aubombarely/Organelle_PBA

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

sanvva opened this issue · 3 comments

sanvva commented

$ OrganelleRef_PBA -i artha_pacbioSRR1284093_c025k.fastq -r artha_refchl01_artha.fa -o artha_chl

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OrganelleRef_PBA Starts (Mon Apr 16 11:18:32 CST 2018)

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0) Checking arguments (Mon Apr 16 11:18:32 CST 2018)

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 (/usr/bin/bedtools)
blasr is available in the PATH (/usr/bin/blasr)
blastn is available in the PATH (/home/hzs/bin/ncbi-blast-2.7.1+/bin/blastn)
makeblastdb is available in the PATH (/home/hzs/bin/ncbi-blast-2.7.1+/bin/makeblastdb)
runCA is available in the PATH (/home/hzs/bin/wgs/Linux-amd64/bin/runCA)
pacBioToCA is available in the PATH (/home/hzs/bin/wgs/Linux-amd64/bin/pacBioToCA)
PBcR is available in the PATH (/home/hzs/bin/wgs/Linux-amd64/bin/PBcR)
samtools is available in the PATH (/usr/bin/samtools)
ezez_vx1.pl is available in the PATH (/home/hzs/bin/sprai/bin/ezez_vx1.pl)
ezez4qsub_vx1.pl is available in the PATH (/home/hzs/bin/sprai/bin/ezez4qsub_vx1.pl)
bfmt72s is available in the PATH (/home/hzs/bin/sprai/bin/bfmt72s)
m52bfmt7 is available in the PATH (/home/hzs/bin/sprai/bin/m52bfmt7)
myrealigner is available in the PATH (/home/hzs/bin/sprai/bin/myrealigner)
nss2v_v3 is available in the PATH (/home/hzs/bin/sprai/bin/nss2v_v3)
fa2fq.pl is available in the PATH (/home/hzs/bin/sprai/bin/fa2fq.pl)
check_circularity.pl is available in the PATH (/home/hzs/bin/sprai/bin/check_circularity.pl)
dfq2fq_v2.pl is available in the PATH (/home/hzs/bin/sprai/bin/dfq2fq_v2.pl)
SSPACE-LongRead.pl is available in the PATH (/home/hzs/bin/SSPACE-LongRead_v1-1/SSPACE-LongRead.pl)

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  1. Running BlasR (Mon Apr 16 11:18:33 CST 2018)
    ============================================================

    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) (Mon Apr 16 11:28:07 CST 2018)

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.

sanvva commented

----------------------------------------START Mon Apr 16 11:28:07 2018
/home/hzs/bin/wgs/Linux-amd64/bin/gatekeeper -o /home/hzs/bin/Organelle_PBA/testdata/artha_chl/result_20180416_112807//CA/asm_CA_01_20180416_112807.gkpStore.BUILDING -T -F /home/hzs/bin/Organelle_PBA/testdata/artha_chl/result_20180416_112807//CA/c01.fin.top20x.frg > /home/hzs/bin/Organelle_PBA/testdata/artha_chl/result_20180416_112807//CA/asm_CA_01_20180416_112807.gkpStore.err 2>&1
----------------------------------------END Mon Apr 16 11:28:08 2018 (1 seconds)
ERROR: Failed with signal ABRT (6)

runCA failed.

Stack trace:

at /home/hzs/bin/wgs/Linux-amd64/bin//runCA line 1628.
main::caFailure("gatekeeper failed", "/home/hzs/bin/Organelle_PBA/testdata/artha_chl/result_2018041"...) called at /home/hzs/bin/wgs/Linux-amd64/bin//runCA line 1957
main::preoverlap("/home/hzs/bin/Organelle_PBA/testdata/artha_chl/result_2018041"...) called at /home/hzs/bin/wgs/Linux-amd64/bin//runCA line 6250

Last few lines of the relevant log file (/home/hzs/bin/Organelle_PBA/testdata/artha_chl/result_20180416_112807//CA/asm_CA_01_20180416_112807.gkpStore.err):

Failure message:

gatekeeper failed

amit4mchiba commented

Hi Sanvva,

Did you got solution for the problem that you metioned. I have got same problem and not being able to solve. Please let me know things that you tried and things that helped you to make it work.

best regards
Amit

sanvva commented

@amit4mchiba Sorry, I got help from our serve administrator to install the software on the HPC instead of on my desktop PC. I don't know how he worked it out.