I used this command metaphlan -1 ./rawdata_fq/SRR5898908_1.fastq -2 ./rawdata_fq/SRR5898908_2.fastq --input_type fastq --subsampling_paired 5327757 > ./R_Taxonomy/SRR5898908.txt, but it reported an error. Can’t it recognize paired-end data? This is the error content: Sun Jul 20 12:39:21 2025: [Warning] It seems that you do not have Internet access.
Sun Jul 20 12:39:21 2025: [Warning] Cannot connect to the database server. The latest available local database will be used.
Traceback (most recent call last):
File “/home/huanglin/anaconda3/envs/Metagenome/bin/metaphlan”, line 10, in
sys.exit(main())
File “/home/huanglin/anaconda3/envs/Metagenome/lib/python3.9/site-packages/metaphlan/metaphlan.py”, line 2263, in main
metaphlan_runner.run_metaphlan()
File “/home/huanglin/anaconda3/envs/Metagenome/lib/python3.9/site-packages/metaphlan/metaphlan.py”, line 1907, in run_metaphlan
self.mapping_controller.run_mapping()
File “/home/huanglin/anaconda3/envs/Metagenome/lib/python3.9/site-packages/metaphlan/metaphlan.py”, line 933, in run_mapping
self.init_mapping_arguments()
File “/home/huanglin/anaconda3/envs/Metagenome/lib/python3.9/site-packages/metaphlan/metaphlan.py”, line 759, in init_mapping_arguments
self.init_mapout()
File “/home/huanglin/anaconda3/envs/Metagenome/lib/python3.9/site-packages/metaphlan/metaphlan.py”, line 697, in init_mapout
elif stat.S_ISFIFO(os.stat(self.inp).st_mode):
FileNotFoundError: [Errno 2] No such file or directory: ‘/tmp/tmp5jaxfmgi,/tmp/tmp99lke42_’
Hi @linhuang
MetaPhlAn uses the paired information only when performing the paired subsampling as you are doing. The issue seems to be with the intermediate mapping file, you can try to explicitly specify it (with –bowtie2out until 4.1.*, with –mapout since 4.2.*). To be safe, I suggest you download the latest version of metaphlan (4.2.2)