Merge branch 'master' of https://github.com/biobakery/MetaPhlAn

CHANGELOG.md

@@ -7,6 +7,7 @@
 * [MetaPhlAn] Implementation of the option `--subsampling_paired [N_PAIRED_READS]` to subsample paired-end input reads. It needs to be used in conjunction with `-1 [FORWARD_READS_FILE]` and `-2 [REVERSE_READS_FILE]`
 ### Fixes
 * [MetaPhlAn] Fixed a bug that would halt MetaPhlAn execution when the option `--profile_vsc` was used but had no viral hits
+* [MetaPhlAn] Fixed a bug that would halt MetaPhlAn execution when the number of reads to map was zero
 * [StrainPhlAn] Fixed a bug in the new implementation (since v4.1) of `–-print_clades_only`
   <br/>
 
@@ -55,7 +56,7 @@
 * [StrainPhlAn] Improved StrainPhlAn's speed when running with the --print_clades_only option
 ### Missing features
 * [MetaPhlAn] The GTDB taxonomic assignment for the vOct22 database is not available yet (expected release: end of Feb 2023)
-* [MetaPhlAn] The phylogenetic tree of life for the vOct22 database is not available yet (expected release: TBD).
+* [MetaPhlAn] The phylogenetic tree of life for the vOct22 database is not available yet (expected release: TBD)
 
 <br/>
 

metaphlan/utils/fix_relab_mpa4.py

@@ -7,7 +7,7 @@
 
 import os, time
 try:
-    from .util_fun import info, error, warning
+    from .util_fun import info, error, warning, openrt
 except ImportError:
     from util_fun import info, error, warning, openrt
 import argparse as ap

metaphlan/utils/read_fastx.py

@@ -114,10 +114,15 @@ def read_and_write_raw_int(fd, min_len=None, prefix_id=""):
     #         avg_read_length = len(l) + avg_read_length
     #         _ = sys.stdout.write(ignore_spaces(l))
 
+    if not idx:
+        sys.stderr.write('Error: no reads found.\n')
+        sys.exit(1)
+
     nreads = idx - discarded
 
     if not nreads:
-        nreads, avg_read_length = 0, 0
+        sys.stderr.write('Error: no reads longer than {} bp found.\n'.format(min_len))
+        sys.exit(1)
 
     return (nreads, avg_read_length)