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Merge branch 'master' of https://github.com/biobakery/MetaPhlAn
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Cengoni committed Jun 19, 2024
2 parents cda4f3e + a8c2971 commit 6570549
Showing 3 changed files with 9 additions and 3 deletions.
3 changes: 2 additions & 1 deletion CHANGELOG.md
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@@ -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)

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2 changes: 1 addition & 1 deletion metaphlan/utils/fix_relab_mpa4.py
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@@ -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
7 changes: 6 additions & 1 deletion metaphlan/utils/read_fastx.py
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@@ -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)

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