Hi,
I’m using Humann 3.9 coupled with metaphlan 4.1.
I’ve downloaded the demo.fastq.gz + the demo databases.
When i run the demo file i receive different results than what is mentioned in the Humann tutorial.
My run looks like this:
Running metaphlan ........
Found g__GGB1511.s__GGB1511_SGB2091 : 81.49% of mapped reads ( )
Found t__SGB1871 : 16.03% of mapped reads ( s__Bacteroides_ovatus,g__Bacteroides.s__Bacteroides_sp_2_2_4,g__Bacteroides.s__Bacteroides_sp_AM56_10ce,g__Bacteroides.s__Bacteroides_sp_AF32_8BH,g__Bacteroides.s__Bacteroides_sp_KFT8,g__Bacteroides.s__Bacteroides_sp_HMSC073E02,g__Bacteroides.s__Bacteroides_sp_3_1_23,g__Bacteroides.s__Bacteroides_kribbi,g__Bacteroides.s__Bacteroides_sp_OF03_11BH,g__Bacteroides.s__Bacteroides_sp_MSK_17_76,g__Bacteroides.s__Bacteroides_sp_MSK_18_37 )
Found t__SGB2301 : 2.03% of mapped reads ( s__Alistipes_finegoldii,g__Alistipes.s__Alistipes_sp_HGB5 )
Found t__SGB1814 : 0.45% of mapped reads ( s__Bacteroides_vulgatus,g__Phocaeicola.s__Phocaeicola_dorei )
Total species selected from prescreen: 19
Selected species explain 100.00% of predicted community composition
Creating custom ChocoPhlAn database ........
Running bowtie2-build ........
Running bowtie2 ........
Total bugs from nucleotide alignment: 1
g__Bacteroides.s__Bacteroides_vulgatus: 25357 hits
Total gene families from nucleotide alignment: 838
Unaligned reads after nucleotide alignment: 82.3496655367 %
Running diamond ........
Aligning to reference database: uniref90_demo_prots_v201901b.dmnd
Total bugs after translated alignment: 1
g__Bacteroides.s__Bacteroides_vulgatus: 25357 hits
Total gene families after translated alignment: 838
Unaligned reads after translated alignment: 82.3496655367 %
Computing gene families ...
Computing pathways abundance and coverage ...
Output files created:
/home/ec2-user/humann3_test/demo3_fastq/demo3_genefamilies.tsv
/home/ec2-user/humann3_test/demo3_fastq/demo3_pathabundance.tsv
/home/ec2-user/humann3_test/demo3_fastq/demo3_pathcoverage.tsv```
Can you share whether this output is OK since it does not match what appears in the toturial.
Thanks