User: russianconcussion

Reputation:
30
Status:
New User
Location:
United States
Last seen:
1 month ago
Joined:
7 years ago
Email:
r****************@gmail.com

PhD candidate in microbiology at Oregon State University.  Wrangling metagenomes, mostly with other people's code (isn't that the definition of hell: other people's code? haha!  Anyhow, thank you if you help me with my own).

Posts by russianconcussion

<prev • 17 results • page 1 of 2 • next >
0
votes
0
answers
137
views
0
answers
Comment: C: Manage expected successful job exit but no output file in Snakemake
... I'll just edit the post to show all of the snakemake rules above. ...
written 5 weeks ago by russianconcussion30
1
vote
0
answers
137
views
0
answers
Manage expected successful job exit but no output file in Snakemake
... Hi, I'm trying to subsample a large collection of processed fastq files in a Snakemake workflow. I want to sequentially subsample these files by one third, a total of six times. All my fastq files are different sizes, so I expect that some of the subsamples will be empty before the sixth iteration ...
python snakemake shell written 5 weeks ago by russianconcussion30
0
votes
0
answers
1.1k
views
0
answers
Comment: C: "out" parameter for _Fasttree module in Bio.Phylo.Applications from Biopython 1.
... Oops! Yes, you're right; I wrote the command wrong. Regardless, after updating to FastTree 2.1.10, the Biopython wrapper works! It was my ancient version of FastTree that was causing me trouble. Thank you for your help, Rodrigo! ...
written 3.1 years ago by russianconcussion30
0
votes
0
answers
1.1k
views
0
answers
Comment: C: "out" parameter for _Fasttree module in Bio.Phylo.Applications from Biopython 1.
... Hmmm. It definitely doesn't have an '-out' option in my version of FastTree (2.1.3 SSE3). For example, if I try: FastTree -nt -gtr test.codon Works fine and yields a tree in stdout: FastTree Version 2.1.3 SSE3 Alignment: test.codon Nucleotide distances: Jukes-Cantor Joins: balance ...
written 3.1 years ago by russianconcussion30
0
votes
0
answers
1.1k
views
0
answers
Comment: C: "out" parameter for _Fasttree module in Bio.Phylo.Applications from Biopython 1.
... Hi Rodrigo. Actually, my codon alignment is in nucleotides, not amino acids. In a codon alignment, you use a protein alignment to constrain the cognate nucleotide alignment. So I'm sure that the -gtr and -nt options are fine. Here is the head of the codon alignment file: >ID:AMR59844.1 ...
written 3.1 years ago by russianconcussion30
4
votes
0
answers
1.1k
views
0
answers
"out" parameter for _Fasttree module in Bio.Phylo.Applications from Biopython 1.68 doesn't work
... Hi, When I try to run the FastTree wrapper from Bio.Phylo.Applications, it fails, giving me this message: ApplicationError: Non-zero return code 1 from '/home/fetz/genome/phylosift_v1.0.1/bin/FastTree -nt -gtr -out 245_hypothetical_protein.tre 245_hypothetical_protein.codon', message 'Unknown ...
biopython fasttree written 3.1 years ago by russianconcussion30 • updated 3.0 years ago by Biostar ♦♦ 20
0
votes
4
answers
4.5k
views
4
answers
Comment: C: How to make a custom blast db with taxon IDs from a taxid_map file
... Thanks! Upgrading solved this issue for me too. ...
written 3.1 years ago by russianconcussion30
0
votes
1
answer
1.4k
views
1
answers
Comment: C: Need help interpreting gdb backtrace from a SAMtools segmentation fault (or help
... Thanks to John Marshall's help with interpreting the samtools segmentation fault, I was able to fix the error. Here is the code that I ended up using to put reads mapped to individual bacterial/phage genes from a multifasta file (a transcriptome bam file from kallisto) onto the bacterial/phage geno ...
written 3.8 years ago by russianconcussion30
0
votes
1
answer
1.4k
views
1
answers
Comment: C: Need help interpreting gdb backtrace from a SAMtools segmentation default (or he
... Thanks very much, John. I'll start digging into the gdb tutorials, but in the meantime, I'll just try to replicate the steps you took to diagnose the problem and then address that pesky mtid error! (Oh, and I'll update samtools on my laptop. *blush*) ...
written 3.8 years ago by russianconcussion30
3
votes
1
answer
1.4k
views
1
answer
Need help interpreting gdb backtrace from a SAMtools segmentation fault (or help editing SAM/BAM files!)
... Hi, I'm editing the header, RNAME, POS, and PNEXT of a bam file so that I can transfer read mappings on individual CDS's directly to the complete genome containing those CDS's. To do that, I am using pysam to iterate through a bam file alignment-by-alignment and then building a new alignment to be ...
bam samtools pysam written 3.8 years ago by russianconcussion30

Latest awards to russianconcussion

Popular Question 22 months ago, created a question with more than 1,000 views. For How to write FULL genbank files with Biopython SeqIO module?
Popular Question 2.9 years ago, created a question with more than 1,000 views. For How to write FULL genbank files with Biopython SeqIO module?
Supporter 3.1 years ago, voted at least 25 times.
Autobiographer 4.7 years ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1960 users visited in the last hour