Something went wrong with indexing the assembly

[PhoebeCc]

Here is my running code:

time metawrap quant_bins -b temp/bin_refinement2/ref4/metawrap_70_5_bins/ \
    -t 48 -o temp/bin_arg/quant/summer \
    -a result/megahit/summer.contigs.fa \
    temp/qc/summer/*.R1.raw_kneaddata_paired_?.fastq

Here is the results:

11 forward and 11 reverse read files detected                                -----
------------------------------------------------------------------------------------------------------------------------


########################################################################################################################
#####                                    SETTING UP OUTPUT AND INDEXING ASSEMBLY                                   #####
########################################################################################################################

mkdir: cannot create directory ‘temp/bin_quant/summer’: File exists

------------------------------------------------------------------------------------------------------------------------
-----                            Indexing assembly file with salmon. Ignore any warnings                           -----
------------------------------------------------------------------------------------------------------------------------

[2024-05-18 20:47:21.847] [jLog] [info] building index
[2024-05-18 20:47:21.848] [jointLog] [info] [Step 1 of 4] : counting k-mers
**Version Info: Could not resolve upgrade information in the alotted time.
Check for upgrades manually at https://combine-lab.github.io/salmon**
counted k-mers for 320,000 transcripts[2024-05-18 20:50:32.699] [jointLog] [info] Building rank-select dictionary and saving to disk
[2024-05-18 20:50:32.947] [jointLog] [info] done
[2024-05-18 20:50:32.983] [jointLog] [info] Writing sequence data to file . . . 

************************************************************************************************************************
*****                           Something went wrong with indexing the assembly. Exiting.                          *****
************************************************************************************************************************

I have tried updating salmon and it is not compatible.
I would like to know how to solve the above problem.
Or how to use individual salmon for quantification.

Thank you~

[PhoebeCc]

I tried to run bin_quant in individual salmon environment (py3) and got the following results：

Traceback (most recent call last):
  File "/gpfs/share/home/1701111743/metaWRAP/bin/metawrap-scripts/split_salmon_out_into_bins.py", line 4, in <module>
    import numpy as np
ImportError: No module named numpy

************************************************************************************************************************
*****                     something went wrong with making summary abundance table. Exiting...                     *****
************************************************************************************************************************

numpy was already installed in salmon environment, presumably due to version incompatibility.
Is there a way to run split_salmon_out_into_bins.py in py2.7 after this step？

Also, I am re-trying to install metawrap-mg=1.2.0 (I have installed this version before and can run quant_bin successfully), but it seems that neither conda nor mamba installation can successfully install this version, nor can I install the dependent software using the git method.

I'm sorry that my computer skills are really limited, but I still can't solve this problem after many attempts, and I didn't find a solution in the previous issue.

If anyone can figure it out, thank you very much~