I am using Pseudopipe, and met some errors. I do have reset the path of blast (version2.13), fasta (version35.4), python (version 2.7) in env.sh. The err.log is below.

the err.log in the directory which I run the command

nohup: ignoring input /public1/user/zhurr/software/pgenes/pseudopipe/bin/pseudopipe.sh: line 8: ./../bin/env.sh: No such file or directory ### This is where I install the software /public1/user/zhurr/software/pgenes/pseudopipe/bin/pseudopipe.sh: line 153: /public1/user/zhurr/genome/analysis/30_pseudogene/pseudopipe/ppipe_output: Is a directory
/public1/user/zhurr/software/pgenes/pseudopipe/bin/pseudopipe.sh: line 154: /public1/user/zhurr/genome/analysis/30_pseudogene/pseudopipe/ppipe_output: Is a directory

And I read the FAQs, some one has a similar but maybe a little different question with me. https://faq.gersteinlab.org/2020/03/09/query-regarding-pseudopipe/ In this question's replay, someone metioned that check the output directory in the blast.output folder, and I did it. The output directory in the blast.output folder do exist many split000*.out files. But I still have nothing in my ppipe_output_pgenes.align.gz file. See the picture below.

And I found another logfile, which has err content.

the log file in ppipe_output/pgenes/plus/log/Psorted.log

cannot open "/public1/user/zhurr/genome/analysis/30_pseudogene/pseudopipe/pugr/ppipe_input/mysql/Psorted.exLocs". need to document overlap parameter (30) and dependency on mask array files. mask fields [2, 3] running filterEnsemblGene.py failed during filterEnsemblGene.py stage.

If you can provide some solution, I will be very grateful. Thanks a lot.