Problem creating salmon index

Question

[dylannicoembros]

Good evening,

I need to align some rna sequences from some data with salmon. I am trying to create an index with salmon using this command:

salmon index -t GRCh38_latest_rna.fna.gz --index tindex 

where the zipped file is downloaded from this link: https://www.ncbi.nlm.nih.gov/projects/genome/guide/human/index.shtml

selecting the transcriptome file.

I am new to this field and I am approaching it for research purposes. Thus, the main point is that it gives me this error:

[2023-07-24 16:16:23.388] [jLog] [warning] The salmon index is being built without any decoy sequences.  It 
is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the 
organism) be provided during indexing. Further details can be found at 
https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.
[2023-07-24 16:16:23.388] [jLog] [info] building index
out : tindex
[2023-07-24 16:16:23.389] [puff::index::jointLog] [info] Running fixFasta

[Step 1 of 4] : counting k-mers

[2023-07-24 16:16:23.390] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides
[2023-07-24 16:16:23.390] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts
wrote 0 cleaned references
[2023-07-24 16:16:23.390] [puff::index::jointLog] [info] Filter size not provided; estimating from number of 
distinct k-mers
[2023-07-24 16:16:23.391] [puff::index::jointLog] [info] ntHll estimated 47270 distinct k-mers, setting filter 
size to 2^20
Threads = 2
Vertex length = 31
Hash functions = 5
Filter size = 1048576
Capacity = 2
Files: 
tindex/ref_k31_fixed.fa
--------------------------------------------------------------------------------
Round 0, 0:1048576
Pass    Filling Filtering
terminate called without an active exception
Aborted

Can someone please help me figuring out ?

[Rob]

What version of salmon are you using? Can you first make sure you are using the latest version?

[dylannicoembros]

I updated it to the latest, 1.10.1

Answer 1

[dsull]

The number of k-mers seems low for a transcript index. Can you make sure that your .fna.gz file is intact, isn't broken, and is the right file (maybe the download stopped in the middle)?

[dylannicoembros]

Seems like the file was damaged during the copy from local to remote server. I basically decompressed in local and then loaded into the remote server. Thank you all.

[GenoMax]

You can accept @dsull answer (green check mark) to provide closure to this thread.