Humann3 intermediate output file (sam) for strainphlan

Microbial community profiling StrainPhlAn
1

Hi all, I ran humann3 in the following manner:

humann3 --input “$0” --output “$1”_humann3_out --input-format fastq --nucleotide-database /data/databases/Humann3/chocophlan/ --protein-database /data/databases/Humann3/uniref/ --diamond /install/software/anaconda3.6.a/bin/ --metaphlan /install/software/mincondas/3.7/instance2/bin/metaphlan --metaphlan-options “–bowtie2db /data/databases/MetaPhlAn3/ --index mpa_v30_CHOCOPhlAn_201901” --search-mode uniref90 --threads 9 --memory-use maximum"

The intermediate output folder thus formed has an aligned sam file. Can this file be used to produce consensus marker sequences and run strainphlan? Or will I have to run metaphlan again as described in the tutorial and generate a sam file and run strainphlan? Will these 2 files be different?

Apologies for the basic question, any help would be appreciated.
Thank you

Best
DP

2

Hi @Dhrati_Patangia
Thanks for getting in touch. Could you share the first lines of the sam file to understand whether that is the sam file containing the mapping of the MetaPhlAn marker genes or the one for the Humann pangenomes.
Thanks

3

Hi @aitor.blancomiguez , sure. The start of one of the files looks like this:

@HD VN:1.0 SO:unsorted
@SQ SN:817__A0A374W6K5__M132_1536|k__Bacteria.p__Bacteroidetes.c__Bacteroidia.o__Bacteroidales.f__Bacteroidaceae.g__Bacteroides.s__Bacteroides_fragilis|UniRef90_A0A374W6K5|UniRef50_U2MJZ6|300 LN:300
@SQ SN:817__F3PU10__M132_4381|k__Bacteria.p__Bacteroidetes.c__Bacteroidia.o__Bacteroidales.f__Bacteroidaceae.g__Bacteroides.s__Bacteroides_fragilis|UniRef90_F3PU10|UniRef50_P59916|1242 LN:1242
@SQ SN:817__Q5LG69__M132_1046|k__Bacteria.p__Bacteroidetes.c__Bacteroidia.o__Bacteroidales.f__Bacteroidaceae.g__Bacteroides.s__Bacteroides_fragilis|UniRef90_Q5LG69|UniRef50_Q5LG69|480 LN:480
@SQ SN:817__UPI00044762BA__M132_4718|k__Bacteria.p__Bacteroidetes.c__Bacteroidia.o__Bacteroidales.f__Bacteroidaceae.g__Bacteroides.s__Bacteroides_fragilis|UniRef90_UPI00044762BA|UniRef50_UPI00044762BA|408 LN:408
@SQ SN:817__A0A396ED79__M132_2610|k__Bacteria.p__Bacteroidetes.c__Bacteroidia.o__Bacteroidales.f__Bacteroidaceae.g__Bacteroides.s__Bacteroides_fragilis|UniRef90_A0A396ED79|UniRef50_A0A396ED79|327 LN:327
@SQ SN:817__A0A015WAV5__M132_2651|k__Bacteria.p__Bacteroidetes.c__Bacteroidia.o__Bacteroidales.f__Bacteroidaceae.g__Bacteroides.s__Bacteroides_fragilis|UniRef90_A0A015WAV5|UniRef50_A0A015WAV5|960 LN:960
@SQ SN:817__A0A0E2SYD2__M132_2141|k__Bacteria.p__Bacteroidetes.c__Bacteroidia.o__Bacteroidales.f__Bacteroidaceae.g__Bacteroides.s__Bacteroides_fragilis|UniRef90_A0A0E2SYD2|UniRef50_A0A0E2SYD2|156 LN:156
@SQ SN:817__B3CC52__M132_2606|k__Bacteria.p__Bacteroidetes.c__Bacteroidia.o__Bacteroidales.f__Bacteroidaceae.g__Bacteroides.s__Bacteroides_fragilis|UniRef90_B3CC52|UniRef50_B3CC52|123 LN:123
@SQ SN:817__A0A0K6BV26__M132_2136|k__Bacteria.p__Bacteroidetes.c__Bacteroidia.o__Bacteroidales.f__Bacteroidaceae.g__Bacteroides.s__Bacteroides_fragilis|UniRef90_A0A0K6BV26|UniRef50_D1QQK5|1098 LN:1098

Thank you for your help
DP

4

Hi @Dhrati_Patangia
That seems to be the mapping results against the full pangenomes. Unfortunately, you will have to run MetaPhlAn again with the -s / --samout option.

Best,
Aitor

5

Hi @aitor.blancomiguez
Thank you very much for clarifying this, I will do so.
Best
Dhrati