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tseemann / nullarbor

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology
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make: *** [3960_Saga/sketch.msh] Error 127 #292

Open naikd0 opened 2 years ago

naikd0 commented 2 years ago

Hello everyone, I am running a Nullarbor analysis on S. Agalctiae fastq files, was able to get to this [14:02:51] Hello dn927558 [14:02:51] This is nullarbor.pl 2.0.20191013 [14:02:51] Send complaints to Torsten Seemann [14:02:51] Scanning --ref for problematic sequence IDs... [14:02:51] Using reference genome: /network/rit/lab/andamlab/Dowd/Vet_strep_Agalactiae/nullarbor_Agalactiae/NZ_CP012480.1.fna [14:02:51] Loaded 10 isolates: 2438_Saga 282_Saga 3717_Saga 3917_Saga 3960_Saga 6020_Saga 6501_Saga 6742_Saga 7359_Saga 91C_Saga [14:02:51] Found 'mlst' => /network/rit/lab/andamlab/bin/miniconda3/envs/nullarbor/bin/mlst [14:02:51] Found 134 MLST schemes [14:02:51] Using scheme: sagalactiae [14:02:51] Making output folder: /network/rit/lab/andamlab/Dowd/Vet_strep_Agalactiae/nullarbor_Agalactiae/Agalctiae_output [14:02:51] Found Perl module: Bio::SeqIO [14:02:51] Found Perl module: Cwd [14:02:51] Found Perl module: Sys::Hostname [14:02:51] Found Perl module: Time::Piece [14:02:51] Found Perl module: List::Util [14:02:51] Found Perl module: YAML::Tiny [14:02:51] Found Perl module: Moo [14:02:51] Found Perl module: Path::Tiny [14:02:51] Found Perl module: File::Copy [14:02:51] Found Perl module: File::Which [14:02:51] Found Perl module: File::Basename [14:02:51] Found Perl module: File::Spec [14:02:51] Found Perl module: File::Path [14:02:51] Found Perl module: Data::Dumper [14:02:51] Found Perl module: Term::ANSIColor [14:02:51] Found Perl module: SVG [14:02:51] Found Perl module: Text::CSV [14:02:51] Found Perl module: List::MoreUtils [14:02:51] Found Perl module: IO::File [14:02:51] Found 'head' => /usr/bin/head [14:02:51] Found 'cat' => /usr/bin/cat [14:02:51] Found 'install' => /usr/bin/install [14:02:51] Found 'env' => /usr/bin/env [14:02:51] Found 'nl' => /usr/bin/nl [14:02:51] Found 'grep' => /usr/bin/grep [14:02:51] Found 'touch' => /usr/bin/touch [14:02:51] Found 'tr' => /usr/bin/tr [14:02:51] Found 'seqtk' => /network/rit/lab/andamlab/bin/miniconda3/envs/nullarbor/bin/seqtk [14:02:51] Found 'trimmomatic' => /network/rit/lab/andamlab/bin/miniconda3/envs/nullarbor/bin/trimmomatic [14:02:51] Found 'prokka' => /network/rit/lab/andamlab/bin/miniconda3/envs/nullarbor/bin/prokka [14:02:51] Found 'roary' => /network/rit/lab/andamlab/bin/miniconda3/envs/nullarbor/bin/roary [14:02:51] Found 'mlst' => /network/rit/lab/andamlab/bin/miniconda3/envs/nullarbor/bin/mlst [14:02:51] Found 'abricate' => /network/rit/lab/andamlab/bin/miniconda3/envs/nullarbor/bin/abricate [14:02:51] Found 'any2fasta' => /network/rit/lab/andamlab/bin/miniconda3/envs/nullarbor/bin/any2fasta [14:02:51] Found 'skesa' => /network/rit/lab/andamlab/bin/miniconda3/envs/nullarbor/bin/skesa [14:02:51] Found 'megahit' => /network/rit/lab/andamlab/bin/miniconda3/envs/nullarbor/bin/megahit [14:02:51] Found 'spades.py' => /network/rit/lab/andamlab/bin/miniconda3/envs/nullarbor/bin/spades.py [14:02:51] Found 'shovill' => /network/rit/lab/andamlab/bin/miniconda3/envs/nullarbor/bin/shovill [14:02:51] Found 'snippy' => /network/rit/lab/andamlab/bin/miniconda3/envs/nullarbor/bin/snippy [14:02:51] Found 'snp-dists' => /network/rit/lab/andamlab/bin/miniconda3/envs/nullarbor/bin/snp-dists [14:02:51] Found 'nw_order' => /network/rit/lab/andamlab/bin/miniconda3/envs/nullarbor/bin/nw_order [14:02:51] Found 'nw_display' => /network/rit/lab/andamlab/bin/miniconda3/envs/nullarbor/bin/nw_display [14:02:51] Found 'iqtree' => /network/rit/lab/andamlab/bin/miniconda3/envs/nullarbor/bin/iqtree [14:02:51] Found 'FastTree' => /network/rit/lab/andamlab/bin/miniconda3/envs/nullarbor/bin/FastTree [14:02:51] Found 'quicktree' => /network/rit/lab/andamlab/bin/miniconda3/envs/nullarbor/bin/quicktree [14:02:51] Found 'kraken' => /network/rit/lab/andamlab/bin/miniconda3/envs/nullarbor/bin/kraken [14:02:51] Found 'kraken-report' => /network/rit/lab/andamlab/bin/miniconda3/envs/nullarbor/bin/kraken-report [14:02:51] Found 'kraken2' => /network/rit/lab/andamlab/bin/kraken2/kraken2 [14:02:51] Found 'centrifuge' => /network/rit/lab/andamlab/bin/miniconda3/envs/nullarbor/bin/centrifuge [14:02:51] Found 'centrifuge-kreport' => /network/rit/lab/andamlab/bin/miniconda3/envs/nullarbor/bin/centrifuge-kreport [14:02:51] Found 'fq' => /network/rit/lab/andamlab/bin/miniconda3/envs/nullarbor/bin/fq [14:02:51] Found 'fa' => /network/rit/lab/andamlab/bin/miniconda3/envs/nullarbor/bin/fa [14:02:51] Found 'roary2svg.pl' => /network/rit/lab/andamlab/bin/miniconda3/envs/nullarbor/bin/roary2svg.pl [14:02:52] Parsed shovill 1.1 from 'shovill 1.1.0' [14:02:54] Parsed megahit 1.2 from 'MEGAHIT v1.2.9' [14:02:54] Parsed skesa 2.4 from 'SKESA 2.4.0' [14:02:55] Parsed snippy 4.6 from 'snippy 4.6.0' [14:02:55] Parsed prokka 1.14 from 'prokka 1.14.6' [14:02:55] Parsed quicktree 2.5 from 'quicktree 2.5' [14:02:56] Parsed iqtree 2.0 from 'IQ-TREE multicore version 2.0.3 for Linux 64-bit built Dec 20 2020' [14:02:59] Parsed roary 3.13 from '3.13.0' [14:02:59] Parsed mlst 2.19 from 'mlst 2.19.0' [14:02:59] Parsed abricate 1.0 from 'abricate 1.0.1' [14:03:00] Parsed snp-dists 0.7 from 'snp-dists 0.7.0' [14:03:01] Parsed trimmomatic 0.39 from '0.39' [14:03:02] Parsed spades.py 3.14 from 'SPAdes genome assembler v3.14.1' [14:03:02] Parsed kraken 1.1 from 'Kraken version 1.1.1' [14:03:02] Parsed mash 2.2 from '2.2.2' [14:03:02] Parsed centrifuge 1.0 from 'Centrifuge version 1.0.4 by the Centrifuge developer team (centrifuge.metagenomics@gmail.com)' [14:03:02] Found kraken env-var KRAKEN_DEFAULT_DB=/network/rit/lab/andamlab/bin/minikraken_20171019_8GB [14:03:02] Found file required by kraken: /network/rit/lab/andamlab/bin/minikraken_20171019_8GB/database.idx [14:03:02] Found file required by kraken: /network/rit/lab/andamlab/bin/minikraken_20171019_8GB/database.kdb [14:03:02] Found centrifuge env-var CENTRIFUGE_DEFAULT_DB=/network/rit/lab/andamlab/bin/centrifuge-db/p_compressed+h+v [14:03:02] Found file required by centrifuge: /network/rit/lab/andamlab/bin/centrifuge-db/p_compressed+h+v.1.cf [14:03:02] Found file required by centrifuge: /network/rit/lab/andamlab/bin/centrifuge-db/p_compressed+h+v.2.cf [14:03:02] Found file required by centrifuge: /network/rit/lab/andamlab/bin/centrifuge-db/p_compressed+h+v.3.cf [14:03:02] All nullarbor.pl 2.0.20191013 dependencies are installed. [14:03:02] You deserve a medal! [14:03:03] Loaded YAML config: /network/rit/lab/andamlab/bin/miniconda3/envs/nullarbor/bin/../conf/nullarbor.conf [14:03:03] - prefill = HASH(0x55edd1f93c80) [14:03:03] - trimmomatic = ILLUMINACLIP:/network/rit/lab/andamlab/bin/miniconda3/envs/nullarbor/conf/trimmomatic.fa:1:30:11 LEADING:10 TRAILING:10 MINLEN:30 [14:03:03] - nw_display = -S -s -w 1024 -l 'font-size:12;font-family:sans-serif;' -i 'opacity:0' -b 'opacity:0' -v 16 [14:03:03] - publish = /network/rit/home/dn927558/public_html/MDU [14:03:03] Optimizing use of 80 cores for 10 isolates. [14:03:03] Will run concurrent 10 jobs with 8 threads each. [14:03:03] Preparing isolate rules and creating isolates.txt [14:03:03] Saving /network/rit/lab/andamlab/Dowd/Vet_strep_Agalactiae/nullarbor_Agalactiae/Agalctiae_output/nullarbor.log

but when tried to implement make preview this happened mash sketch -m 5 -s 10000 -r -o 3960_Saga/sketch -I 3960_Saga -C 3960_Saga/R1.fq.gz 3960_Saga/R1.fq.gz /bin/bash: mash: command not found make: *** [3960_Saga/sketch.msh] Error 127

This error also came up when I used nullarbor on E.coli samples. Is the problem with Nullarbor itself or with my files? Any help would be greatly appreciated.

Dowd Naik