build database

[Alice-yyt]

Hi Jason, I am sorry to bother you. When I run the ./GT_Pro build --in test/build.list --out ./test/my_db --dbname tri_db --threads 4, I got following errors. Do you know why I got those errors? Thank you for time!

[zjshi]

Hi Alice-yyt, sorry for my late response. Would you please paste here the content of one of the log files, e.g. ./test/my_db/temp/ss_kmers/100001.ss.hq.log?

[Alice-yyt]

Hi Alice-yyt, sorry for my late response. Would you please paste here the content of one of the log files, e.g. ./test/my_db/temp/ss_kmers/100001.ss.hq.log?

Hi Jason, thank you for your reply! Following are the contents in 100001.ss.hq.log: db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0196 Encrypted checksum: no encryption key specified db_dump: BDB0210 ./test/my_db/temp/ss_kmers/100001.ss.hq.bin: metadata page checksum error db_dump: BDB5115 open: ./test/my_db/temp/ss_kmers/100001.ss.hq.bin: Invalid argument

Thanks again!

[zjshi]

Thanks Alice-yyt. Unfortunately, I was not able to reproduce the issue you faced. Could you please also let me know which OS did you run the program as well as type in ls -l ./test/my_db/temp/ss_kmers/ and paste the output here?

[Alice-yyt]

Thanks Alice-yyt. Unfortunately, I was not able to reproduce the issue you faced. Could you please also let me know which OS did you run the program as well as type in ls -l ./test/my_db/temp/ss_kmers/ and paste the output here?

Thank you for your reply! My OS is CentOS Linux release 7.6.1810 (Core). And here is the output of ls -l ./test/my_db/temp/ss_kmers/. Thank for your help!

.

[zjshi]

Hi Alice-yyt, thanks for posting output of ls but could you please do ls -l. So I was mainly wondering whether the intermediate files are empty before the final database building.

[qbdong122]

Hi Jason, I am sorry to bother you. I wonder to know how to get the "msa.fa" and "core_snps.vcf" files before building my own database, because the CallM doesn't work well so I had to try Mummer4, but I can not get these files directly.

[zjshi]

Hi qbdong122, thanks for trying GT-Pro and CallM. Using the CallM would be the easiest way to build a customized database for GT-Pro, since that is one of the purposes of CallM. Are your experiencing any issues with CallM? I would be happy to help with troubleshooting CallM.

[qbdong122]

Thank you very much! When I run CallM, i only get this .... [clustering] done Traceback (most recent call last): File "/Business/NJMU_company/njmu-staff/soft/CallM/bin/CallM.py", line 1239, in main() File "/Business/NJMU_company/njmu-staff/soft/CallM/bin/CallM.py", line 1230, in main call_snps_main(args) File "~/soft/CallM/bin/CallM.py", line 1116, in call_snps_main site_assembly = msa.monolithic_parse(args['msa_path'], args['msa_type'], args['max_samples']) File "~/soft/CallM/bin/align_io/msa.py", line 17, in monolithic_parse return parse_control(msa_path, msa_type, max_sample) File "~/soft/CallM/bin/align_io/msa.py", line 14, in parse_control return parse(msa_path, max_sample) File "~/soft/CallM/bin/align_io/xmfa_mummer4_io.py", line 30, in parse cur_aln.ncols = len(cur_aln.seqs[0].seq) IndexError: list index out of range

[lvxsen]

Hi Alice-yyt, thanks for posting output of ls but could you please do ls -l. So I was mainly wondering whether the intermediate files are empty before the final database building.

Hi Jason, I am sorry to bother you. I got the same error as Alice-yyt. Here is my output of ls -l ./test/my_db/temp/ss_kmers/. Could you please give me some advice?

[qbdong122]

I get the same error, you have solved this?

Hi Jason, I am sorry to bother you. I got the same error as Alice-yyt. Here is my output of ls -l ./test/my_db/temp/ss_kmers/. Could you please give me some advice?

[lvxsen]

I get the same error, you have solved this?

Hi Jason, I am sorry to bother you. I got the same error as Alice-yyt. Here is my output of ls -l ./test/my_db/temp/ss_kmers/. Could you please give me some advice?

Sorry, I haven't solved this problem yet.

[zjshi]

Happy to help! Could you either of you share the genomes sequences used for the database building as well as the following files: reference.fna, msa.fa/tag_msa.fa, core_snps.vcf and coords.tsv? I would like to start an investigation of this issue by reproducing the error at my end. Thanks.

[qbdong122]

Happy to help! Could you either of you share the genomes sequences used for the database building as well as the following files: reference.fna, msa.fa/tag_msa.fa, core_snps.vcf and coords.tsv? I would like to start an investigation of this issue by reproducing the error at my end. Thanks.

I use the test/ data and follow these commands: tar xzvf test/100035.tar.gz && tar xzvf test/101747.tar.gz && tar xzvf test/102779.tar.gz _./GT_Pro build --in test/build.list --out ./test/my_db --dbname tridb then I get these error