No SNPs left after intersection of partitions (--min-partition-size option)

[doy-pin]

Hi,

I ran the command: parsnp -r ref.fna -d fna_files/*.fna -p 20 -c -x --min-partition-size 40

Portions of the output is below: (this is the first few lines) /home/doy.pinili/.conda/envs/parsnp2/bin/parsnp:147: SyntaxWarning: invalid escape sequence '\d' hdr_block_pattern = re.compile("##SequenceIndex (\d+)\n##SequenceFile (.+)\n##SequenceHeader >\s*(\S+).*\n##SequenceLength (\d+)bp") /home/doy.pinili/.conda/envs/parsnp2/bin/parsnp:153: SyntaxWarning: invalid escape sequence '\d' seq_count = int(re.match("#SequenceCount (\d+)\n", line).groups()[0]) 01:29:48 - ESC[1;37mINFOESC[0m - |--Parsnp 2.0.5--|

(this is the part where min-partition-size ran) 01:30:08 - ESC[1;37mINFOESC[0m - Setting the partition size to 40 01:30:08 - ESC[1;37mINFOESC[0m - Running partitions... 01:30:08 - ESC[1;37mINFOESC[0m - 0%| | 0/13 [00:00<?, ?it/s] 01:34:45 - ESC[1;37mINFOESC[0m - 8%|7 | 1/13 [04:36<55:19, 276.62s/it] 01:34:47 - ESC[1;37mINFOESC[0m - 92%|#########2| 12/13 [04:38<00:23, 23.20s/it] 01:34:47 - ESC[1;37mINFOESC[0m - Computing intersection of all partition LCBs... 01:35:00 - ESC[1;37mINFOESC[0m - Partition stats: Mean bp covered = 1361113.23 Mean LCB count = 1397.46 01:35:00 - ESC[1;37mINFOESC[0m - After intersection: 0 reference bases over 0 clusters 01:35:00 - ESC[1;37mINFOESC[0m - Trimming partitioned XMFAs back to intersected intervals...

Can you help me on this? I will try to run without the --min-partition-size option also

[bkille]

Hi @doy-pin!

Hmmm, you may have some bad input files. Each partitioned run is covering an average of 1.3Mbp, but there are no aligned regions common to all partitions. This likely means that one (or more) of your partitions contains at least one problematic fasta file (i.e. either a low-quality or very divergent assembly).

What happens if you run without the curated flag? (without -c).