Open Alice-yyt opened 2 years ago
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 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!
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?
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!
.
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 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.
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.
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
Hi Alice-yyt, thanks for posting output of
ls
but could you please dols -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?
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?
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.
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.
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
andcoords.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
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!