Hi, i met some problem extracting species marker genes from metaphlan4 database in step 2 of tutorial identifying strain transmission event
The version information was as follows:
$ strainphlan -v
Wed May 3 20:42:37 2023: StrainPhlAn version 4.0.3 (24 Oct 2022)
when i run
module load Anaconda3
source activate metaphlan4
module load Bowtie2
filename=$(cat ~/WORKSPACE/result/wzy/mother_infant/metaphlan4/SGB_input_transmission.txt | tail -n+2 | awk ‘{print $1}’)
db_markers=~/WORKSPACE/result/wzy/mother_infant/metaphlan4/db_markers
metaphlan4_database=~/WORKSPACE/database/metaphlan4_database/mpa_vJan21_CHOCOPhlAnSGB_202103.pkl
mkdir ~/WORKSPACE/result/wzy/mother_infant/metaphlan4/db_markers
for i in $filename
do
extract_markers.py -c ${i} -o ${db_markers} -d ${metaphlan4_database}
done
i encountered the error
Wed May 3 19:43:11 2023: Start extract markers execution
Wed May 3 19:43:11 2023: Extracting markers from the Bowtie2 database…
Wed May 3 19:54:43 2023: Done.
Wed May 3 19:54:43 2023: Loading MetaPhlAn mpa_vJan21_CHOCOPhlAnSGB_202103 database…
".Wed May 3 19:55:13 2023: Stop StrainPhlAn execution.: [Error] No markers were found for the clade "t__SGB10068
Wed May 3 19:55:14 2023: Start extract markers execution
Wed May 3 19:55:14 2023: Extracting markers from the Bowtie2 database…
Wed May 3 20:06:44 2023: Done.
Wed May 3 20:06:44 2023: Loading MetaPhlAn mpa_vJan21_CHOCOPhlAnSGB_202103 database…
".Wed May 3 20:07:13 2023: Stop StrainPhlAn execution.: [Error] No markers were found for the clade "t__SGB6148
i have referred to another previous issue and checked the SGB marker information of t__SGB10068 by ruuning
cat mpa_vJan21_CHOCOPhlAnSGB_202103_marker_info.txt | grep “t__SGB10068” | awk ‘{print $1, $3}’
and i do found a lot of SGB marker:
SGB10068__DKCKNNOD_02965 ‘t__SGB10068’,
SGB10068__BOKFPOAE_00433 ‘t__SGB10068’,
SGB10068__KKFLDMED_01050 ‘t__SGB10068’,
SGB10068__PPJOBBMP_00387 ‘t__SGB10068’,
SGB10068__ACFBEDFH_01712 ‘t__SGB10068’,
SGB10068__GIPCMNHK_02102 ‘t__SGB10068’,
SGB10068__NEHLOBGE_03055 ‘t__SGB10068’,
SGB10068__EMBPIGEI_03969 ‘t__SGB10068’,
SGB10068__NIEECKMC_04630 ‘t__SGB10068’,
SGB10068__KEDMLLKM_03350 ‘t__SGB10068’,
SGB10068__PGNBEFEI_01923 ‘t__SGB10068’,
SGB10068__FDOFALBO_00426 ‘t__SGB10068’,
SGB10068__LDAKBCFB_03173 ‘t__SGB10068’,
SGB10068__EJCLKCOE_01256 ‘t__SGB10068’,
SGB10068__EJPOHGHF_03821 ‘t__SGB10068’,
so it seems not the problem of without prefix _group.
could you figure out this issue for me? thanks a lot.
hope to hear from you soon.