Host_prediction_to_genus_m90.csv and Host_prediction_to_genome_m90.csv doens't apper at the end

[CAIO RAPOSO]

Hi, I’m having a problem with iphop, I already use it with no problem but these lasts attempts the program isn’t generate the Host_prediction_to_genus_m90.csv and Host_prediction_to_genome_m90.csv. I think it’s because “the The blastn output file was empty, this may be ok, but is still unusual, so you may want to check the blastn log” but I already use this program with these samples and I already I’m trying to run it in differents terminals. What can I do to solve this?

command: nohup iphop predict --fa_file /root/caio/virus_identificados/GPp2/00_VIBRANT_VirSorter_DeepVirFinder_GuanduPp2/Overlap_GuanduPp2/final_overlapped_virus.fasta --db_dir /root/ViWrap/datbase/iPHoP_db/Aug_2023_pub_rw/ --out_dir /root/caio/virus_identificados/ &

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iphop.log

Looks like everything is now set up, we will first clean up the input file, and then we will start the host prediction steps themselves
[1/1/Skip] Skipping computation of blastn against microbial genomes...
[1/3/Run] Get relevant blast matches...
The blastn output file was empty, this may be ok, but is still unusual, so you may want to check the blastn log (Wdir/blastgenomes.tsv.log)
[2/1/Run] Running blastn against CRISPR...
Looks like everything is now set up, we will first clean up the input file, and then we will start the host prediction steps themselves
[1/1/Run] Running blastn against genomes...
[1/3/Run] Get relevant blast matches...
No hits were included in the result file after parsing the blast, this may be ok, but is still unusual, so you may want to check the blastn log (Wdir/blastgenomes.tsv.log)
[2/1/Run] Running blastn against CRISPR...
[2/2/Run] Get relevant crispr matches...
[3/1/Run] Running (recoded)WIsH...

Welcome to iPHoP

ls -ls result directory

-rw-r--r--. 1 root root 21K Sep 10 18:59 blastcrispr.tsv
-rw-r--r--. 1 root root 480 Sep 10 18:59 blastcrispr.tsv.cmd
-rw-r--r--. 1 root root 0 Sep 10 18:59 blastcrispr.tsv.log
-rw-r--r--. 1 root root 4.9K Sep 10 18:59 blastgenomes.tsv
-rw-r--r--. 1 root root 428 Sep 10 18:58 blastgenomes.tsv.cmd
-rw-r--r--. 1 root root 0 Sep 10 18:58 blastgenomes.tsv.log
-rw-r--r--. 1 root root 268 Sep 10 18:59 blastparsed.csv
-rw-r--r--. 1 root root 1.2K Sep 10 18:59 crisprparsed.csv
drwxr-xr-x. 2 root root 52 Sep 10 18:59 split_input
-rw-r--r--. 1 root root 0 Sep 10 18:59 wish.cmd
-rw-r--r--. 1 root root 0 Sep 10 18:59 wish.log
drwxr-xr-x. 2 root root 16K Sep 10 22:07 wish_results

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[Simon Roux]

Hi,

It looks like iPHoP is still processing (or stuck ?) at the WIsH stage. How many input sequences are you trying to process ? And do you see any error message ?

[CAIO RAPOSO]

In this case i run 8 different samples at same type, but I use a capable stance to run it all toguether. Days ago I did run it with only one sample on another terminal and I got the same problem, I use the htop to see what is running and it was finished. I didin’t find any error mensage in all cases. Today I will try to re install the IPHOP and see what happens.

[Simon Roux]

In the results directory, the wish.log file looks empty, so that suggests to me that iPHoP either encountered an error or stalled in the middle of a run. Re-install is worth trying, then you may want to look into the content of the “wish_results” folder.

[CAIO RAPOSO]

The reinstallation works, for the most part. In one of the terminals it’s stays endlessly at the solving environment part, but it’s ok. Thank you for the help.

[Simon Roux]

Thanks for sharing the good news !