Joseph Fass

I used GENCODE's GRCh38 primary assembly fasta file, without an obvious problem: ``` ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_31/GRCh38.primary_assembly.genome.fa.gz ```

I'll second this; I'm still seeing this error with the command: ``` docker run --rm -v /home/ubuntu/TCRseq/downsampled:/scratch -w /scratch teichlab/tracer assemble -m assembly -p 48 -s Hsap /scratch/$fwd $rev $base...

I'm using 5.3: **$ blasr --version blasr 5.3.061bd35** I've been running with this (above) blasr, installed from pitchfork (within the last two weeks), and I'm still getting errors because there...

Yah that was dumb - I should have posted it. It was just the call to blasr in unzip.py, but with single dashes instead of double dashes. I called 'fc_unzip.py...

I think the current sticking point is independent of blasr ... I'm getting errors in the calling hasm.sh, which I'll research and then post as a separate issue if I...

I found another single dash, full word option issue ... in: ``` Python_venv/lib/python2.7/site-packages/falcon_unzip-0.1.0-py2.7.egg/falcon_unzip/run_quiver.py ``` on line 211, pbalign is called with almost all word options having two dashes, except for...

I listed two locations that have this single-dash error, in comments above. I changed both and it didn't bother me after that, but it's possible I forgot one. If you...

@adamtongji Thank you! Your patched version https://github.com/adamtongji/kma works for me. Interesting side note: GitHub's internal search doesn't find that repo when you search "adamtongji/kma" (all of GitHub). So I spent...

I get the same warnings as @hjack123 , but the real issue is the error: ``` Error in LogNorm(data = tf.idf, display_progress = verbose, scale_factor = 10000) : No such...

looks like it moved again, to: ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_genbank/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh38/seqs_for_alignment_pipelines/GCA_000001405.15_GRCh38_full_analysis_set.fna.gz