Jun 15 11:07]  fun3tax_50.wranks
    ├── [739K Jun 15 11:07]  fun3tax_51.noidfilter.wranks
    ├── [665K Jun 15 11:07]  fun3tax_51.wranks
    ├── [735K Jun 15 11:08]  fun3tax_52.noidfilter.wranks
    ├── [661K Jun 15 11:08]  fun3tax_52.wranks
    ├── [735K Jun 15 11:07]  fun3tax_53.noidfilter.wranks
    ├── [660K Jun 15 11:07]  fun3tax_53.wranks
    ├── [733K Jun 15 11:09]  fun3tax_54.noidfilter.wranks
    ├── [660K Jun 15 11:09]  fun3tax_54.wranks
    ├── [737K Jun 15 11:07]  fun3tax_55.noidfilter.wranks
    ├── [658K Jun 15 11:07]  fun3tax_55.wranks
    ├── [735K Jun 15 11:07]  fun3tax_56.noidfilter.wranks
    ├── [660K Jun 15 11:07]  fun3tax_56.wranks
    ├── [723K Jun 15 11:08]  fun3tax_57.noidfilter.wranks
    ├── [650K Jun 15 11:08]  fun3tax_57.wranks
    ├── [734K Jun 15 11:08]  fun3tax_58.noidfilter.wranks
    ├── [658K Jun 15 11:08]  fun3tax_58.wranks
    ├── [724K Jun 15 11:09]  fun3tax_59.noidfilter.wranks
    ├── [650K Jun 15 11:09]  fun3tax_59.wranks
    ├── [721K Jun 15 11:06]  fun3tax_5.noidfilter.wranks
    ├── [646K Jun 15 11:06]  fun3tax_5.wranks
    ├── [739K Jun 15 11:10]  fun3tax_60.noidfilter.wranks
    ├── [663K Jun 15 11:10]  fun3tax_60.wranks
    ├── [719K Jun 15 11:09]  fun3tax_61.noidfilter.wranks
    ├── [647K Jun 15 11:09]  fun3tax_61.wranks
    ├── [725K Jun 15 11:09]  fun3tax_62.noidfilter.wranks
    ├── [658K Jun 15 11:09]  fun3tax_62.wranks
    ├── [729K Jun 15 11:09]  fun3tax_63.noidfilter.wranks
    ├── [657K Jun 15 11:09]  fun3tax_63.wranks
    ├── [727K Jun 15 11:09]  fun3tax_64.noidfilter.wranks
    ├── [653K Jun 15 11:09]  fun3tax_64.wranks
    ├── [735K Jun 15 11:10]  fun3tax_65.noidfilter.wranks
    ├── [659K Jun 15 11:10]  fun3tax_65.wranks
    ├── [732K Jun 15 11:08]  fun3tax_66.noidfilter.wranks
    ├── [657K Jun 15 11:08]  fun3tax_66.wranks
    ├── [722K Jun 15 11:09]  fun3tax_67.noidfilter.wranks
    ├── [650K Jun 15 11:09]  fun3tax_67.wranks
    ├── [725K Jun 15 11:08]  fun3tax_68.noidfilter.wranks
    ├── [652K Jun 15 11:08]  fun3tax_68.wranks
    ├── [738K Jun 15 11:09]  fun3tax_69.noidfilter.wranks
    ├── [663K Jun 15 11:09]  fun3tax_69.wranks
    ├── [727K Jun 15 11:07]  fun3tax_6.noidfilter.wranks
    ├── [651K Jun 15 11:07]  fun3tax_6.wranks
    ├── [736K Jun 15 11:09]  fun3tax_70.noidfilter.wranks
    ├── [662K Jun 15 11:09]  fun3tax_70.wranks
    ├── [731K Jun 15 11:10]  fun3tax_71.noidfilter.wranks
    ├── [658K Jun 15 11:10]  fun3tax_71.wranks
    ├── [738K Jun 15 11:07]  fun3tax_72.noidfilter.wranks
    ├── [664K Jun 15 11:07]  fun3tax_72.wranks
    ├── [728K Jun 15 11:07]  fun3tax_73.noidfilter.wranks
    ├── [654K Jun 15 11:07]  fun3tax_73.wranks
    ├── [741K Jun 15 11:09]  fun3tax_74.noidfilter.wranks
    ├── [665K Jun 15 11:09]  fun3tax_74.wranks
    ├── [732K Jun 15 11:09]  fun3tax_75.noidfilter.wranks
    ├── [654K Jun 15 11:09]  fun3tax_75.wranks
    ├── [729K Jun 15 11:09]  fun3tax_76.noidfilter.wranks
    ├── [652K Jun 15 11:09]  fun3tax_76.wranks
    ├── [725K Jun 15 11:09]  fun3tax_77.noidfilter.wranks
    ├── [653K Jun 15 11:09]  fun3tax_77.wranks
    ├── [732K Jun 15 11:09]  fun3tax_78.noidfilter.wranks
    ├── [654K Jun 15 11:09]  fun3tax_78.wranks
    ├── [736K Jun 15 11:08]  fun3tax_79.noidfilter.wranks
    ├── [658K Jun 15 11:08]  fun3tax_79.wranks
    ├── [723K Jun 15 11:09]  fun3tax_7.noidfilter.wranks
    ├── [650K Jun 15 11:09]  fun3tax_7.wranks
    ├── [733K Jun 15 11:09]  fun3tax_80.noidfilter.wranks
    ├── [660K Jun 15 11:09]  fun3tax_80.wranks
    ├── [734K Jun 15 11:09]  fun3tax_81.noidfilter.wranks
    ├── [656K Jun 15 11:09]  fun3tax_81.wranks
    ├── [726K Jun 15 11:09]  fun3tax_82.noidfilter.wranks
    ├── [653K Jun 15 11:09]  fun3tax_82.wranks
    ├── [739K Jun 15 11:07]  fun3tax_83.noidfilter.wranks
    ├── [660K Jun 15 11:07]  fun3tax_83.wranks
    ├── [732K Jun 15 11:09]  fun3tax_84.noidfilter.wranks
    ├── [655K Jun 15 11:09]  fun3tax_84.wranks
    ├── [729K Jun 15 11:09]  fun3tax_85.noidfilter.wranks
    ├── [654K Jun 15 11:09]  fun3tax_85.wranks
    ├── [738K Jun 15 11:09]  fun3tax_86.noidfilter.wranks
    ├── [660K Jun 15 11:09]  fun3tax_86.wranks
    ├── [725K Jun 15 11:09]  fun3tax_87.noidfilter.wranks
    ├── [653K Jun 15 11:09]  fun3tax_87.wranks
    ├── [734K Jun 15 11:09]  fun3tax_88.noidfilter.wranks
    ├── [660K Jun 15 11:09]  fun3tax_88.wranks
    ├── [734K Jun 15 11:08]  fun3tax_89.noidfilter.wranks
    ├── [659K Jun 15 11:08]  fun3tax_89.wranks
    ├── [730K Jun 15 11:07]  fun3tax_8.noidfilter.wranks
    ├── [657K Jun 15 11:07]  fun3tax_8.wranks
    ├── [745K Jun 15 11:08]  fun3tax_90.noidfilter.wranks
    ├── [665K Jun 15 11:08]  fun3tax_90.wranks
    ├── [724K Jun 15 11:09]  fun3tax_91.noidfilter.wranks
    ├── [650K Jun 15 11:09]  fun3tax_91.wranks
    ├── [734K Jun 15 11:09]  fun3tax_92.noidfilter.wranks
    ├── [659K Jun 15 11:09]  fun3tax_92.wranks
    ├── [728K Jun 15 11:10]  fun3tax_93.noidfilter.wranks
    ├── [650K Jun 15 11:10]  fun3tax_93.wranks
    ├── [733K Jun 15 11:09]  fun3tax_94.noidfilter.wranks
    ├── [655K Jun 15 11:09]  fun3tax_94.wranks
    ├── [725K Jun 15 11:10]  fun3tax_95.noidfilter.wranks
    ├── [649K Jun 15 11:10]  fun3tax_95.wranks
    ├── [731K Jun 15 11:09]  fun3tax_96.noidfilter.wranks
    ├── [657K Jun 15 11:09]  fun3tax_96.wranks
    ├── [740K Jun 15 11:09]  fun3tax_97.noidfilter.wranks
    ├── [665K Jun 15 11:09]  fun3tax_97.wranks
    ├── [738K Jun 15 11:10]  fun3tax_98.noidfilter.wranks
    ├── [659K Jun 15 11:10]  fun3tax_98.wranks
    ├── [733K Jun 15 11:09]  fun3tax_99.noidfilter.wranks
    ├── [658K Jun 15 11:09]  fun3tax_99.wranks
    ├── [726K Jun 15 11:07]  fun3tax_9.noidfilter.wranks
    ├── [653K Jun 15 11:07]  fun3tax_9.wranks
    ├── [2.7K Jun 14 17:25]  mito.gff
    ├── [3.1K Jun 14 17:25]  mito.gff.mod
    ├── [299K Jun 14 17:29]  trna.gff.mod
    ├── [ 22M Jun 14 17:29]  trnas.aragorn
    └── [  68 Jun 15 09:18]  wc

10 directories, 474 files

Progress file output:

1       01.run_all_assemblies.pl (megahit)
2       02.rnas.pl
3       03.run_prodigal.pl
4       04.rundiamond.pl
5       05.run_hmmer.pl
6       06.lca.pl

My nohup output error file:

Input and filter stats:
        Input sequences: 762,723
        Input bases: 452,994,294
        Input mean length: 593.92
        Good sequences: 762,723 (100.00%)
        Good bases: 452,994,294
        Good mean length: 593.92
        Bad sequences: 0 (0.00%)
        Sequences filtered by specified parameters:
        none
-p destination: Broken pipe
Died at /apps/chpc/bio/anaconda3-2020.02/envs/SqueezeMeta-1.6.3/bin/SqueezeMeta.pl line 941.

My nohup output normal file(basically local syslog):

SqueezeMeta v1.6.3, September 2023 - (c) J. Tamames, F. Puente-Sánchez CNB-CSIC, Madrid, SPAIN

Please cite: Tamames & Puente-Sanchez, Frontiers in Microbiology 9, 3349 (2019). doi: https://doi.org/10.3389/fmicb.2018.03349

Run started Fri Jun 14 13:50:47 2024 in sequential mode
1 metagenomes found: SW_sample

--- SAMPLE SW_sample ---
Now creating directories
Reading configuration from /home/maloo/SW_sample/SqueezeMeta_conf.pl
  Running trimmomatic (Bolger et al 2014, Bioinformatics 30(15):2114-20) for quality filtering
  Parameters: 
[0 seconds]: STEP1 -> RUNNING ASSEMBLY: 01.run_all_assemblies.pl (megahit)
  Working for sample SW_sample
  Preparing files for pair1: cat /mnt/lustre/users/maloo/euMwanza/George/marwahsab/raw_data/SW/SW_clean_data1.fq.gz > /home/maloo/SW_sample/data/raw_fastq/par1.fastq.gz
  Running assembly with megahit: perl /apps/chpc/bio/anaconda3-2020.02/envs/SqueezeMeta-1.6.3/SqueezeMeta/lib/SqueezeMeta/assembly_megahit.pl /home/maloo/SW_sample SW_sample /home/maloo/SW_sample/data/raw_fastq/par1.fastq.gz 
  Running prinseq (Schmieder et al 2011, Bioinformatics 27(6):863-4) for selecting contigs longer than 200 
  Renaming contigs in /home/maloo/SW_sample/results/01.SW_sample.fasta
Running prinseq for contig statistics: /apps/chpc/bio/anaconda3-2020.02/envs/SqueezeMeta-1.6.3/SqueezeMeta/bin/prinseq-lite.pl -fasta /home/maloo/SW_sample/results/01.SW_sample.fasta -stats_len -stats_info -stats_assembly > /home/maloo/SW_sample/intermediate/01.SW_sample.stats
    Counting length of contigs
  Contigs stored in /home/maloo/SW_sample/results/01.SW_sample.fasta
  Number of contigs: 762723
[3 hours, 32 minutes, 54 seconds]: STEP2 -> RNA PREDICTION: 02.rnas.pl
  Running barrnap (Seeman 2014, Bioinformatics 30, 2068-9) for predicting RNAs:  Bacteria Archaea Eukaryote Mitochondrial
  Running RDP classifier (Wang et al 2007, Appl Environ Microbiol 73, 5261-7)
  Running Aragorn (Laslett & Canback 2004, Nucleic Acids Res 31, 11-16) for tRNA/tmRNA prediction
[3 hours, 38 minutes, 52 seconds]: STEP3 -> ORF PREDICTION: 03.run_prodigal.pl
  Running prodigal (Hyatt et al 2010, BMC Bioinformatics 11: 119) for predicting ORFs
  ORFs predicted: 997580
[4 hours, 19 minutes, 18 seconds]: STEP4 -> HOMOLOGY SEARCHES: 04.rundiamond.pl
  Setting block size for Diamond
  AVAILABLE (free) RAM memory: 109.56 Gb
  We will set Diamond block size to 13.7 (Gb RAM/8, Max 16).
  You can override this setting using the -b option when starting the project, or changing
  the $blocksize variable in SqueezeMeta_conf.pl
  Working with taxonomy database in /mnt/lustre/bsp/DB/SqueezeMeta-1.6.3/db/nr.dmnd
 taxa COGS   Running Diamond (Buchfink et al 2015, Nat Methods 12, 59-60) for KEGG

[12 hours, 24 minutes, 32 seconds]: STEP5 -> HMMER/PFAM: 05.run_hmmer.pl
  Running HMMER3 (Eddy 2009, Genome Inform 23, 205-11) for Pfam
[19 hours, 27 minutes, 39 seconds]: STEP6 -> TAXONOMIC ASSIGNMENT: 06.lca.pl
  AVAILABLE (free) RAM memory: 109.26 Gb
  We will set the number of threads to 107 for this step
  Splitting Diamond file
  Starting multithread LCA in 107 threads
  Creating /home/maloo/SW_sample/results/06.SW_sample.fun3.tax.wranks file
  Creating /home/maloo/SW_sample/results/06.SW_sample.fun3.tax.noidfilter.wranks file
Stopping in STEP6 -> 06.lca.pl. File /home/maloo/SW_sample/results/06.SW_sample.fun3.tax.wranks is empty!

  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/maloo/SW_sample/syslog file (zip it first)
fpusan commented 2 weeks ago

Hi!

You need to add -p to your restart command.

SqueezeMeta.pl /home/maloo/SW_sample --restart -step 4 should be SqueezeMeta.pl -p /home/maloo/SW_sample --restart -step 4

Also you can not use more than one node for the same sample. You should instead run several samples in parallel, each in one node. The sequential mode can not achieve this, so you will need to

  1. Make a different samples file for each sample, containing only the fwd and rev fastq files for that sample
  2. Launch adifferent SqueezeMeta job for each sample. You can use the coassembly mode for this (though it will not really do a coassembly since you will only have one sample per job).
jtamames commented 2 weeks ago

Hello Sequential projects must be restarted individually, specifying the project name, as Fernando said. Besides, I would recommend updating to 1.6.4, that will be released very shortly, where several issues were corrected. Best, J

EorgeKit commented 1 week ago

Hello Sequential projects must be restarted individually, specifying the project name, as Fernando said. Besides, I would recommend updating to 1.6.4, that will be released very shortly, where several issues were corrected. Best, J

Oh yeah thanks, I managed to deploy the restart mode.

EorgeKit commented 1 week ago

Hi!

You need to add -p to your restart command.

SqueezeMeta.pl /home/maloo/SW_sample --restart -step 4 should be SqueezeMeta.pl -p /home/maloo/SW_sample --restart -step 4

Also you can not use more than one node for the same sample. You should instead run several samples in parallel, each in one node. The sequential mode can not achieve this, so you will need to

  1. Make a different samples file for each sample, containing only the fwd and rev fastq files for that sample
  2. Launch adifferent SqueezeMeta job for each sample. You can use the coassembly mode for this (though it will not really do a coassembly since you will only have one sample per job).

Hi, thanks a lot , I manage to get a hold of a big memory node which kind took care of the problem

EorgeKit commented 1 week ago

Hi there again, I managed to run all my samples using the sequential mode after getting the bigmemory node.

Particularly I am ONLY interested in the cyanobacteria present in the three environmental samples. My proposed method is, after I am done with the assembly and all the steps, I mine all the contigs that classify as cyanobacteria and reanalyze their functional and taxonomy profiles independently. Do you think this is the right way or can you advise a better one?

Thank you in advance

jtamames commented 1 week ago

That's ok. The subset functions in SQMtools are devised to help you on that Best,

EorgeKit commented 1 week ago

Perfect , Thanks

EorgeKit commented 1 week ago

Hi there once again, One of my sample had a low mappingstat so decided to use the sqm_reads.pl script. Code:

sqm_reads.pl \
-p SW_sample_reads_based \
-s $SAMPLE_FILES/SW.samples \
-f $RAW_DATA_DIR/SW \
-t 52 -b 100

Project directory structure:

ls SW_sample_reads_based/
creator.txt  SW_sample_reads_based.out.allreads          SW_sample_reads_based.out.allreads.mcount
methods.txt  SW_sample_reads_based.out.allreads.funcog   SW_sample_reads_based.out.mappingstat
SW_sample    SW_sample_reads_based.out.allreads.funkegg

When trying to run sqm2pavian.pl script: Code:

sqm2pavian.pl SW_sample_reads_based/
You can now use these data in your R pavian or in the web app https://fbreitwieser.shinyapps.io/pavian

But no pavian file is produced, it is worth noting that sqm2pavian.pl produces a pavian file for the Squeezemeta.pl runs . Please advise on what might be the issue.

Best, G