more info on failing gmap_build

ablab · Aug 1, 2023 · 25d40ad · 25d40ad
1 parent 0fa7d8f
commit 25d40ad
Showing 1 changed file with 8 additions and 3 deletions.
diff --git a/general/UtilsTools.py b/general/UtilsTools.py
@@ -214,10 +214,15 @@ def run_gmap(args_reference, genome_len, args_transcripts, args_labels, args_thr
                    log_out_1=gmap_build_logger_out_path, log_out_2=gmap_build_logger_err_path)
         exit_code = subprocess.call(command, shell=True)
 
-        logger.info('  logs can be found in {} and {}.'.format(gmap_build_logger_out_path, gmap_build_logger_err_path))
+        logger.info('  logs can be found in {} and {}'.format(gmap_build_logger_out_path, gmap_build_logger_err_path))
 
         if exit_code != 0:
-            logger.error(message='{} failed!'.format(gmap_build), exit_with_code=exit_code, to_stderr=True)
+            gmap_build_logger_err_file = open(gmap_build_logger_err_path, "r")
+            logger.error(message='{} failed with the following error: '.format(gmap_build))
+            gmap_build_logger_err_file = open(gmap_build_logger_err_path, "r")
+            logger.error(gmap_build_logger_err_file.read())
+            gmap_build_logger_err_file.close()
+            logger.error(message='{} failed! Check you gmap installation. '.format(gmap_build), exit_with_code=exit_code, to_stderr=True)
 
         end_time = datetime.datetime.now()
         spent_time = end_time - start_time
@@ -590,4 +595,4 @@ def get_genome_bowtie2_index(reference_path, logger, log_dir):
     #
     # logger.info('  saved to {}'.format(isoforms_fa_path))
     #
-    # return isoforms_fa_path
+    # return isoforms_fa_path