How to fix "Please indicate the file directory in 'setting' file?" for MaxBin2?

Question

[O.rka]

I can't figure out why this is happening. I'm running the same command for all of my samples but I'm only getting the error on some. I've even found the setting file and put the directories for the programs it's complaining about.

What could be the issue here?

Here's my script:

IDENTIFIERS=$(python -c "import os; print(*set(map(lambda x: x.split('_RD1')[0], os.listdir('./Fastq'))))")
N_JOBS=4

for ID in $IDENTIFIERS;
    do CONTIGS=assembly_output/${ID}/scaffolds.gt1000.fasta;
    COV=./mapping_output/${ID}.coverage.maxbin2.tsv;
    OUT=maxbin2_output/${ID}
    mkdir -p ${OUT}
    qsub -pe threaded ${N_JOBS} -l centos7 -cwd -P 0714 -N maxbin2_${ID} -o logs/${ID}__maxbin2.o -e logs/${ID}__maxbin2.e "source activate binning_env && run_MaxBin.pl -abund ${COV} -contig ${CONTIGS} -markerset 107 -out ${OUT}/bin -thread ${N_JOBS}"
        #run_MaxBin.pl -abund ${COV} -contig ${CONTIGS} -markerset 107 -out ${OUT}/bin -thread ${N_JOBS};
    done

Here's an example of some of the errors:

for FP in  logs/*maxbin2.e ; do echo $FP; cat $FP; echo " "; done | less

logs/1059.1__maxbin2.o
MaxBin 2.2.7
Located abundance file [./mapping_output/1059.1.coverage.maxbin2.tsv]
Input contig: assembly_output/1059.1/scaffolds.gt1000.fasta
out header: maxbin2_output/1059.1/bin
Thread: 4
Searching against 107 marker genes to find starting seed contigs for [assembly_output/1059.1/scaffolds.gt1000.fasta]...
Running FragGeneScan....
Running HMMER hmmsearch....
Done data collection. Running MaxBin...
Command: /local/ifs2_devel/ANNOTATION/jespinoz/anaconda3/envs/binning_env/opt/MaxBin-2.2.7/src/MaxBin -fasta maxbin2_output/1059.1/bin.contig.tmp  -abund maxbin2_output/1059.1/bin.contig.tmp.abund1 -seed maxbin2_output/1059.1/bin.seed -out maxbin2_output/1059.1/bin -min_contig_length 1000 -thread 4

logs/1059.2__maxbin2.o
Cannot run Bowtie2. Please indicate the file directory in 'setting' file.

logs/1082.1__maxbin2.o
Cannot run Bowtie2. Please indicate the file directory in 'setting' file.

logs/1082.2__maxbin2.o
Cannot run FragGeneScan. Please indicate the file directory in 'setting' file.

logs/1086.1__maxbin2.o
Cannot run FragGeneScan. Please indicate the file directory in 'setting' file.

logs/1086.2__maxbin2.o
Cannot run Bowtie2. Please indicate the file directory in 'setting' file.

[serene.s]

Did you solve the above error? I am also getting the same error while using MaxBin2 script run_MaxBin.pl. Please respond if you were able to run it properly?

Thanks

[Sunguk]

Cannot run FragGeneScan. Please indicate the file directory in 'setting' file.

I only got above error mesages about FragGeneScan. I did chmod 755 "all files" in FragGeneScan folder. I just fixed it and didn't check the result. But it will work, probably. run_MaxBin.pl requires not only main FragGeneScan but also run_FragGeneScan.pl or others.

Answer 1

[Charlie]

Just ran into the same issue when installing MaxBin2 with the tarball. Looking into the setting file, I think I found the issue:

[FragGeneScan] /home/yuwwu/work/MaxBin/auxiliary/FragGeneScan1.30
[Bowtie2] /home/yuwwu/work/MaxBin/auxiliary/bowtie2-2.2.3
[HMMER3] /home/yuwwu/work/MaxBin/auxiliary/hmmer-3.1b1/src

These paths need to be updated to point to the programs wherever you have them installed