Arkadiy-Garber

bit-genbank-to-gene-seqs.py takes a genbank file, and writes nucleotides seqs for all genes. check it out ;)

What is this file: bn_17.sn_360.epoch_9.ckpt.data-00000-of-00001

2

I am downloading the trained models, but I am not getting any files ending with .ckpt. Here are the contents of one of the directories: ``` bn_17.sn_360.epoch_9.ckpt.data-00000-of-00001 bn_17.sn_360.epoch_9.ckpt.index bn_17.sn_360.epoch_9.ckpt.meta checkpoint...

Added sequences to a total of 0 reads.

1

Getting the following output. Some help would be appreciated. `(deepsignalenv) MAB@Axceleron-WKS:~/2748_NP_methylation/fast5_pass$ tombo preprocess annotate_raw_with_fastqs --fast5-basedir single_barcode12/ --fastq-filenames barcode12/barcode12.guppy.fastq` [16:00:39] Preparing reads and extracting read identifiers. 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 110340/110340 [03:07

--allow-outies by default ON

1

Hi! I've been running flash2 that I installed via conda. There does not appear to be a way to turn off the --allow-outies option. Flash2 combines both in innie and...

Could not load dynamic library

3

Getting some errors, likely not caused by the program but by my system, so jsut wondering if you have a solution: ~/bin/DeepMP$ `DeepMP combine-extraction -fr docs/reads/untreated/ -re docs/output_example/error_features/untreated/tmp/ -rp docs/ref/Escherichia_coli_str_k_12_substr_mg1655.ASM584v2.dna.toplevel.fa...

TypeError: 'NoneType' object is not subscriptable

2

Any insight in what is causing this error would be appreciated. Thanks, Arkadiy ``` Command: python /data/MAB/bin/DeepMod2/deepmod2 detect-guppy --threads 24 --fast5 ../../../fast5_pass/single_barcode12 --ref assembly.fasta --bam assembly.bam RuntimeError: module compiled against...