diff options
| -rw-r--r-- | Code/BUGS.txt | 3 | ||||
| -rw-r--r-- | Code/configure.py | 2 | ||||
| -rw-r--r-- | Code/download_and_map.py | 2 |
3 files changed, 5 insertions, 2 deletions
diff --git a/Code/BUGS.txt b/Code/BUGS.txt new file mode 100644 index 0000000..acb5476 --- /dev/null +++ b/Code/BUGS.txt @@ -0,0 +1,3 @@ +[20250721A] Confirmed +SRR11093798 has small size (as it was in the file Data/log/download_log_small_sized_ids.txt), but salmon has been called to map it. +Expectation: salmon should not be called to map small-sized rna-seq data. diff --git a/Code/configure.py b/Code/configure.py index 34446c3..f12eed9 100644 --- a/Code/configure.py +++ b/Code/configure.py @@ -6,7 +6,7 @@ SALMON_MAP_RESULT_DIR = '../Data/temp/salmon_map_result' KMER = 31 # From download_and_map.py -DAILY_MAP_NUMBER = 10 # download this many samples each time. I have tested the values of 3, 4, 5, 8. +DAILY_MAP_NUMBER = 2 # download this many samples each time. I have tested the values of 3, 4, 5, 8. MIN_FASTQ_FILE_SIZE = 200000000 # in bytes, approximately 200MB INFO_DIR = '../Data/information/' ENA_RECORDS_READ_RUN = '../Data/information/ena_read_run.xml' diff --git a/Code/download_and_map.py b/Code/download_and_map.py index 7bc0dee..502b5e5 100644 --- a/Code/download_and_map.py +++ b/Code/download_and_map.py @@ -156,7 +156,7 @@ def has_no_more_time(times): first_time = times[0] now_time = datetime.now() time_diff = now_time - first_time - if time_diff.total_seconds()/3600 > 8: # started 8 hours ago, should stop now, let the machine rest for 16 hours + if time_diff.total_seconds()/3600 > 4: # started 8 hours ago, should stop now, let the machine rest for 20 hours return True return False |