Can't locate Fasta/Parser.pm

[AMMMachado]

Dear thackl , First of all thank you for the program. It is a very useful program to build genomes with few resources available. Im working on cluster, centos 7, 512Gb ram and 32 cpus.

I tried to run the "make sample-yeast" to test the installation of the program, without success.

Seems to have all programs in the bashrc, but give me always the error below, and the mp files are empty.

5 Log.file

make sample-yeast hash bwa || { echo "bwa required in PATH" 1>&2 && exit 1; } hash curl || { echo "curl required in PATH" 1>&2 && exit 1; } hash fastq-dump || { echo "fastq-dump required in PATH" && exit 1; } cd samples/yeast && ../../bin/cross-mates -s -t 4 -i 500,2000,5000,10000 S228c.fa CLIB324.fq [18:30:39] bwa .. ok [18:30:39] samtools .. ok [18:30:39] bcftools .. ok [18:30:39] vcfutils.pl .. ok [18:30:39] seq-frag .. ok [18:30:39] interleaved-split .. ok [bwa_index] Pack FASTA... 0.14 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 7.06 seconds elapse. [bwa_index] Update BWT... 0.09 sec [bwa_index] Pack forward-only FASTA... 0.07 sec [bwa_index] Construct SA from BWT and Occ... 2.26 sec [main] Version: 0.7.17-r1198-dirty [main] CMD: bwa index S228c.fa [main] Real time: 12.414 sec; CPU: 9.628 sec [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 396040 sequences (40000040 bp)... [M::process] read 396040 sequences (40000040 bp)... [M::mem_process_seqs] Processed 396040 reads in 36.060 CPU sec, 8.922 real sec [M::mem_process_seqs] Processed 396040 reads in 36.115 CPU sec, 8.918 real sec [M::process] read 396040 sequences (40000040 bp)... [M::process] read 396040 sequences (40000040 bp)... [M::mem_process_seqs] Processed 396040 reads in 36.844 CPU sec, 9.019 real sec [M::mem_process_seqs] Processed 396040 reads in 37.512 CPU sec, 9.280 real sec [M::process] read 396040 sequences (40000040 bp)... [M::process] read 396040 sequences (40000040 bp)... [M::mem_process_seqs] Processed 396040 reads in 38.666 CPU sec, 9.490 real sec [M::mem_process_seqs] Processed 396040 reads in 36.277 CPU sec, 8.954 real sec [M::process] read 396040 sequences (40000040 bp)... [M::process] read 396040 sequences (40000040 bp)... [M::mem_process_seqs] Processed 396040 reads in 36.093 CPU sec, 8.841 real sec [M::process] read 396040 sequences (40000040 bp)... [M::mem_process_seqs] Processed 396040 reads in 36.962 CPU sec, 9.055 real sec [M::process] read 126279 sequences (12754179 bp)... [M::mem_process_seqs] Processed 396040 reads in 36.274 CPU sec, 8.939 real sec [M::mem_process_seqs] Processed 126279 reads in 11.582 CPU sec, 2.864 real sec [main] Version: 0.7.17-r1198-dirty [main] CMD: bwa mem -t 4 S228c.fa /dev/fd/63 [main] Real time: 100.592 sec; CPU: 344.304 sec [bam_sort_core] merging from 0 files and 4 in-memory blocks... [warning] samtools mpileup option u is functional, but deprecated. Please switch to using bcftools mpileup in future. [mpileup] 1 samples in 1 input files Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid bash -c seq-frag pe -p -s -i 500 -l 100 -c 10 <cross-mates-2019-05-03/target-cns.fq | interleaved-split 1>cross-mates-2019-05-03/CLIB324-pe-500_1.fq 2>cross-mates-2019-05-03/CLIB324-pe-500_2.fq bash -c seq-frag mp -p -s -i 2000 -l 100 -c 10 <cross-mates-2019-05-03/target-cns.fq | interleaved-split 1>cross-mates-2019-05-03/CLIB324-mp-2000_1.fq 2>cross-mates-2019-05-03/CLIB324-mp-2000_2.fq bash -c seq-frag mp -p -s -i 5000 -l 100 -c 10 <cross-mates-2019-05-03/target-cns.fq | interleaved-split 1>cross-mates-2019-05-03/CLIB324-mp-5000_1.fq 2>cross-mates-2019-05-03/CLIB324-mp-5000_2.fq bash -c seq-frag mp -p -s -i 10000 -l 100 -c 10 <cross-mates-2019-05-03/target-cns.fq | interleaved-split 1>cross-mates-2019-05-03/CLIB324-mp-10000_1.fq 2>cross-mates-2019-05-03/CLIB324-mp-10000_2.fq Can't locate Fasta/Parser.pm in @INC (@INC contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /home/amachado/SW/cs-scaffolding/bin//../util//seq-scripts/bin/seq-frag line 8. BEGIN failed--compilation aborted at /home/amachado/SW/cs-scaffolding/bin//../util//seq-scripts/bin/seq-frag line 8. Can't locate Fasta/Parser.pm in @INC (@INC contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /home/amachado/SW/cs-scaffolding/bin//../util//seq-scripts/bin/seq-frag line 8. BEGIN failed--compilation aborted at /home/amachado/SW/cs-scaffolding/bin//../util//seq-scripts/bin/seq-frag line 8. Can't locate Fasta/Parser.pm in @INC (@INC contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /home/amachado/SW/cs-scaffolding/bin//../util//seq-scripts/bin/seq-frag line 8. BEGIN failed--compilation aborted at /home/amachado/SW/cs-scaffolding/bin//../util//seq-scripts/bin/seq-frag line 8. Can't locate Fasta/Parser.pm in @INC (@INC contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /home/amachado/SW/cs-scaffolding/bin//../util//seq-scripts/bin/seq-frag line 8. BEGIN failed--compilation aborted at /home/amachado/SW/cs-scaffolding/bin//../util//seq-scripts/bin/seq-frag line 8. [18:40:59] Generated the following libraries: /home/amachado/SW/cs-scaffolding/samples/yeast/cross-mates-2019-05-03/CLIB324-mp-2000_1.fq /home/amachado/SW/cs-scaffolding/samples/yeast/cross-mates-2019-05-03/CLIB324-mp-2000_2.fq /home/amachado/SW/cs-scaffolding/samples/yeast/cross-mates-2019-05-03/CLIB324-mp-5000_1.fq /home/amachado/SW/cs-scaffolding/samples/yeast/cross-mates-2019-05-03/CLIB324-mp-5000_2.fq /home/amachado/SW/cs-scaffolding/samples/yeast/cross-mates-2019-05-03/CLIB324-mp-10000_1.fq /home/amachado/SW/cs-scaffolding/samples/yeast/cross-mates-2019-05-03/CLIB324-mp-10000_2.fq /home/amachado/SW/cs-scaffolding/samples/yeast/cross-mates-2019-05-03/CLIB324-pe-500_1.fq /home/amachado/SW/cs-scaffolding/samples/yeast/cross-mates-2019-05-03/CLIB324-pe-500_2.fq [18:40:59] Possible SOAP-denovo config for libraries: [LIB] avg_ins=500 reverse_seq=0 asm_flags=2 rank=4 q1=cross-mates-2019-05-03/CLIB324-pe-500_1.fq q2=cross-mates-2019-05-03/CLIB324-pe-500_2.fq [LIB] avg_ins=2000 reverse_seq=1 asm_flags=2 rank=5 q1=cross-mates-2019-05-03/CLIB324-mp-2000_1.fq q2=cross-mates-2019-05-03/CLIB324-mp-2000_2.fq [LIB] avg_ins=5000 reverse_seq=1 asm_flags=2 rank=6 q1=cross-mates-2019-05-03/CLIB324-mp-5000_1.fq q2=cross-mates-2019-05-03/CLIB324-mp-5000_2.fq [LIB] avg_ins=10000 reverse_seq=1 asm_flags=2 rank=7 q1=cross-mates-2019-05-03/CLIB324-mp-10000_1.fq q2=cross-mates-2019-05-03/CLIB324-mp-10000_2.fq

Thank you in advance for all help. André

[thackl]

I'm assuming you did not use make dependencies to install the external programs. That would have also downloaded the perl libraries you are missing. The easiest fix should be to go into you cross-species-scaffolding install directory and run the following lines

mkdir -p lib
cd lib
git clone https://github.com/BioInf-Wuerzburg/perl5lib-Fastq.git Fastq
git clone https://github.com/BioInf-Wuerzburg/perl5lib-Fasta.git Fasta

Let me know if that doesn't work

[AMMMachado]

Hi thackl, During the instalation of software i used the make dependencies instruction.

Now i deleted the folder and applied again the commands that you recommended.

" mkdir -p lib cd lib git clone https://github.com/BioInf-Wuerzburg/perl5lib-Fastq.git Fastq git clone https://github.com/BioInf-Wuerzburg/perl5lib-Fasta.git Fasta " but the error continues to happen.

"Can't locate Fasta/Parser.pm in @INC (@INC contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /home/amachado/SW/cs-scaffolding/bin//../util//seq-scripts/bin/seq-frag line 8. BEGIN failed--compilation aborted at /home/amachado/SW/cs-scaffolding/bin//../util//seq-scripts/bin/seq-frag line 8. Can't locate Fasta/Parser.pm in @INC (@INC contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /home/amachado/SW/cs-scaffolding/bin//../util//seq-scripts/bin/seq-frag line 8. BEGIN failed--compilation aborted at /home/amachado/SW/cs-scaffolding/bin//../util//seq-scripts/bin/seq-frag line 8. Can't locate Fasta/Parser.pm in @INC (@INC contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /home/amachado/SW/cs-scaffolding/bin//../util//seq-scripts/bin/seq-frag line 8. BEGIN failed--compilation aborted at /home/amachado/SW/cs-scaffolding/bin//../util//seq-scripts/bin/seq-frag line 8. Can't locate Fasta/Parser.pm in @INC (@INC contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /home/amachado/SW/cs-scaffolding/bin//../util//seq-scripts/bin/seq-frag line 8. BEGIN failed--compilation aborted at /home/amachado/SW/cs-scaffolding/bin//../util//seq-scripts/bin/seq-frag line 8."

In the basch i have the paths..

export PATH=/home/amachado/SW/cs-scaffolding:/home/amachado/SW/cs-scaffolding/util/bcftools:/home/amachado/SW/cs-scaffolding/util/htslib:/home/amachado/SW/cs-scaffolding/util/samtools:/home/amachado/SW/cs-scaffolding/util/seq-scripts/bin:/home/amachado/SW/cs-scaffolding/util/seqtk:/home/amachado/SW/cs-scaffolding/util/bcftools/misc:/home/amachado/SW/cs-scaffolding/lib

I should include other path's of cs-scaffolding?

Thank you again for all the support. André

[AMMMachado]

Hi again dear thackl, Apparently i solved the problem. I moved the /lib/Fastq and /lib/Fasta folders to /usr/share/perl5 directory. The test, runned without problems and generate all the outputs. Thank you again for all the support. André

[hughcross]

Hello, I am having the same problem. @INC contains the folder with those perl modules (full install done) and still says it is not loaded. I have added to perl5 directories (all listed in @INC), with no success. I also tried changing the use line in the seq-frag script to: use lib '/path/to/lib/fasta/';

Nothing has worked so far. Anything else I can try? Thanks,

Hugh

[thackl]

Hm. I don't really have an idea. This sounds like it's a general perl issue, and how libraries are loaded on your system. I can't think of anything that would make this an issue with my libraries specifically. Can you run the following and send me the output?

find /path/to/where/you/installed/Fasta -name "*.pm"
perl -e 'print @INC; use Fasta::Parser'

[tshori]

The Bash Script is not exporting the env Variable $PERL5LIB If you export it manually, ut fixes it, like so: export PERL5LIB=/path/to/cross-species-scaffolding/lib/Fasta/lib:/path/to/cross-species-scaffolding/lib/Fastq/lib:$PERL5LIB

You can also edit the shell script cross-mates to export that variable every time it run.