I am following [This tutorial][1] to test the working of salmon on my RNASeq dataset.
I am using the RNA-Seq dataset from [SRA][2], for testing I am just using the first run that is "SRR5938419"(about 4.85 GB), so after downloading this file , I used [SRAToolkit][3] and using the following ommand, it gave me two fasta files of size(1.45 GB each)

    E:\SRAs>fastq-dump --split-files --fasta  60 --gzip E:\SRAs\SRR5938419
    Read 36388169 spots for /E/SRAs/SRR5938419
    Written 36388169 spots for /E/SRAs/SRR5938419

Then I downloaded the salmon docker as I am in my windows 10 environment using the following command

    docker pull combinelab/salmon

So after running the docker for the downloaded image I was able to test if the salmon was working or not so I ran the following commands

    root@d6fc32919494:/home# ls
    SRAs  salmon-0.14.1  salmon-v0.14.1.tar.gz
    root@d6fc32919494:/home# salmon
    salmon v0.14.1
    
    Usage:  salmon -h|--help or
            salmon -v|--version or
            salmon -c|--cite or
            salmon [--no-version-check] <COMMAND> [-h | options]
    
    Commands:
         index Create a salmon index
         quant Quantify a sample
         alevin single cell analysis
         swim  Perform super-secret operation
         quantmerge Merge multiple quantifications into a single file
    root@d6fc32919494:/home#     

                                     
then I shared the folder in for my windows host so that I could access fasta files in my docker salmon environment. After that I downloaded the human reference transcriptome using  [This][4] link and executed the following commands in my docker to save the 

    root@d6fc32919494:/home# wget ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz -o human.fa.gz
    root@d6fc32919494:/home# ls
    Homo_sapiens.GRCh38.cdna.all.fa.gz  SRAs  human.fa.gz  salmon-0.14.1  salmon-v0.14.1.tar.gz
    root@d6fc32919494:/home#
Then I build the index  using the following command.

    root@d6fc32919494:/home# salmon index -t human.fa.gz -i human_index
    Version Info: Could not resolve upgrade information in the alotted time.
    Check for upgrades manually at https://combine-lab.github.io/salmon
    index ["human_index"] did not previously exist  . . . creating it
    [2019-10-24 09:47:41.438] [jLog] [info] building index
    [2019-10-24 09:47:41.449] [jointLog] [info] [Step 1 of 4] : counting k-mers
    Elapsed time: 0.0048599s
    
    [2019-10-24 09:47:41.454] [jointLog] [info] Replaced 97776 non-ATCG nucleotides
    [2019-10-24 09:47:41.454] [jointLog] [info] Clipped poly-A tails from 0 transcripts
    [2019-10-24 09:47:41.454] [jointLog] [info] Building rank-select dictionary and saving to disk
    [2019-10-24 09:47:41.454] [jointLog] [info] done
    Elapsed time: 3.77e-05s
    [2019-10-24 09:47:41.454] [jointLog] [info] Writing sequence data to file . . .
    [2019-10-24 09:47:41.454] [jointLog] [info] done
    Elapsed time: 6.93e-05s
    [2019-10-24 09:47:41.454] [jointLog] [info] Building 32-bit suffix array (length of generalized text is 97845)
    [2019-10-24 09:47:41.454] [jointLog] [info] Building suffix array . . .
    success
    saving to disk . . . done
    Elapsed time: 0.0001873s
    done
    Elapsed time: 0.0101487s
    processed 0 positions[2019-10-24 09:47:41.490] [jointLog] [info] khash had 97814 keys
    [2019-10-24 09:47:41.490] [jointLog] [info] saving hash to disk . . .
    [2019-10-24 09:47:41.496] [jointLog] [info] done
    Elapsed time: 0.0052422s
    [2019-10-24 09:47:41.496] [jLog] [info] done building index
    root@d6fc32919494:/home# ls
    Homo_sapiens.GRCh38.cdna.all.fa.gz  SRAs  human.fa.gz  human_index  salmon-0.14.1  salmon-v0.14.1.tar.gz
    root@d6fc32919494:/home#

After that I ran the salmon with the created human_index on my fasta files using the following command

    root@d6fc32919494:/home# salmon quant -i human_index -l A -1 SRAs/SRR5938419_1.fasta.gz  -2 SRAs/SRR5938419_2.fasta.gz -p 8 --validateMappings -o quants/SRR5938419_qunats
    Version Info: Could not resolve upgrade information in the alotted time.
    Check for upgrades manually at https://combine-lab.github.io/salmon
    ### salmon (mapping-based) v0.14.1
    ### [ program ] => salmon
    ### [ command ] => quant
    ### [ index ] => { human_index }
    ### [ libType ] => { A }
    ### [ mates1 ] => { SRAs/SRR5938419_1.fasta.gz }
    ### [ mates2 ] => { SRAs/SRR5938419_2.fasta.gz }
    ### [ threads ] => { 8 }
    ### [ validateMappings ] => { }
    ### [ output ] => { quants/SRR5938419_qunats }
    Logs will be written to quants/SRR5938419_qunats/logs
    [2019-10-24 09:51:04.203] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
    [2019-10-24 09:51:04.203] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
    [2019-10-24 09:51:04.203] [jointLog] [info] Usage of --validateMappings, without --hardFilter implies use of range factorization. rangeFactorizationBins is being set to 4
    [2019-10-24 09:51:04.203] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.2.
    [2019-10-24 09:51:04.203] [jointLog] [info] parsing read library format
    [2019-10-24 09:51:04.203] [jointLog] [info] There is 1 library.
    [2019-10-24 09:51:04.237] [jointLog] [info] Loading Quasi index
    [2019-10-24 09:51:04.237] [jointLog] [info] Loading 32-bit quasi index
    [2019-10-24 09:51:04.242] [jointLog] [info] done
    [2019-10-24 09:51:04.242] [jointLog] [info] Index contained 1 targets
    [2019-10-24 09:51:04.237] [stderrLog] [info] Loading Suffix Array
    [2019-10-24 09:51:04.237] [stderrLog] [info] Loading Transcript Info
    [2019-10-24 09:51:04.237] [stderrLog] [info] Loading Rank-Select Bit Array
    [2019-10-24 09:51:04.237] [stderrLog] [info] There were 1 set bits in the bit array
    [2019-10-24 09:51:04.237] [stderrLog] [info] Computing transcript lengths
    [2019-10-24 09:51:04.237] [stderrLog] [info] Waiting to finish loading hash
    [2019-10-24 09:51:04.242] [stderrLog] [info] Done loading index


I got the following message after few minutes

    processed 36000000 fragments
    hits: 0, hits per frag:  0[2019-10-24 09:55:35.561] [jointLog] [warning] salmon was only able to assign 0 fragments to transcripts in the index, but the minimum number of required assigned fragments (--minAssignedFrags) was 10. This could be indicative of a mismatch between the reference and sample, or a very bad sample.  You can change the --minAssignedFrags parameter to force salmon to quantify with fewer assigned fragments (must have at least 1).
    root@d6fc32919494:/home#

So I did not find and TSV file as was claimed in the tutorial link as I mentioned in the first line of post , instead I got following information in the file

    root@d6fc32919494:/home# ls
    Homo_sapiens.GRCh38.cdna.all.fa.gz  SRAs  human.fa.gz  human_index  quants  salmon-0.14.1  salmon-v0.14.1.tar.gz
    root@d6fc32919494:/home# cd quants
    root@d6fc32919494:/home/quants# ls
    SRR5938419_qunats
    root@d6fc32919494:/home/quants# cd SRR5938419_qunats/
    root@d6fc32919494:/home/quants/SRR5938419_qunats# ls
    aux_info  cmd_info.json  libParams  logs  quant.sf
    root@d6fc32919494:/home/quants/SRR5938419_qunats# cat quant.sf
    Name    Length  EffectiveLength TPM     NumReads
            97844   97844.000       0.000000        0.000
    root@d6fc32919494:/home/quants/SRR5938419_qunats#


Now after all this effort, please somebody tell me what is the problem, why I am not getting the TPMs or counts and what went wrong, I would be extremely humbled if somebody could guide me the way out of this problem.

Regards
  [1]: https://combine-lab.github.io/salmon/getting_started/
  [2]: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA398545&o=acc_s%3Aa
  [3]: https://ncbi.github.io/sra-tools/install_config.html
  [4]: https://www.biostars.org/p/257180/




In `wget` command, `-o` is used to specify the file to record the log messages, so you should use `Homo_sapiens.GRCh38.cdna.all.fa.gz` to index not `human.fa.gz`, `human.fa.gz` only contains log messages instead of fasta sequence.