aubombarely/Organelle_PBA

erron when Running SSPACE-Long

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sanvva commented

  1. Running assembly (Sprai) (Wed Oct 28 11:56:12 CST 2020)

    2.1- Creating the ec.spec file for Sprai.

    2.2- Creating the pbasm.spec file for Sprai.

    2.3- Running Sprai.

    2.3- Analyzing the results
    Scaffold output file: nymph929_5_Organelle_PBA_5sequel_mt/02_1_result_20201028_115612/CA/9-terminator/asm_CA_01_20201028_130720.scf.fasta

    Assembly Step 1 Results

    • Total scaffolds: 2

    • Total size (bp): 367070

    • Total gaps size (Ns): 0

    • Longest scaffold size (bp): 336728

    • Longest scaffold gap size (Ns): 0

    • Longest scaffold id: scf7180000000018

    • Total assembly ref. fraction: 0.59

    • Longest assembly ref. fraction: 0.55

    • Different in size with ref. (bp): 280467

  2. Running scaffolding (SSPACE) (Wed Oct 28 14:40:12 CST 2020)

    3.1- Running SSPACE-Long

  • EXCEPTION
    MSG: Could not read file 'nymph929_5_Organelle_PBA_5sequel_mt/03_1_organelle_assembly.fasta': No such file or directory
    STACK Bio::Root::IO::_initialize_io /usr/local/share/perl5/Bio/Root/IO.pm:268
    STACK Bio::SeqIO::_initialize /usr/local/share/perl5/Bio/SeqIO.pm:513
    STACK Bio::SeqIO::fasta::_initialize /usr/local/share/perl5/Bio/SeqIO/fasta.pm:87
    STACK Bio::SeqIO::new /usr/local/share/perl5/Bio/SeqIO.pm:389
    STACK Bio::SeqIO::new /usr/local/share/perl5/Bio/SeqIO.pm:435
    STACK main::get_seqstats /ds3200_1/users_root/hezhengshan/bin/Organelle_PBA/OrganelleRef_PBA:2169
    STACK toplevel /ds3200_1/users_root/hezhengshan/bin/Organelle_PBA/OrganelleRef_PBA:1061

Files In the output directory
-rw-r--r-- 1 19G Oct 28 11:14 01_1_BlasR_in.fasta
-rw-r--r-- 1 12M Oct 28 11:52 01_2_BlasR_out.txt
-rw-r--r-- 1 2.0M Oct 28 11:52 01_3_BlasR_hit_ids.txt
-rw-r--r-- 1 679M Oct 28 11:56 02_0_Sprai_in.fastq
-rw-r--r-- 1 423 Oct 28 11:56 02_1_Sprai_ec.spec
-rw-r--r-- 1 947 Oct 28 11:56 02_1_Sprai_pbasm.spec
-rw-r--r-- 1 1.8K Oct 28 13:07 02_1_Sprai_log.txt
drwxr-xr-x 4 98 Oct 28 13:07 02_1_result_20201028_115612
-rw-r--r-- 1 364K Oct 28 14:40 02_3_organelle_assembly01.fasta
drwxr-xr-x 3 96 Oct 28 14:40 03_1_sspacelong_out

There is no 03_1_organelle_assembly.fasta, only 02_3_organelle_assembly01.fasta.

HELP!