Segmentation fault (core dumped) on /makeSummaryTables.sh

[Леонид Солнцев]

CALRK 1.2.5.1

Linux srv-lab 4.15.0-39-generic #42~16.04.1-Ubuntu SMP Wed Oct 24 17:09:54 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

www_adm@srv-lab:~/metagen/CLARKSCV1.2.5.1$  ./makeSummaryTables.sh 10 1 /home/www_adm/metagen/2018/00_CLARK/26_S4_PAIRED_ORIG_ABUNDANCE.csv /home/www_adm/metagen/2018/00_CLARK/27_S5_PAIRED_ORIG_ABUNDANCE.csv

Segmentation fault (core dumped)

from journalctl

srv-lab kernel: makeSummaryTabl[28120]: segfault at 8 ip 00007f5681ca336e sp 00007ffc4f5b6330 error 4 in libstdc++.so.6.0.21[7f5681b84000+172000]

https://yadi.sk/d/pQ14MklHHmkMFQ for CSV reports

produced by

ID1=['S1','S2','S3','S4','S1','S2','S3','S4','S5','S5']

ID2=['2','3','4','6','7','8','9','26','27','42']

BASE_PATH='/home/www_adm/metagen/2018/'

RESULT_DIR_NAME='00_CLARK/'

shutil.rmtree(BASE_PATH+RESULT_DIR_NAME, ignore_errors=True)

os.mkdir(BASE_PATH+RESULT_DIR_NAME)

for AA,BB in zip (ID1,ID2):

    F1='/home/www_adm/UPLOAD/2018/src/'+BB+'_'+AA+'_L001_R1_001.fastq'

    F2='/home/www_adm/UPLOAD/2018/src/'+BB+'_'+AA+'_L001_R2_001.fastq'

    FF_OUT=BASE_PATH+RESULT_DIR_NAME + BB + '_' + AA + '_PAIRED_ORIG_RAW'

    FF_EST_OUTPUT=BASE_PATH+RESULT_DIR_NAME + BB + '_' + AA + '_PAIRED_ORIG_ABUNDANCE' 

    os.chdir('/home/www_adm/metagen/CLARKSCV1.2.5.1/')

    

    cmd_set='./set_targets.sh DBDT bacteria viruses'     

    cmd_class_cnt='./classify_metagenome.sh -k 20 -P ' + F1 + ' ' + F2 + ' -R ' + FF_OUT + ' -m 0 -n 24 --extended'

    cmd_est_cnt='./estimate_abundance.sh -F '+ FF_OUT + '.csv -D DBDT --krona --highconfidence > ' + FF_EST_OUTPUT + '.csv'

    cmd_krona_cnt='ktImportTaxonomy -o ' + BASE_PATH+RESULT_DIR_NAME + BB + '_' + AA + '_PAIRED_ORIG_KRONA.html /home/www_adm/metagen/CLARKSCV1.2.5.1/results.krn'

    

    subprocess.check_call(cmd_set,shell=True)

    subprocess.check_call(cmd_class_cnt,shell=True)

    subprocess.check_call(cmd_est_cnt,shell=True)

    subprocess.check_call(cmd_krona_cnt,shell=True)

[Леонид Солнцев]

libstdc++6  (5.4.0-6ubuntu1~16.04.11).