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.