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  • What is the specific syntax needed for Trans-ABySS to analyze both SE and PE files?

    I have been trying for days to get Trans-ABySS to run a set of paired-end and single-end fastq files. The paired in data is stored in two files, one with the forward reads and the other with the reverse reads. There are also two single-end files, one for the reverse reads and one for the forward reads. All four files were generated using Trimmomatic to filter the original, raw Illumina fastq files to remove low-quality reads.

    Despite numerous reading the tutorial several times and trying many permutations of my input code, I keep getting the following error:
    Trans-ABySS 1.5.1
    CMD: /usr/local/trans-ABySS-1.5.1/transabyss --se /home/gwilymh/data/transabyss_test/SRR573708_Unpaired_1.fq /home/gwilymh/data/transabyss_test/SRR573708_Unpaired_2.fq /home/gwilymh/data/transabyss_test/SRR573708_Paired_1.fq /home/gwilymh/data/transabyss_test/SRR573708_Paired_2.fq --pe /home/gwilymh/data/transabyss_test/SRR573708_Paired_1.fq /home/gwilymh/data/transabyss_test/SRR573708_Paired_2.fq --name SRR573708 --outdir /home/gwilymh/data/transabyss_test/SRR573708 --kmer 64 --length 200 --threads 4 --qends 20
    =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
    # CPU(s) available: 24
    # thread(s) requested: 4
    # thread(s) to use: 4
    CMD: abyss-pe --directory=/home/gwilymh/data/transabyss_test/SRR573708 k=64 name=SRR573708 E=0 e=2 c=2 j=4 SRR573708-1.fa SRR573708-1.adj q=20 se="/home/gwilymh/data/transabyss_test/SRR573708_Paired_1.fq /home/gwilymh/data/transabyss_test/SRR573708_Paired_2.fq /home/gwilymh/data/transabyss_test/SRR573708_Unpaired_1.fq /home/gwilymh/data/transabyss_test/SRR573708_Unpaired_2.fq /home/gwilymh/data/transabyss_test/SRR573708_Paired_1.fq /home/gwilymh/data/transabyss_test/SRR573708_Paired_2.fq"
    /bin/sh: abyss-pe: command not found
    ERROR: CMD ended with status code 127


    My last input code was:
    module load abyss
    module load trans-ABySS/1.5.1
    SAMPLE=SRR573708
    WORKING_DIR="${HOME}/data/transabyss_test/${SAMPLE}"
    FORWARD_PE="${HOME}/data/transabyss_test/${SAMPLE}_Paired_1.fq"
    REVERSE_PE="${HOME}/data/transabyss_test/${SAMPLE}_Paired_2.fq"
    FORWARD_SE="${HOME}/data/transabyss_test/${SAMPLE}_Unpaired_1.fq"
    REVERSE_SE="${HOME}/data/transabyss_test/${SAMPLE}_Unpaired_2.fq"
    cd $WORKING_DIR

    transabyss --se "${FORWARD_SE}" "${REVERSE_SE}" "${FORWARD_PE}" "${REVERSE_PE}" \
    --pe "${FORWARD_PE}" "${REVERSE_PE}" \
    --name "${SAMPLE}" --outdir "${WORKING_DIR}" \
    --kmer 64 --length 200 --threads 4 --qends 20


    I would very much appreciate any insights into why my code is failing to execute Trans-ABySS successfully.

  • #2
    The following code worked. I dropped the unpaired reads.

    transabyss --se $INPUT_F $INPUT_R --pe $INPUT_F $INPUT_R --outdir $WORKING_DIR --name $OUTPUT_FILE --threads 10 --mpi 10 --indel 4

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