Salmon quant output is missing index_seq_hash variable

[samuelmontgomery]

Description of the bug

The meta_info.json file for each sample quantified using salmon is missing the values for the index hashes required for tximeta import etc.

It is present in the info.json in the salmon index, but not in the metadata for each quant.sf file

Command used and terminal output

No response

Relevant files

{
"salmon_version": "1.10.1",
"samp_type": "none",
"opt_type": "vb",
"quant_errors": [],
"num_libraries": 1,
"library_types": [
"ISR"
],
"frag_dist_length": 1001,
"frag_length_mean": 131.06035147965313,
"frag_length_sd": 41.948120867161687,
"seq_bias_correct": false,
"gc_bias_correct": false,
"num_bias_bins": 4096,
"mapping_type": "alignment",
"num_valid_targets": 252798,
"num_decoy_targets": 0,
"num_eq_classes": 432137,
"serialized_eq_classes": false,
"eq_class_properties": [
"range_factorized",
"gzipped"
],
"length_classes": [
549,
773,
1399,
2648,
109224
],
"index_seq_hash": "",
"index_name_hash": "",
"index_seq_hash512": "",
"index_name_hash512": "",
"index_decoy_seq_hash": "",
"index_decoy_name_hash": "",
"num_bootstraps": 0,
"num_processed": 24186572,
"num_mapped": 24186572,
"num_decoy_fragments": 0,
"num_dovetail_fragments": 0,
"num_fragments_filtered_vm": 0,
"num_alignments_below_threshold_for_mapped_fragments_vm": 0,
"percent_mapped": 100.0,
"call": "quant",
"start_time": "Sun Aug 06 05:15:44 2023",
"end_time": "Sun Aug 06 05:34:38 2023"
}

System information

No response

[samuelmontgomery]

Just following up - this is really only an issue when importing data into R using tximeta to create a linked transcriptome database
I have written a python script to parse the salmon index info.json file for the hash values, and iteratively edit the meta.json files in each quant.sf file for each sample to add the hash values in
Happy to share if this is helpful
When running salmon outside the pipeline, it is no issue