No new spacers in added custom MAGs

[Zhichao Zhou]

Hi iPHoP authors,

I found an error report when adding custom MAGs to the db:

In lines 1104-1108:

[4] Get CRISPR arrays from new MAGs and add to database...
python /home/zhichao/miniconda3/envs/Test-iPHoP/lib/python3.8/site-packages/iphop/utils/CRISPR/identify_crispr.folder.py -i /storage1/data11/Test/Guaymas_bins -o /storage1/data11/Test/Test_db/iPHoP_db_custom/db/Tmp_CRISPRs
python /home/zhichao/miniconda3/envs/Test-iPHoP/lib/python3.8/site-packages/iphop/utils/CRISPR/get_crispr_database.py -d /storage1/data11/Test/Test_db/iPHoP_db_custom/db/Tmp_CRISPRs
Count total new spacers -> 0
No new spacers, we just link to the old db

In the last lines:

Traceback (most recent call last):
File "/home/zhichao/miniconda3/envs/Test-iPHoP/bin/iphop", line 10, in <module>
sys.exit(cli())
File "/home/zhichao/miniconda3/envs/Test-iPHoP/lib/python3.8/site-packages/iphop/iphop.py", line 121, in cli
args"func"
File "/home/zhichao/miniconda3/envs/Test-iPHoP/lib/python3.8/site-packages/iphop/modules/master_predict.py", line 70, in main
blast_crispr.run_and_parse_blast_to_crispr(args)
File "/home/zhichao/miniconda3/envs/Test-iPHoP/lib/python3.8/site-packages/iphop/modules/blast_crispr.py", line 25, in run_and_parse_blast_to_crispr
get_crispr_results(args["crisprparsed"],args["blastcrisprout"],args["array_file"],args["spacer_complexity"],args["messages"])
File "/home/zhichao/miniconda3/envs/Test-iPHoP/lib/python3.8/site-packages/iphop/modules/blast_crispr.py", line 59, in get_crispr_results
with open(array_file, "r", newline='') as f:
FileNotFoundError: [Errno 2] No such file or directory: './Test_db/iPHoP_db_custom/db_infos/All_CRISPR_array_size.tsv'

I am wondering if this is the reason that no new crisprs were found in added custom MAGs caused the error

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[Simon Roux]

Hi,

Thanks for reporting. Do you expect CRISPR arrays/spacers to be detected in the new MAGs ? And does the addition of custom MAGs still complete successfully despite this absence of CRISPR spacer ?

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[Zhichao Zhou]

I am not intentionally expecting CRISPR arrays/spacers to be detected to add more potential host matches, it is OK if there are none in the input new MAGs. It is OK if the CRISPR part is not practical but other parts (for example blastn against genomes, kmer-based viral-host associations) work

[Simon Roux]

Ok, let me know if the new database works as expected then, even without CRISPR spacer. If that is the case, then it’s just an exception we have to better handle, but that would not be a major issue.

[Zhichao Zhou]

I found that it is not the result of no CRISPR detected in custom MAGs.

It is that one has to provide the full path to the directory of database since custom db will link the files from the standard db and full paths are needed to make links

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[Zhichao Zhou]

The issue has been solved

[Simon Roux]

Good point, because the database is very large we opted to use symbolic links rather than copying all files over, but it is true that you need to provide the full path. I’ll update the README, thanks !