Can Kockan
- Total activity 35
- Last activity
- Member since
- Following 0 users
- Followed by 0 users
- Votes 1
- Subscriptions 16
Activity overview
Latest activity by Can Kockan-
Can Kockan commented,
Quick note, I saw the following in the logs: picard.PicardException: /data/putnamlab/dbecks/DeNovo_transcriptome/2023_A.pul/output/stranded_output/trinity_out_dir.Trinity.dict already exists. Dele...
-
Can Kockan commented,
Thanks Andrew Wicks for posting your solution! I would say that the forum is a perfect place for questions like these. There are a lot of GATK tools that require passing a sequence dictionary for p...
-
Can Kockan commented,
I see a few possible scenarios here. This could be perfectly normal depending on how many chromosomes you have. If I look at my hg38 fasta index and sequence dictionary files, I see that they are a...
-
Can Kockan commented,
Chances are you don't have the sequence dictionary for your reference. Could you try running CreateSequenceDictionary (details here: https://gatk.broadinstitute.org/hc/en-us/articles/27007990059931...
-
Can Kockan commented,
Looking at your original reference index Mus_musculus.GRCm38.dna_sm.primary_assembly.fa.fai , it seems that the contigs are using the 1, 2, ..., X, Y, MT convention unless I'm missing something. Us...
-
Can Kockan commented,
Just a tiny addition to Gökalp Çelik's suggestions regarding potential whitespace issues; the last two replies on this thread might be worth checking out: https://gatk.broadinstitute.org/hc/en-us/c...
-
Can Kockan commented,
Might still be a good idea, just to make sure that whitespaces, etc. don't get mangled during the download process. Your system information and the command-line you are using these files with would...
-
Can Kockan commented,
Hi Nikola Antić , essentially you'll want to:- Fork the repo- Clone the fork to your system- Create a new branch for your feature- Make your changes- Push your changes back to your fork- Create a P...
-
Can Kockan commented,
It might be a whitespace related issue, I recall seeing something similar here: https://gatk.broadinstitute.org/hc/en-us/community/posts/21369679658267-Tribble-can-t-find-CHROM-header-but-line-is-p...
-
Can Kockan commented,
gabriele tosadori That could still be an early termination, I'd expect an exit status as well. I'd check the output VCF to make sure but I highly suspect that this is similar to the following issue...