Cannot find .SR_evidence.list1

[concscid]

Hello

When I try to run prophage tracer, it stops after generating the candidate prophage table (see below) because awk can't find the table .SR_evidence.list1. The files .SR_evidence.list and prophage.WGS.sr-drp.temp.out are empty so I wonder whether none of the candidates are identified as prophages and that is why the file is not generated or whether there is a problem. I haven't been able to find any detailed information on how the script works and I don't understand all the commands in the script, could you please help me?

candidate_1 0 1 1 958602 958608 1036233 1036239 77631 contig_1 0 0 0
candidate_2 1 0 1 2158714 2158725 2231241 2231252 72527 contig_1 0 0 0
candidate_3 0 1 1 3466080 3466082 3534407 3534409 68327 contig_1 0 0 0

[WangLab-SCSIO]

I have updated our codes and provided test data ( see README file). Please try to download the new shell scripts and the test data. Try to run on the test data.
Refer to the problem you met, it is probable that no split reads or discordant read pairs derived from prophages were found in your data.

[WangLab-SCSIO]

Hello

When I try to run prophage tracer, it stops after generating the candidate prophage table (see below) because awk can't find the table .SR_evidence.list1. The files .SR_evidence.list and prophage.WGS.sr-drp.temp.out are empty so I wonder whether none of the candidates are identified as prophages and that is why the file is not generated or whether there is a problem. I haven't been able to find any detailed information on how the script works and I don't understand all the commands in the script, could you please help me?

candidate_1 0 1 1 958602 958608 1036233 1036239 77631 contig_1 0 0 0 candidate_2 1 0 1 2158714 2158725 2231241 2231252 72527 contig_1 0 0 0 candidate_3 0 1 1 3466080 3466082 3534407 3534409 68327 contig_1 0 0 0

It should be noted that some users reported that blast+ 2.16.0 on Ubuntu may generate error and exit the shell script when using makeblastdb. However, this bulit DB is ok for downstream command. Therefore, I have updated the shell script to ignore this error message and continue with the following command. I also suggest to install blast+ 2.6.0 as mentioned in "System and software requirements".