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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
    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'


    -- Trans-ABySS --

    -- 1

    Because the $ 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.


    -- 2

    The setup file was set as follow


    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

    And this is the output of sh <TA_DIR>/

    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/
    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/
    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] LIB PATH -g GENOME
    blat: TARGET QUERY OUTPUT.psl -repMatch=1024 -minScore=0 -minIdentity=90 CONFIG_FILE -a blat -n LIB-TYPE -f CONTIGS -t GENOME -o OUT_DIR -s -b -q 1000 -c CLUSTER -m MEM BLAT_DIR blat -n 1 -u -m 90 -d -k TRACK_NAME -o PSL -f CONTIGS -g GENOME 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 -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 TRACK GENOME -l -d -o OUTDIR -f PATH/merge/LIB-contigs.fa -r -C PATH/reads_to_contigs/LIB-contigs.bam COVERAGE R2C TRACK OUTPUT CLUSTER MQSUB CLUSTERDIR JOB NAME MEM all.q EMAIL CONTIGS READSLIST -p LIB -P PROJECT -o PATH/reads_to_contigs -t 8 -x
    num_reads_per_fastq: NA

    fem: 2.5G
    xa2multi: 8G 5G 15G 6G 5G 5G 5G 5G
    snv_caller.py_filter: 10G 6G 1G
    blat: 5G
    convert_reads: 3.8G
    r2c_index: 4G
    r2c_aln: 2G
    r2c_sam: 10G
    r2c_merge: 4G

    hg19: /path/to/your/hg19/fasta_file/here

    contact: [email protected]

    topdir: /home/outputs/PP_M_Gonad/trans-abyss
    reference: none

    -- 4


    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

    ./ -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


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