Issue while running test run

[amit4mchiba]

Hi,

I am writing here to seek your help in using this tool. After installing all its dependencies, I started running test run, but seems not working. Here is what I did-
amit8chiba@amit8chiba-Precision-Tower-7910:/mnt/HD1/Organelle_PBA/testdata/artha_chl$ ../../OrganelleRef_PBA -i artha_pacbioSRR1284093_c025k.fastq -r artha_refchl01_artha.fa -o artha_chl

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OrganelleRef_PBA Starts (2018年 9月 8日 土曜日 01:53:36 JST)

############################################################

============================================================
0) Checking arguments (2018年 9月 8日 土曜日 01:53:36 JST)

    Input PacBio reads file: artha_pacbioSRR1284093_c025k.fastq
    Input type: fastq
    Output directory: artha_chl
    Organelle reference fasta file: artha_refchl01_artha.fa
            Organelle reference size: 154478 bp
            Repeat block size coverage detection: 1000
            Coverage ratio to define repeatitive region: 1.6
    Completeness fraction: 1.0
    Breaks overlap: 0
    Highest position to set up origin: 1
    Starting-End margin to check circularity: 10
    Overlap length to check circularity: 100
    Minimum BlasR alignment percentage: 5

    bedtools is available in the PATH (/mnt/md0/HiC_analysis_and_tools/bedtools2/bin/bedtools)
    blasr is available in the PATH (/mnt/HD1/pacbio/smrtlink/smrtcmds/bin/blasr)
    blastn is available in the PATH (/mnt/HD1/Organelle_PBA/build_dependensies/ncbi-blast-2.7.1+/bin/blastn)
    makeblastdb is available in the PATH (/mnt/HD1/Organelle_PBA/build_dependensies/ncbi-blast-2.7.1+/bin/makeblastdb)
    runCA is available in the PATH (/mnt/HD1/Organelle_PBA/build_dependensies/wgs-8.3rc2/Linux-amd64/bin/runCA)
    pacBioToCA is available in the PATH (/mnt/HD1/Organelle_PBA/build_dependensies/wgs-8.3rc2/Linux-amd64/bin/pacBioToCA)
    PBcR is available in the PATH (/mnt/HD1/Organelle_PBA/build_dependensies/wgs-8.3rc2/Linux-amd64/bin/PBcR)
    samtools is available in the PATH (/mnt/HD1/pacbio/smrtlink/smrtcmds/bin/samtools)
    ezez_vx1.pl is available in the PATH (/mnt/HD1/Organelle_PBA/build_dependensies/sprai/bin/ezez_vx1.pl)
    ezez4qsub_vx1.pl is available in the PATH (/mnt/HD1/Organelle_PBA/build_dependensies/sprai/bin/ezez4qsub_vx1.pl)
    bfmt72s is available in the PATH (/mnt/HD1/Organelle_PBA/build_dependensies/sprai/bin/bfmt72s)
    m52bfmt7 is available in the PATH (/mnt/HD1/Organelle_PBA/build_dependensies/sprai/bin/m52bfmt7)
    myrealigner is available in the PATH (/mnt/HD1/Organelle_PBA/build_dependensies/sprai/bin/myrealigner)
    nss2v_v3 is available in the PATH (/mnt/HD1/Organelle_PBA/build_dependensies/sprai/bin/nss2v_v3)
    fa2fq.pl is available in the PATH (/mnt/HD1/Organelle_PBA/build_dependensies/sprai/bin/fa2fq.pl)
    check_circularity.pl is available in the PATH (/mnt/HD1/Organelle_PBA/build_dependensies/sprai/bin/check_circularity.pl)
    dfq2fq_v2.pl is available in the PATH (/mnt/HD1/Organelle_PBA/build_dependensies/sprai/bin/dfq2fq_v2.pl)
    SSPACE-LongRead.pl is available in the PATH (/mnt/HD1/Organelle_PBA/build_dependensies/SSPACE-LongRead_v1-1/SSPACE-LongRead.pl)

============================================================

1. Running BlasR (2018年 9月 8日 土曜日 01:53:36 JST)
   ============================================================

   1.1- Converting Fastq to Fasta.
         Using Seqtk to convert Fastq to Fasta.
        Input PacBio read file contains 24903 reads
   
   1.2- Running BlasR mapping.
   
   1.3- Processing the BlasR output.
         1263 reads (13909469 bp) will be selected
         Estimated depth (reference based): 90 X.
   
   1.4- Selecting reads from the fastq file
         Using Seqtk to select reads from fastq.
   

============================================================
2) Running assembly (Sprai) (2018年 9月 8日 土曜日 02:03:33 JST)

    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

ERROR: Sprai/CA didnt produced an output 9-terminator. Check log.

Log is as follows-
#>- params -<#
input_for_database artha_chl/02_0_Sprai_in.fastq
estimated_genome_size 308956
estimated_depth 90
partition 12
evalue 1e-50
num_threads 2
valid_voters 30
trim 42
use_one_subread 0
ca_path /mnt/HD1/Organelle_PBA/build_dependensies/wgs-8.3rc2/Linux-amd64/bin/
sprai_path /mnt/HD1/Organelle_PBA/build_dependensies/sprai/bin/
blast_path /mnt/HD1/Organelle_PBA/build_dependensies/ncbi-blast-2.7.1+/bin/
word_size 18
min_len_for_query 1000
max_len_for_query 1000000000000000
max_target_seqs 100
#>- params -<#
sh: 1: set: Illegal option -o pipefail
Redundant argument in sprintf at /mnt/HD1/Organelle_PBA/build_dependensies/sprai/bin/ezez_vx1.pl line 341.
sh: 1: set: Illegal option -o pipefail
sh: 1: set: Illegal option -o pipefail
sh: 1: set: Illegal option -o pipefail
sh: 1: set: Illegal option -o pipefail
cat: /mnt/HD1/Organelle_PBA/testdata/artha_chl/result_20180908_020333//tmp//c00.refined_0000.fin.idfq.gz: No such file or directory
cat: /mnt/HD1/Organelle_PBA/testdata/artha_chl/result_20180908_020333//tmp//c00.refined_0001.fin.idfq.gz: No such file or directory
cat: /mnt/HD1/Organelle_PBA/testdata/artha_chl/result_20180908_020333//tmp//c00.refined_0002.fin.idfq.gz: No such file or directory
cat: /mnt/HD1/Organelle_PBA/testdata/artha_chl/result_20180908_020333//tmp//c00.refined_0003.fin.idfq.gz: No such file or directory
cat: /mnt/HD1/Organelle_PBA/testdata/artha_chl/result_20180908_020333//tmp//c00.refined_0004.fin.idfq.gz: No such file or directory
cat: /mnt/HD1/Organelle_PBA/testdata/artha_chl/result_20180908_020333//tmp//c00.refined_0005.fin.idfq.gz: No such file or directory
cat: /mnt/HD1/Organelle_PBA/testdata/artha_chl/result_20180908_020333//tmp//c00.refined_0006.fin.idfq.gz: No such file or directory
cat: /mnt/HD1/Organelle_PBA/testdata/artha_chl/result_20180908_020333//tmp//c00.refined_0007.fin.idfq.gz: No such file or directory
cat: /mnt/HD1/Organelle_PBA/testdata/artha_chl/result_20180908_020333//tmp//c00.refined_0008.fin.idfq.gz: No such file or directory
cat: /mnt/HD1/Organelle_PBA/testdata/artha_chl/result_20180908_020333//tmp//c00.refined_0009.fin.idfq.gz: No such file or directory
cat: /mnt/HD1/Organelle_PBA/testdata/artha_chl/result_20180908_020333//tmp//c00.refined_0010.fin.idfq.gz: No such file or directory
cat: /mnt/HD1/Organelle_PBA/testdata/artha_chl/result_20180908_020333//tmp//c00.refined_0011.fin.idfq.gz: No such file or directory
gzip: /mnt/HD1/Organelle_PBA/testdata/artha_chl/result_20180908_020333//c01.fin.idfq.gz: No such file or directory
Command exited with non-zero status 1
0.00user 0.00system 0:00.00elapsed ?%CPU (0avgtext+0avgdata 1680maxresident)k
0inputs+0outputs (0major+78minor)pagefaults 0swaps

Then I checked sprai-run results, and here is details of error-
----------------------------------------START Sat Sep 8 02:03:34 2018
/mnt/HD1/Organelle_PBA/build_dependensies/wgs-8.3rc2/Linux-amd64/bin/gatekeeper -o /mnt/HD1/Organelle_PBA/testdata/artha_chl/result_20180908_020333//CA/asm_CA_01_20180908_020334.gkpStore.BUILDING -T -F /mnt/HD1/Organelle_PBA/testdata/artha_chl/result_20180908_020333//CA/c01.fin.top20x.frg > /mnt/HD1/Organelle_PBA/testdata/artha_chl/result_20180908_020333//CA/asm_CA_01_20180908_020334.gkpStore.err 2>&1
----------------------------------------END Sat Sep 8 02:03:34 2018 (0 seconds)
ERROR: Failed with signal ABRT (6)

runCA failed.

---

Stack trace:

at /mnt/HD1/Organelle_PBA/build_dependensies/wgs-8.3rc2/Linux-amd64/bin//runCA line 1628.
main::caFailure("gatekeeper failed", "/mnt/HD1/Organelle_PBA/testdata/artha_chl/result_20180908_020"...) called at /mnt/HD1/Organelle_PBA/build_dependensies/wgs-8.3rc2/Linux-amd64/bin//runCA line 1957
main::preoverlap("/mnt/HD1/Organelle_PBA/testdata/artha_chl/result_20180908_020"...) called at /mnt/HD1/Organelle_PBA/build_dependensies/wgs-8.3rc2/Linux-amd64/bin//runCA line 6250

---

Last few lines of the relevant log file (/mnt/HD1/Organelle_PBA/testdata/artha_chl/result_20180908_020333//CA/asm_CA_01_20180908_020334.gkpStore.err):

---

Failure message:

gatekeeper failed

When I checked logfile for CA run, here is what I have got-
CA version 8.3rc2 ($Id: AS_GKP_main.C 4640 2015-04-21 00:12:47Z brianwalenz $).

Error Rates:
AS_OVL_ERROR_RATE 0.015000
AS_CNS_ERROR_RATE 0.250000
AS_CGW_ERROR_RATE 0.250000
AS_MAX_ERROR_RATE 0.400000

Current Working Directory:
/mnt/HD1/Organelle_PBA/testdata/artha_chl/result_20180908_020333/CA

Command:
/mnt/HD1/Organelle_PBA/build_dependensies/wgs-8.3rc2/Linux-amd64/bin/gatekeeper
-o /mnt/HD1/Organelle_PBA/testdata/artha_chl/result_20180908_020333//CA/asm_CA_01_20180908_020334.gkpStore.BUILDING
-T
-F /mnt/HD1/Organelle_PBA/testdata/artha_chl/result_20180908_020333//CA/c01.fin.top20x.frg

I am not able to figure out what really is the main problem here. Please help me. I think I have installed all correct dependensies, and all the versions as said or suggested. For Sprai, I am using sprai-0.9.9.23.

Please let me know if you need any further information to advise me.

Thanks in Advance,

with best regards
Amit