marcelauliano
commented
9 months ago Hi,
The -r parameter can take several reads, or the -c can take several contigs. But the -f and -g only take one fasta and gb sequence, respectively.
Em sex., 2 de fev. de 2024 às 11:51, xuxiaodong111 @.***> escreveu:
Hi, when I used Pacbio sequencing data, I met the problem: mitogenome file has more than one sequence. I want to obtain all these mitogenomes. How should I adjust the parameters?
START AT: Thu Feb 1 14:34:23 CST 2024 INFO: Converting SIF file to temporary sandbox... WARNING: underlay of /etc/localtime required more than 50 (109) bind mounts 2024-02-01 14:34:29 [INFO] Welcome to MitoHifi v2. Starting pipeline... Traceback (most recent call last): File "/opt/MitoHiFi/src/mitohifi.py", line 567, in main() File "/opt/MitoHiFi/src/mitohifi.py", line 94, in main rel_mito_len = getMitoLength.get_mito_length(args.f) File "/opt/MitoHiFi/src/getMitoLength.py", line 20, in get_mito_length raise Exception("failed because mitogenome file has more than one sequence. {} sequences were found".format(str(num_sequences))) Exception: failed because mitogenome file has more than one sequence. 15 sequences were found INFO: Cleaning up image... END AT: Thu Feb 1 14:34:31 CST 2024
— Reply to this email directly, view it on GitHub https://github.com/marcelauliano/MitoHiFi/issues/72, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA7M5RHUTEM2FC3Q3SGZARLYRTHKRAVCNFSM6AAAAABCWRQE22VHI2DSMVQWIX3LMV43ASLTON2WKOZSGEYTINZVHE3TAMY . You are receiving this because you are subscribed to this thread.Message ID: @.***>
-- Marcela Uliano da Silva, PhD
Senior Bioinformatician - Wellcome Sanger Institute
Darwin Tree of Life Project (DToL)
Churchill College Postdoctoral By-Fellow, University of Cambridge
Cambridge, UK
Hi, when I used Pacbio sequencing data, I met the problem: mitogenome file has more than one sequence. I want to obtain all these mitogenomes. How should I adjust the parameters?
START AT: Thu Feb 1 14:34:23 CST 2024 INFO: Converting SIF file to temporary sandbox... WARNING: underlay of /etc/localtime required more than 50 (109) bind mounts 2024-02-01 14:34:29 [INFO] Welcome to MitoHifi v2. Starting pipeline... Traceback (most recent call last): File "/opt/MitoHiFi/src/mitohifi.py", line 567, in
main()
File "/opt/MitoHiFi/src/mitohifi.py", line 94, in main
rel_mito_len = getMitoLength.get_mito_length(args.f)
File "/opt/MitoHiFi/src/getMitoLength.py", line 20, in get_mito_length
raise Exception("failed because mitogenome file has more than one sequence. {} sequences were found".format(str(num_sequences)))
Exception: failed because mitogenome file has more than one sequence. 15 sequences were found
INFO: Cleaning up image...
END AT: Thu Feb 1 14:34:31 CST 2024