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  • Stage 0 - cannot find topdir under project

    Hi everyone,

    I'm trying to locally run stage 0 of Trans-ABySS version_1.3.5, but when I try to run the programme it shows me the following:


    input: /home/programas/trans-abyss/trans-ABySS-v1.3.5/input/input_transAbyss_2012_10_02.txt
    /home/programas/trans-abyss/trans-ABySS-v1.3.5/wrappers
    cannot find topdir under project transAbyss_2012_10_02


    I already read other similar topics in this forum, but it seems that I got everything right until now, meaning I cannot find the source of the problem. Can you tell me if there's something missing or if I'm doing something wrong.

    Here's what I did:


    -- ABySS running --

    I ran successfully the ABySS as follow:

    export k

    for k in {45,49,53,57,61,65,69,73,77,81,85,89}; do

    mkdir k$k

    /home/programas/abyss/abyss_installation/bin/abyss-pe j=12 -C k$k name=PP_F_Brain in='/home/outputs/PP_F_Brain/prinseq/PP_F_Brain_L1_1_file_passed.fastq /home/outputs/PP_F_Brain/prinseq/PP_F_Brain_L1_2_file_passed.fastq ' OVERLAP_OPTIONS='--no-scaffold' SIMPLEGRAPH_OPTIONS='--no-scaffold'

    done


    -- Trans-ABySS --


    -- 1

    Because the $name.in file was not necessary to run ABySS and was not outputted by it, I created it myself as suggested in Trans-ABySS manual and placed it into the directory containing the library's multi-k-mer assemblies. Anyway, this problem appeared with and without this file.

    PP_F_Brain.in

    /home/outputs/PP_F_Brain/prinseq/PP_F_Brain_L1_1_file_passed.fastq
    /home/outputs/PP_F_Brain/prinseq/PP_F_Brain_L1_2_file_passed.fastq


    -- 2

    The setup file was set as follow

    <TA>/setup

    export TRANSABYSS_VERSION=1.3.5
    export TRANSABYSS_PATH=/home/programas/trans-abyss/trans-ABySS-v1.3.5
    export PERL5LIB=$TRANSABYSS_PATH/wrappers:$PERL5LIB:/usr/lib64/perl5
    export PYTHONPATH=/usr/local/bin/python:$PYTHONPATH:$TRANSABYSS_PATH
    export ABYSSPATH=/home/FC/jgpinho/programas/abyss/abyss_installation/bin
    export LD_LIBRARY_PATH="/lib:/usr/lib":$LD_LIBRARY_PATH
    export PATH=$TRANSABYSS_PATH/bin:$ABYSSPATH:$LD_LIBRARY_PATH:$PYTHONPATH:$PATH

    And this is the output of sh <TA_DIR>/check-prereq.sh


    ABYSS and related....................
    abyss-pe: /home/programas/abyss/abyss_installation/bin/abyss-pe
    abyss-index: /home/programas/abyss/abyss_installation/bin/abyss-index
    abyss-map: /home/programas/abyss/abyss_installation/bin/abyss-map
    abyss-filtergraph: /home/programas/trans-abyss/trans-ABySS-v1.3.5/bin/abyss-filtergraph
    abyss-junction: /home/programas/trans-abyss/trans-ABySS-v1.3.5/bin/abyss-junction
    MergeContigs: /home/programas/abyss/abyss_installation/bin/MergeContigs

    Alignment and related................
    blat: N/A
    bowtie: N/A
    bwa: N/A
    xa2multi: /usr/local/bin/xa2multi.pl
    samtools: N/A
    pysam: N/A

    Trans-ABySS wrappers and related.....
    perl: /usr/bin/perl
    python: /usr/local/bin/python
    trans-abyss: /home/programas/trans-abyss/trans-ABySS-v1.3.5/wrappers/trans-abyss.sh
    mqsub: /home/programas/trans-abyss/trans-ABySS-v1.3.5/bin/mqsub
    qsub: N/A



    -- 3

    To configure the <TA>/configs/transcriptome.cfg file, just the project part was modified:


    [commands]
    copy_bam.py: LIB PATH -g GENOME
    blat: TARGET QUERY OUTPUT.psl -repMatch=1024 -minScore=0 -minIdentity=90
    cluster_align.py: CONFIG_FILE -a blat -n LIB-TYPE -f CONTIGS -t GENOME -o OUT_DIR -s -b -q 1000 -c CLUSTER -m MEM
    align_parser.py: BLAT_DIR blat -n 1 -u -m 90 -d -k TRACK_NAME -o PSL -f CONTIGS -g GENOME
    fusion.py: INPUT PATH/fusions -B TOPDIR/LIB/Reads_to_genome/GENOME_BAM -b PATH/reads_to_contigs/LIB-contigs.bam -G GENOME k -k apollo
    fusion.py_filter: PATH/fusions/cluster PATH/fusions -X -F
    snv_caller.py: -a ALIGNS -c CONTIGS -g GENOME -o PATH/snv -m k -C PATH/reads_to_contigs/LIB-contigs.bam -k apollo -O -A -VL
    snv_caller.py_filter: -f PATH/snv/cluster -o PATH/snv -X
    model_matcher.py: TRACK GENOME -l -d -o OUTDIR -f PATH/merge/LIB-contigs.fa -r -C PATH/reads_to_contigs/LIB-contigs.bam
    gene_coverage.py: COVERAGE R2C TRACK OUTPUT
    submitjobs.sh: CLUSTER MQSUB CLUSTERDIR JOB NAME MEM all.q EMAIL
    ta-r2c.py: CONTIGS READSLIST -p LIB -P PROJECT -o PATH/reads_to_contigs -t 8 -x
    convert_reads: ta-qseq2fastq.py
    num_reads_per_fastq: NA

    [memory]
    fem: 2.5G
    xa2multi: 8G
    fusion.py: 5G
    model_matcher.py: 15G
    reads_to_contigs.py: 6G
    align_parser.py: 5G
    cluster_align.py: 5G
    gene_coverage.py: 5G
    snv_caller.py: 5G
    snv_caller.py_filter: 10G
    anchor_pipeline.py: 6G
    copy_bam.py: 1G
    blat: 5G
    convert_reads: 3.8G
    r2c_index: 4G
    r2c_aln: 2G
    r2c_sam: 10G
    r2c_merge: 4G

    [genomes]
    hg19: /path/to/your/hg19/fasta_file/here

    [contact]
    contact: [email protected]

    [transAbyss_2012_10_02]
    topdir: /home/outputs/PP_M_Gonad/trans-abyss
    reference: none


    -- 4

    <TA>/input/input_file


    Created the file input_transAbyss_2012_10_02.txt with


    PP_F_Brain 1.3.4 /home/outputs/PP_F_Brain/PP_F_Brain transAbyss_2012_10_02


    -- 5

    Trans-ABySS was ran locally with the following command

    ./trans-abyss.sh -n 1 -e [email protected] -i /home/programas/trans-abyss/trans-ABySS-v1.3.5/input/input_transAbyss_2012_10_02.txt -0


    Moreover, I didn´t set the anchor since I only want to produce transcripts sequences and it won't be run in clusters.


    I really hope you could help

    Best regards

    Joana

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