Open GM110Z opened 2 years ago
Hello
I have been trying to run roary to build a tree for a whole genus. The program starts fine, it built the 'clustered' and 'combined' files ok. It started running BLAST and at the beginning it was generating the *.out files too. However at one point it stopped running throwing the following error: sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error awk: fatal: cannot open file `_blast_results' for reading: Input/output error Couldnt write output file:blast_identity_frequency.Rtabcannot fetch initial working directory: Input/output error at /usr/lib/x86_64-linux-gnu/perl-base/File/Temp.pm line 2632. cannot fetch initial working directory: Input/output error at /usr/lib/x86_64-linux-gnu/perl-base/File/Temp.pm line 2632. cannot fetch initial working directory: Input/output error at /usr/lib/x86_64-linux-gnu/perl-base/File/Temp.pm line 2632.
I installed the program through conda so I was assuming the dependencies were all there? Can you help me fix it?
Thanks
Hello
I have been trying to run roary to build a tree for a whole genus. The program starts fine, it built the 'clustered' and 'combined' files ok. It started running BLAST and at the beginning it was generating the *.out files too. However at one point it stopped running throwing the following error: sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error sh: 1: cannot create _blast_results: Input/output error sh: 0: getcwd() failed: Input/output error awk: fatal: cannot open file `_blast_results' for reading: Input/output error Couldnt write output file:blast_identity_frequency.Rtabcannot fetch initial working directory: Input/output error at /usr/lib/x86_64-linux-gnu/perl-base/File/Temp.pm line 2632. cannot fetch initial working directory: Input/output error at /usr/lib/x86_64-linux-gnu/perl-base/File/Temp.pm line 2632. cannot fetch initial working directory: Input/output error at /usr/lib/x86_64-linux-gnu/perl-base/File/Temp.pm line 2632.
I installed the program through conda so I was assuming the dependencies were all there? Can you help me fix it?
Thanks