update README.md

README.md

@@ -114,7 +114,7 @@ Singularity Image
 
 The easiest way to run GALBA is using singuarlity. We provide a docker container to build a singularity image (tested with singularity version 3.10.0-dirty). **We only include Miniprot in Docker & Singularity!** GenomeThreader is not included.
 
-Build as follows (requires 1.2 GB disk space):
+Build as follows (requires 1.4 GB disk space):
 
 ```
 singularity build galba.sif docker://katharinahoff/galba-notebook:latest
@@ -126,23 +126,6 @@ Execute GALBA from galba.sif like this (i.e. it automatically mounts the user's
 singularity exec galba.sif galba.pl
 ```
 
-Known issue with partitionLargeSeqeunces or partitionLargeSequences
--------------------------------------------------------------------
-
-The AUGUSTUS developers team is currenlty transitioning between versions. One (very minor) change in Augustus is that we fixed a typo in the term "partionLargeSeqeunces (which is now of course partitionLargeSequences). It is a Pygustus argument. Pygustus looks for possible arguments in two places: if there is no json file with the required parameters in the $AUGUSTUS_CONFIG_PATH/parameters, then it uses its own (typo-fixed) json file. If it does find the json file in the $AUGUSTUS_CONFIG_PATH/parameters folder, then it uses that file, and it depends on what age that file has on your system whether our latest-tagged image will work, or not. The latest-tagged image will work for the older (mis-spelled) json file.
-
-If the image built from docker://katharinahoff/galba-notebook:latest dies at pygustus execution, please build the image from a different tag:
-
-```
-singularity build galba.sif docker://katharinahoff/galba-notebook:pygustusbug
-```
-
-and then try execution, again.
-
-In general, the tag docker://katharinahoff/galba-notebook:pygustusbug will probably work on all systems that do not have an older json file in the $AUGUSTUS_CONFIG_PATH/parameters folder.
-
-We will try to put some safeguards into the galba.pl code, later. Right now, you need to simply test which of the two tags works for your system.
-
 Running GALBA in Singularity outside of $HOME
 ---------------------------------------------
 

scripts/galba.pl

@@ -1155,7 +1155,7 @@ sub set_AUGUSTUS_BIN_PATH {
         }
     }
 
-    if ( not( defined($AUGUSTUS_BIN_PATH) ) ) {
+    if( not( defined($AUGUSTUS_BIN_PATH) ) ) {
         my $aug_bin_err;
         $aug_bin_err
             .= "There are 3 alternative ways to set this variable for\n"
@@ -1177,7 +1177,7 @@ sub set_AUGUSTUS_BIN_PATH {
             . "      executable that is available in your \$PATH\n"
             . "      (in this case, the augustus executable is not available).\n";
         $prtStr = "\# " . (localtime) . ": ERROR: in file " . __FILE__
-            . " at line ". __LINE__ . "\n" . "\$AUGUSTUS_BIN_PATH not set!\n";
+            . " at line ". __LINE__ . "\n\$AUGUSTUS_BIN_PATH not set!\n";
         $logString .= $prtStr;
         $logString .= $aug_bin_err if ($v > 0);
         print STDERR $logString;
@@ -3323,7 +3323,7 @@ sub make_prot_hints {
                 }
                 # Currently running miniprot twice, the first run only serves training gene generation
                 $cmdString
-                    .= "$prot_aligner -ut$CPU --outn=1 --gtf $otherfilesDir/genome.mpi $prot_seq_files[$i] >> $alignment_outfile ";
+                    .= "$prot_aligner -ut$CPU --outn=1 --gtf $otherfilesDir/genome.mpi $prot_seq_files[$i] >> $alignment_outfile 2>> $errorfile";
                 print LOG "\# "
                     . (localtime)
                     . ": running Miniprot to produce protein to "
@@ -3460,7 +3460,7 @@ sub make_prot_hints {
 
             # Currently running miniprot twice, the first run only serves training gene generation, the second shall produce the actual hints
             $cmdString
-                .= "$prot_aligner -ut$CPU --outn=1 --aln $otherfilesDir/genome.mpi $prot_seq_files[$i] >> $miniprot_aln_file ";
+                .= "$prot_aligner -ut$CPU --outn=1 --aln $otherfilesDir/genome.mpi $prot_seq_files[$i] >> $miniprot_aln_file 2>> $errorfile";
             print LOG "\# "
                 . (localtime)
                 . ": running Miniprot to produce protein to "