Closed Slugger70 closed 12 years ago
nway is looking for reference.fa in the nesoni working directory. This has been replaced with a directory called reference with reference.fa and other files in it.
Command line example:
nesoni nway Agona_SL483/ arizonae_62_z4_z23_RSK2980/ Choleraesuis_SC_B67/
returns:
IOError: [Errno 2] No such file or directory: 'Agona_SL483/reference.fa'
Checking Agona directory:
[gla048@athena Agona_SL483]$ ll total 393120 -rw-rw-r-- 1 gla048 gla048 9673526 Jun 26 12:52 alignment.maf -rw-rw-r-- 1 gla048 gla048 16823401 Jun 26 12:48 alignments.bam -rw-rw-r-- 1 gla048 gla048 14809603 Jun 26 12:49 alignments_filtered.bam -rw-rw-r-- 1 gla048 gla048 14809603 Jun 26 12:49 alignments_filtered_sorted.bam -rw-rw-r-- 1 gla048 gla048 14608 Jun 26 12:49 alignments_filtered_sorted.bam.bai -rw-rw-r-- 1 gla048 gla048 4905796 Jun 26 12:52 consensus.fa -rw-rw-r-- 1 gla048 gla048 1325 Jun 26 12:52 consensus_log.txt -rw-rw-r-- 1 gla048 gla048 4905796 Jun 26 12:52 consensus_masked.fa -rw-rw-r-- 1 gla048 gla048 4905981 Jun 26 12:44 contigs.fna -rw-rw-r-- 1 gla048 gla048 6983269 Jun 26 12:50 depths.pickle.gz -rw-rw-r-- 1 gla048 gla048 113911 Jun 26 12:50 gi_197247299_ref_NC_0111481-ambiguous-depth.userplot -rw-rw-r-- 1 gla048 gla048 113471 Jun 26 12:50 gi_197247299_ref_NC_0111481-depth.userplot -rw-rw-r-- 1 gla048 gla048 823350 Jun 26 12:50 gi_197247299_ref_NC_0111481-evidence.txt -rw-rw-r-- 1 gla048 gla048 1083 Jun 26 12:50 gi_197247299_ref_NC_0111481.gff -rw-rw-r-- 1 gla048 gla048 14396006 Jun 26 12:50 gi_197247352_ref_NC_0111491-ambiguous-depth.userplot -rw-rw-r-- 1 gla048 gla048 14273285 Jun 26 12:50 gi_197247352_ref_NC_0111491-depth.userplot -rw-rw-r-- 1 gla048 gla048 113511293 Jun 26 12:52 gi_197247352_ref_NC_0111491-evidence.txt -rw-rw-r-- 1 gla048 gla048 1083 Jun 26 12:52 gi_197247352_ref_NC_0111491.gff -rw-rw-r-- 1 gla048 gla048 46 Jun 26 12:50 parameters drwxrwxr-x 2 gla048 gla048 131 Jun 26 12:44 reference -rw-rw-r-- 1 gla048 gla048 1083 Jun 26 12:52 report.gff -rw-rw-r-- 1 gla048 gla048 73 Jun 26 12:52 report.txt -rw-rw-r-- 1 gla048 gla048 5346 Jun 26 12:48 shrimp_log.txt -rw-rw-r-- 1 gla048 gla048 181433975 Jun 26 12:44 s_single.fa -rw-rw-r-- 1 gla048 gla048 0 Jun 26 12:48 unmapped_paired.fq -rw-rw-r-- 1 gla048 gla048 0 Jun 26 12:48 unmapped_single.fq
As can be seen, reference is now a directory not a file...
Fixed by Simon. See diff...
Slugger70
commented
12 years ago
nway is looking for reference.fa in the nesoni working directory. This has been replaced with a directory called reference with reference.fa and other files in it.
Command line example:
nesoni nway Agona_SL483/ arizonae_62_z4_z23_RSK2980/ Choleraesuis_SC_B67/
returns:
IOError: [Errno 2] No such file or directory: 'Agona_SL483/reference.fa'
Checking Agona directory:
[gla048@athena Agona_SL483]$ ll total 393120 -rw-rw-r-- 1 gla048 gla048 9673526 Jun 26 12:52 alignment.maf -rw-rw-r-- 1 gla048 gla048 16823401 Jun 26 12:48 alignments.bam -rw-rw-r-- 1 gla048 gla048 14809603 Jun 26 12:49 alignments_filtered.bam -rw-rw-r-- 1 gla048 gla048 14809603 Jun 26 12:49 alignments_filtered_sorted.bam -rw-rw-r-- 1 gla048 gla048 14608 Jun 26 12:49 alignments_filtered_sorted.bam.bai -rw-rw-r-- 1 gla048 gla048 4905796 Jun 26 12:52 consensus.fa -rw-rw-r-- 1 gla048 gla048 1325 Jun 26 12:52 consensus_log.txt -rw-rw-r-- 1 gla048 gla048 4905796 Jun 26 12:52 consensus_masked.fa -rw-rw-r-- 1 gla048 gla048 4905981 Jun 26 12:44 contigs.fna -rw-rw-r-- 1 gla048 gla048 6983269 Jun 26 12:50 depths.pickle.gz -rw-rw-r-- 1 gla048 gla048 113911 Jun 26 12:50 gi_197247299_ref_NC_0111481-ambiguous-depth.userplot -rw-rw-r-- 1 gla048 gla048 113471 Jun 26 12:50 gi_197247299_ref_NC_0111481-depth.userplot -rw-rw-r-- 1 gla048 gla048 823350 Jun 26 12:50 gi_197247299_ref_NC_0111481-evidence.txt -rw-rw-r-- 1 gla048 gla048 1083 Jun 26 12:50 gi_197247299_ref_NC_0111481.gff -rw-rw-r-- 1 gla048 gla048 14396006 Jun 26 12:50 gi_197247352_ref_NC_0111491-ambiguous-depth.userplot -rw-rw-r-- 1 gla048 gla048 14273285 Jun 26 12:50 gi_197247352_ref_NC_0111491-depth.userplot -rw-rw-r-- 1 gla048 gla048 113511293 Jun 26 12:52 gi_197247352_ref_NC_0111491-evidence.txt -rw-rw-r-- 1 gla048 gla048 1083 Jun 26 12:52 gi_197247352_ref_NC_0111491.gff -rw-rw-r-- 1 gla048 gla048 46 Jun 26 12:50 parameters drwxrwxr-x 2 gla048 gla048 131 Jun 26 12:44 reference -rw-rw-r-- 1 gla048 gla048 1083 Jun 26 12:52 report.gff -rw-rw-r-- 1 gla048 gla048 73 Jun 26 12:52 report.txt -rw-rw-r-- 1 gla048 gla048 5346 Jun 26 12:48 shrimp_log.txt -rw-rw-r-- 1 gla048 gla048 181433975 Jun 26 12:44 s_single.fa -rw-rw-r-- 1 gla048 gla048 0 Jun 26 12:48 unmapped_paired.fq -rw-rw-r-- 1 gla048 gla048 0 Jun 26 12:48 unmapped_single.fq
As can be seen, reference is now a directory not a file...