Error creating abundance table in 'quant_bins' module

[bhunter154]

I keep running into this error running the quant_bins module. Any idea what the issue could be?

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-----                                  1 forward and 1 reverse read files detected                                 -----
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########################################################################################################################
#####                                    SETTING UP OUTPUT AND INDEXING ASSEMBLY                                   #####
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-----                            Indexing assembly file with salmon. Ignore any warnings                           -----
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Version Info: ### PLEASE UPGRADE SALMON ###
### A newer version of salmon with important bug fixes and improvements is available. ####
###
The newest version, available at https://github.com/COMBINE-lab/salmon/releases
contains new features, improvements, and bug fixes; please upgrade at your
earliest convenience.
###
Sign up for the salmon mailing list to hear about new versions, features and updates at:
https://oceangenomics.com/subscribe
###
index ["/mnt/sda/StormData/2019_Storm/metaWRAP/quant_bins/2019_01//assembly_index"] did not previously exist  . . . creating it
[2024-01-16 14:07:34.344] [jLog] [info] building index
[2024-01-16 14:07:34.344] [jointLog] [info] [Step 1 of 4] : counting k-mers
counted k-mers for 400,000 transcriptsElapsed time: 8.14766s

[2024-01-16 14:07:42.492] [jointLog] [info] Replaced 0 non-ATCG nucleotides
[2024-01-16 14:07:42.492] [jointLog] [info] Clipped poly-A tails from 11 transcripts
[2024-01-16 14:07:42.522] [jointLog] [info] Building rank-select dictionary and saving to disk
[2024-01-16 14:07:42.572] [jointLog] [info] done
Elapsed time: 0.0507379s
[2024-01-16 14:07:42.572] [jointLog] [info] Writing sequence data to file . . . 
[2024-01-16 14:07:43.016] [jointLog] [info] done
Elapsed time: 0.443886s
[2024-01-16 14:07:43.017] [jointLog] [info] Building 32-bit suffix array (length of generalized text is 449,166,153)
[2024-01-16 14:07:43.736] [jointLog] [info] Building suffix array . . . 
success
saving to disk . . . done
Elapsed time: 1.67394s
done
Elapsed time: 34.6801s
processed 449,000,000 positions[2024-01-16 14:12:47.344] [jointLog] [info] khash had 418,906,878 keys
[2024-01-16 14:12:47.344] [jointLog] [info] saving hash to disk . . . 
[2024-01-16 14:13:18.727] [jointLog] [info] done
Elapsed time: 31.3826s
[2024-01-16 14:13:22.738] [jLog] [info] done building index

########################################################################################################################
#####                           ALIGNING READS FROM ALL SAMPLES BACK TO BINS WITH SALMON                           #####
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-----                                     processing sample 2019_01 with reads                                     -----
-----               /mnt/sda/StormData/2019_Storm/trimmed_paired_files/gunzipped/2019_01_1.fastq and               -----
-----               /mnt/sda/StormData/2019_Storm/trimmed_paired_files/gunzipped/2019_01_2.fastq...                -----
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Version Info: ### PLEASE UPGRADE SALMON ###
### A newer version of salmon with important bug fixes and improvements is available. ####
###
The newest version, available at https://github.com/COMBINE-lab/salmon/releases
contains new features, improvements, and bug fixes; please upgrade at your
earliest convenience.
###
Sign up for the salmon mailing list to hear about new versions, features and updates at:
https://oceangenomics.com/subscribe
###
### salmon (mapping-based) v0.13.1
### [ program ] => salmon 
### [ command ] => quant 
### [ index ] => { /mnt/sda/StormData/2019_Storm/metaWRAP/quant_bins/2019_01//assembly_index }
### [ libType ] => { IU }
### [ mates1 ] => { /mnt/sda/StormData/2019_Storm/trimmed_paired_files/gunzipped/2019_01_1.fastq }
### [ mates2 ] => { /mnt/sda/StormData/2019_Storm/trimmed_paired_files/gunzipped/2019_01_2.fastq }
### [ output ] => { /mnt/sda/StormData/2019_Storm/metaWRAP/quant_bins/2019_01//alignment_files/2019_01.quant }
### [ meta ] => { }
### [ threads ] => { 1 }
Logs will be written to /mnt/sda/StormData/2019_Storm/metaWRAP/quant_bins/2019_01//alignment_files/2019_01.quant/logs
[2024-01-16 14:13:24.272] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2024-01-16 14:13:24.272] [jointLog] [warning] 

NOTE: It appears you are running salmon without the `--validateMappings` option.
Mapping validation can generally improve both the sensitivity and specificity of mapping,
with only a moderate increase in use of computational resources. 
Mapping validation is planned to become a default option (i.e. turned on by default) in
the next release of salmon.
Unless there is a specific reason to do this (e.g. testing on clean simulated data),
`--validateMappings` is generally recommended.

[2024-01-16 14:13:24.272] [jointLog] [info] parsing read library format
[2024-01-16 14:13:24.273] [jointLog] [info] There is 1 library.
[2024-01-16 14:13:24.338] [stderrLog] [info] Loading Suffix Array 
[2024-01-16 14:13:24.338] [jointLog] [info] Loading Quasi index
[2024-01-16 14:13:24.338] [jointLog] [info] Loading 32-bit quasi index
[2024-01-16 14:13:25.335] [stderrLog] [info] Loading Transcript Info 
[2024-01-16 14:13:25.605] [stderrLog] [info] Loading Rank-Select Bit Array
[2024-01-16 14:13:25.647] [stderrLog] [info] There were 403,725 set bits in the bit array
[2024-01-16 14:13:25.669] [stderrLog] [info] Computing transcript lengths
[2024-01-16 14:13:25.669] [stderrLog] [info] Waiting to finish loading hash




[2024-01-16 14:13:47.087] [stderrLog] [info] Done loading index
[2024-01-16 14:13:47.087] [jointLog] [info] done
processed 36,500,000 fragmentsntLog] [info] Index contained 403,725 targets
hits: 13,013,583, hits per frag:  0.356585









[2024-01-16 14:44:34.242] [jointLog] [info] Computed 505,843 rich equivalence classes for further processing
[2024-01-16 14:44:34.242] [jointLog] [info] Counted 12,136,222 total reads in the equivalence classes 
[2024-01-16 14:44:34.243] [jointLog] [warning] 0.505995% of fragments were shorter than the k used to build the index (31).
If this fraction is too large, consider re-building the index with a smaller k.
The minimum read size found was 2.


[2024-01-16 14:44:34.243] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings : 41,597
[2024-01-16 14:44:34.244] [jointLog] [info] Mapping rate = 32.9235%

[2024-01-16 14:44:34.244] [jointLog] [info] finished quantifyLibrary()
[2024-01-16 14:44:34.244] [jointLog] [info] Starting optimizer
[2024-01-16 14:44:34.346] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2024-01-16 14:44:34.361] [jointLog] [info] iteration = 0 | max rel diff. = 133.186
[2024-01-16 14:44:35.804] [jointLog] [info] iteration = 100 | max rel diff. = 0.0300497
[2024-01-16 14:44:37.242] [jointLog] [info] iteration = 200 | max rel diff. = 0.0199003
[2024-01-16 14:44:38.679] [jointLog] [info] iteration = 300 | max rel diff. = 0.0124077
[2024-01-16 14:44:39.760] [jointLog] [info] iteration = 375 | max rel diff. = 0.00177035
[2024-01-16 14:44:39.763] [jointLog] [info] Finished optimizer
[2024-01-16 14:44:39.763] [jointLog] [info] writing output 


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-----                                           summarize salmon files...                                          -----
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Starting in: /mnt/sda/StormData/2019_Storm/metaWRAP/quant_bins/2019_01/alignment_files
Loading counts from: ./2019_01.quant quant.sf
"2019_01.quant.counts"

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#####                                   EXTRACTING AVERAGE ABUNDANCE OF EACH BIN                                   #####
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-----                            There were 1 samples detected. Making abundance table!                            -----
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Traceback (most recent call last):
  File "/home/becket/miniconda3/envs/metawrap-new/bin/metawrap-scripts/split_salmon_out_into_bins.py", line 8, in <module>
    for line in open(sys.argv[2]+"/"+bin_name):
IOError: [Errno 21] Is a directory: '/mnt/sda/StormData/2019-2022_metaWRAP_bins//log'

************************************************************************************************************************
*****                     something went wrong with making summary abundance table. Exiting...                     *****
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real	37m9.707s
user	38m7.561s
sys	0m51.727s