Closed ymilesz closed 3 years ago
Hi Brant, I'm having the same problem as @ymilesz, also didn't have any issues while running phyluce_snp_bwa_multiple_align or phyluce_snp_phase_uces. I'd be grateful if you could help us on this.
Thank you,
Renata
Hi Retana were you able to resolve this problem?
No, I wasn't, and you?
Not yet.
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No, I wasn't, and you?
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Hi folks,
Please include output to stdout/stderr and all log files that were produced, which may help to diagnose the issue.
thx, b
Hi Brant.
The log file for phyluce_snp_phase_uces.log completed without errors, but alligator_mississippiensis.samtools-bcftools-out.log had the following errors:
/apps/phyluce/20191015/bin/bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
Thanks,
Miles
ok - cool, that helps. you need to reinstall samtools using conda (you may have to force uninstall samtools then reinstall it).
Hi Brant, in my case the log file for phyluce_snp_phase_uces.log completed without errors, but I didn't try with the samples from the tutorial: ------------------ Merging alleles from all loci----------------- 2020-01-03 09:29:16,957 - phyluce_snp_phase_uces - INFO - Wrote 1 loci for Tac_squ5039 2020-01-03 09:29:16,958 - phyluce_snp_phase_uces - INFO - Wrote 1 loci for Aer_mon22904 2020-01-03 09:29:16,959 - phyluce_snp_phase_uces - INFO - Wrote 1 loci for Aer_sax621130 2020-01-03 09:29:16,960 - phyluce_snp_phase_uces - INFO - Wrote 1 loci for Tac_squ650459 2020-01-03 09:29:16,961 - phyluce_snp_phase_uces - INFO - Wrote 1 loci for Aer_and3590 2020-01-03 09:29:16,962 - phyluce_snp_phase_uces - INFO - Wrote 1 loci for Tac_squ45879 2020-01-03 09:29:16,963 - phyluce_snp_phase_uces - INFO - Wrote 1 loci for Tac_pho27024 2020-01-03 09:29:17,011 - phyluce_snp_phase_uces - INFO - ================ Completed phyluce_snp_phase_uces ===============
Thanks for your help in this topic.
Renata
if it works with the samples from the tutorial, then the problem is generally with the data you are using (which is hard for me to help with).
ok, I'll try with the tutorial data and see if I have any problems; a colleague from my lab said it could also be the name of the files, but so far I didn't have any issues running Phyluce.
Thanks Brant mine works now, I will leave this open for Renata.
Hi Brant, I am trying to follow the phasing tutorial, and I realized my joined_allele_sequences_all_samples.fasta file did not seem to work. I didn't notice any errors in the various log files produced from phyluce_snp_bwa_multiple_align either.
When I opened joined_allele_sequences_all_samples.fasta this is what I see:
I know this not terribly helpful, but if you could point me to which file to examine that'd be fantastic.
Thanks,
Miles