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Hi all, thanks for the hard work. I noticed in the ftp zip files for the E. coli genomes, there are only these files :
-rw-r--r-- 1 clb21565 cs6824_f19 69616 Feb 24 14:48 ecoli_aligned_length_ecdf
…
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My command line:
```
phylophlan_write_default_configs.sh
phylophlan \
-i ../../F-06-MAG/03_modify/7_final/ \
-d phylophlan --diversity high -f supertree_aa.cfg \
--genome_extension .…
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The parquet file loaded on my laptop in < 30 min, and the describe() call for this data frame (for all columns) took a few minutes. I am linking the describe() result in this ticket. Its a TSV file bu…
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Dear Javier,
Thanks a ton for developping SqueezeMeta.
I am trying to use SqueezeMeta in order to generate gene catalog from waste water metagenomes.
I followed the installation instructions bu…
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Hi!
I am trying to perform a metagenome assembly with SPAdes v3.14.0.
I only have seven PacBio Filtered Subreads merged in a single fastq. This is the command line I used:
spades.py --meta --pacb…
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Hello,
I know that the assembly with single ends results in lower performance. However, I have data of samples with long reads and single end illumina reads which I would like to use for assembly of …
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Hello, I'm interested in polishing a canu assembly of a metagenome, is it possible to input multiple read files and overlap files? e.g. multiple fastq and .sam files?
Thanks!
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/SqueezeMeta/scripts/SqueezeMeta.pl -m Sequential -s test.samples -f raw/ --minion
SqueezeMeta v1.0.0 - (c) J. Tamames, F. Puente-Sánchez CNB-CSIC, Madrid, SPAIN
Please cite: Tamames & Puente-Sa…
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I run each step separately and in the "atlas run genomes -w working_dir" step I got this message in the pre-dereplication step...
raise ValueError("The number of observations cannot be determined …
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Dear all,
I'm a beginner. When I assembly some metagenomes, it showed like this and some of the assembly succeed but some failed. Could you please help me find out the problems?
Error == something…