After reading through all the topics, I have no idea about the high percentage of unaligned reads.
I am working on the rhizosphere metagenomic data, using uniref50.
humann2 version 0.11.2
metaphlan2 version 2.7.7 (31 May 2018)
my command:
cd /public/home/jkyin/yjk/tomato_micro/raw
source activate humann2
humann2 --input A57RS1T1.fa \
--output ../humann2_uniref50/A57RS1T1 \
--threads 16 \
--verbose \
--taxonomic-profile ../metaphlan2/A57RS1T1_mtph2.txt \
--memory-use maximum \
--remove-temp-output
the output
<< output from stdout >>
Creating output directory: /public/home/jkyin/yjk/tomato_micro/humann2_uniref50/A57RS1T1
Output files will be written to: /public/home/jkyin/yjk/tomato_micro/humann2_uniref50/A57RS1T1
Writing temp files to directory: /public/home/jkyin/yjk/tomato_micro/humann2_uniref50/A57RS1T1/A57RS1T1_humann2_temp_eGo9F8
File ( /public/home/jkyin/yjk/tomato_micro/raw/A57RS1T1.fa ) is of format: fasta
Found g__Sphingobium.s__Sphingobium_unclassified : 24.92% of mapped reads
Found g__Ralstonia.s__Ralstonia_solanacearum : 3.97% of mapped reads
Found g__Sphingomonas.s__Sphingomonas_wittichii : 2.89% of mapped reads
Found g__Pseudomonas.s__Pseudomonas_unclassified : 2.80% of mapped reads
Found g__Asticcacaulis.s__Asticcacaulis_unclassified : 2.31% of mapped reads
Found g__Pseudomonas.s__Pseudomonas_putida : 2.15% of mapped reads
Found g__Burkholderia.s__Burkholderia_unclassified : 2.12% of mapped reads
Found g__Sphaerobacter.s__Sphaerobacter_thermophilus : 1.85% of mapped reads
Found g__Sphingopyxis.s__Sphingopyxis_unclassified : 1.82% of mapped reads
Found g__Thiomonas.s__Thiomonas_unclassified : 1.79% of mapped reads
Found g__Rhodanobacter.s__Rhodanobacter_unclassified : 1.76% of mapped reads
Found g__Cellvibrio.s__Cellvibrio_unclassified : 1.73% of mapped reads
Found g__Actinoplanes.s__Actinoplanes_unclassified : 1.64% of mapped reads
Found g__Paracoccus.s__Paracoccus_unclassified : 1.32% of mapped reads
Found g__Nocardioides.s__Nocardioides_unclassified : 1.31% of mapped reads
Found g__Pseudomonas.s__Pseudomonas_mendocina : 1.28% of mapped reads
Found g__Alicycliphilus.s__Alicycliphilus_unclassified : 1.17% of mapped reads
Found g__Massilia.s__Massilia_unclassified : 1.08% of mapped reads
Found g__Paracoccus.s__Paracoccus_denitrificans : 1.06% of mapped reads
Found g__Oscillatoria.s__Oscillatoria_nigro_viridis : 0.94% of mapped reads
Found g__Azospirillum.s__Azospirillum_lipoferum : 0.92% of mapped reads
Found g__Rhodopseudomonas.s__Rhodopseudomonas_palustris : 0.89% of mapped reads
Found g__Caulobacter.s__Caulobacter_unclassified : 0.87% of mapped reads
Found g__Variovorax.s__Variovorax_unclassified : 0.86% of mapped reads
Found g__Leifsonia.s__Leifsonia_unclassified : 0.85% of mapped reads
Found g__Mesorhizobium.s__Mesorhizobium_unclassified : 0.84% of mapped reads
Found g__Agromyces.s__Agromyces_unclassified : 0.72% of mapped reads
Found g__Microcoleus.s__Microcoleus_vaginatus : 0.66% of mapped reads
Found g__Hyphomicrobium.s__Hyphomicrobium_unclassified : 0.65% of mapped reads
Found g__Sporichthya.s__Sporichthya_polymorpha : 0.64% of mapped reads
Found g__Pseudoxanthomonas.s__Pseudoxanthomonas_unclassified : 0.46% of mapped reads
Found g__Rhizobium.s__Rhizobium_etli : 0.44% of mapped reads
Found g__Bordetella.s__Bordetella_unclassified : 0.40% of mapped reads
Found g__Pseudomonas.s__Pseudomonas_stutzeri : 0.40% of mapped reads
Found g__Bacillus.s__Bacillus_megaterium : 0.39% of mapped reads
Found g__Phenylobacterium.s__Phenylobacterium_zucineum : 0.31% of mapped reads
Found g__Sorangium.s__Sorangium_cellulosum : 0.27% of mapped reads
Found g__Bordetella.s__Bordetella_petrii : 0.26% of mapped reads
Found g__Mycobacterium.s__Mycobacterium_thermoresistibile : 0.25% of mapped reads
Found g__Thiobacillus.s__Thiobacillus_denitrificans : 0.23% of mapped reads
Found g__Rhodanobacter.s__Rhodanobacter_fulvus : 0.23% of mapped reads
Found g__Kribbella.s__Kribbella_unclassified : 0.22% of mapped reads
Found g__Microcoleus.s__Microcoleus_unclassified : 0.22% of mapped reads
Found g__Achromobacter.s__Achromobacter_unclassified : 0.22% of mapped reads
Found g__Singularimonas.s__Singularimonas_variicoloris : 0.20% of mapped reads
Found g__Bradyrhizobium.s__Bradyrhizobium_japonicum : 0.18% of mapped reads
Found g__Methylophilus.s__Methylophilus_methylotrophus : 0.18% of mapped reads
Found g__Streptomyces.s__Streptomyces_chartreusis : 0.16% of mapped reads
Found g__Sphingobacterium.s__Sphingobacterium_unclassified : 0.16% of mapped reads
Found g__Brevundimonas.s__Brevundimonas_unclassified : 0.16% of mapped reads
Found g__Pseudonocardia.s__Pseudonocardia_unclassified : 0.15% of mapped reads
Found g__Dyadobacter.s__Dyadobacter_fermentans : 0.14% of mapped reads
Found g__Mesorhizobium.s__Mesorhizobium_loti : 0.13% of mapped reads
Found g__Azospirillum.s__Azospirillum_unclassified : 0.13% of mapped reads
Found g__Caulobacter.s__Caulobacter_vibrioides : 0.13% of mapped reads
Found g__Rhizobium.s__Rhizobium_leguminosarum : 0.12% of mapped reads
Found g__Nitrosospira.s__Nitrosospira_multiformis : 0.12% of mapped reads
Found g__Pusillimonas.s__Pusillimonas_unclassified : 0.12% of mapped reads
Found g__Alcanivorax.s__Alcanivorax_pacificus : 0.12% of mapped reads
Found g__Oscillatoria.s__Oscillatoria_unclassified : 0.10% of mapped reads
Found g__Delftia.s__Delftia_unclassified : 0.09% of mapped reads
Found g__Nitrosospira.s__Nitrosospira_unclassified : 0.09% of mapped reads
Found g__Nocardia.s__Nocardia_cyriacigeorgica : 0.09% of mapped reads
Found g__Cellulomonas.s__Cellulomonas_unclassified : 0.08% of mapped reads
Found g__Actinomadura.s__Actinomadura_madurae : 0.07% of mapped reads
Found g__Micromonospora.s__Micromonospora_unclassified : 0.07% of mapped reads
Found g__Salinispora.s__Salinispora_unclassified : 0.07% of mapped reads
Found g__Afipia.s__Afipia_unclassified : 0.06% of mapped reads
Found g__Serinicoccus.s__Serinicoccus_unclassified : 0.06% of mapped reads
Found g__Pelagibacterium.s__Pelagibacterium_halotolerans : 0.06% of mapped reads
Found g__Deinococcus.s__Deinococcus_unclassified : 0.06% of mapped reads
Found g__Symbiobacterium.s__Symbiobacterium_thermophilum : 0.06% of mapped reads
Found g__Achromobacter.s__Achromobacter_piechaudii : 0.06% of mapped reads
Found g__Coprothermobacter.s__Coprothermobacter_proteolyticus : 0.05% of mapped reads
Found g__Granulicella.s__Granulicella_unclassified : 0.05% of mapped reads
Found g__Variovorax.s__Variovorax_paradoxus : 0.05% of mapped reads
Found g__Comamonas.s__Comamonas_unclassified : 0.05% of mapped reads
Found g__Hyphomicrobium.s__Hyphomicrobium_denitrificans : 0.04% of mapped reads
Found g__Anaeromyxobacter.s__Anaeromyxobacter_unclassified : 0.04% of mapped reads
Found g__Nitrolancetus.s__Nitrolancetus_hollandicus : 0.03% of mapped reads
Found g__Sphingobium.s__Sphingobium_chinhatense : 0.03% of mapped reads
Found g__Ornithinimicrobium.s__Ornithinimicrobium_pekingense : 0.03% of mapped reads
Found g__Thermomonospora.s__Thermomonospora_curvata : 0.03% of mapped reads
Found g__Mycobacterium.s__Mycobacterium_hassiacum : 0.03% of mapped reads
Found g__Ochrobactrum.s__Ochrobactrum_unclassified : 0.02% of mapped reads
Found g__Mycobacterium.s__Mycobacterium_phlei : 0.01% of mapped reads
Found g__Niastella.s__Niastella_koreensis : 0.01% of mapped reads
Found g__Agrobacterium.s__Agrobacterium_unclassified : 0.01% of mapped reads
Total species selected from prescreen: 88
Selected species explain 75.85% of predicted community composition
Creating custom ChocoPhlAn database ........
/bin/gunzip -c /public/home/jkyin/biosoft/database/chocophlan/g__Achromobacter.s__Achromobacter_piechaudii.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Pseudomonas.s__Pseudomonas_putida.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Symbiobacterium.s__Symbiobacterium_thermophilum.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Ralstonia.s__Ralstonia_solanacearum.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Bacillus.s__Bacillus_megaterium.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Pseudomonas.s__Pseudomonas_mendocina.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Variovorax.s__Variovorax_paradoxus.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Rhizobium.s__Rhizobium_etli.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Pelagibacterium.s__Pelagibacterium_halotolerans.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Streptomyces.s__Streptomyces_chartreusis.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Nitrolancetus.s__Nitrolancetus_hollandicus.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Paracoccus.s__Paracoccus_denitrificans.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Caulobacter.s__Caulobacter_vibrioides.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Microcoleus.s__Microcoleus_vaginatus.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Pseudomonas.s__Pseudomonas_stutzeri.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Coprothermobacter.s__Coprothermobacter_proteolyticus.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Alcanivorax.s__Alcanivorax_pacificus.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Sphaerobacter.s__Sphaerobacter_thermophilus.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Ornithinimicrobium.s__Ornithinimicrobium_pekingense.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Sphingobium.s__Sphingobium_chinhatense.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Dyadobacter.s__Dyadobacter_fermentans.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Hyphomicrobium.s__Hyphomicrobium_denitrificans.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Thiobacillus.s__Thiobacillus_denitrificans.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Rhodanobacter.s__Rhodanobacter_fulvus.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Nitrosospira.s__Nitrosospira_multiformis.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Oscillatoria.s__Oscillatoria_nigro_viridis.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Sporichthya.s__Sporichthya_polymorpha.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Rhizobium.s__Rhizobium_leguminosarum.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Mycobacterium.s__Mycobacterium_hassiacum.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Nocardia.s__Nocardia_cyriacigeorgica.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Bradyrhizobium.s__Bradyrhizobium_japonicum.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Methylophilus.s__Methylophilus_methylotrophus.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Actinomadura.s__Actinomadura_madurae.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Singularimonas.s__Singularimonas_variicoloris.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Phenylobacterium.s__Phenylobacterium_zucineum.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Mesorhizobium.s__Mesorhizobium_loti.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Rhodopseudomonas.s__Rhodopseudomonas_palustris.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Azospirillum.s__Azospirillum_lipoferum.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Bordetella.s__Bordetella_petrii.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Mycobacterium.s__Mycobacterium_thermoresistibile.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Sorangium.s__Sorangium_cellulosum.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Thermomonospora.s__Thermomonospora_curvata.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Sphingomonas.s__Sphingomonas_wittichii.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Niastella.s__Niastella_koreensis.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Mycobacterium.s__Mycobacterium_phlei.centroids.v0.1.1.ffn.gz
TIMESTAMP: Completed custom database creation : 9 seconds
Running bowtie2-build ........
/public/home/jkyin/miniconda3/envs/humann2/bin/bowtie2-build -f /public/home/jkyin/yjk/tomato_micro/humann2_uniref50/A57RS1T1/A57RS1T1_humann2_temp_eGo9F8/A57RS1T1_custom_chocophlan_database.ffn /public/home/jkyin/yjk/tomato_micro/humann2_uniref50/A57RS1T1/A57RS1T1_humann2_temp_eGo9F8/A57RS1T1_bowtie2_index
TIMESTAMP: Completed database index : 673 seconds
Running bowtie2 ........
/public/home/jkyin/miniconda3/envs/humann2/bin/bowtie2 -f -x /public/home/jkyin/yjk/tomato_micro/humann2_uniref50/A57RS1T1/A57RS1T1_humann2_temp_eGo9F8/A57RS1T1_bowtie2_index -U /public/home/jkyin/yjk/tomato_micro/raw/A57RS1T1.fa -S /public/home/jkyin/yjk/tomato_micro/humann2_uniref50/A57RS1T1/A57RS1T1_humann2_temp_eGo9F8/A57RS1T1_bowtie2_aligned.sam -p 16 --very-sensitive
TIMESTAMP: Completed nucleotide alignment : 1187 seconds
TIMESTAMP: Completed nucleotide alignment post-processing : 1673 seconds
Total bugs from nucleotide alignment: 45
g__Pelagibacterium.s__Pelagibacterium_halotolerans: 3766 hits
g__Bacillus.s__Bacillus_megaterium: 10057 hits
g__Hyphomicrobium.s__Hyphomicrobium_denitrificans: 6705 hits
g__Actinomadura.s__Actinomadura_madurae: 260684 hits
g__Caulobacter.s__Caulobacter_vibrioides: 11602 hits
g__Mycobacterium.s__Mycobacterium_hassiacum: 6478 hits
g__Rhodanobacter.s__Rhodanobacter_fulvus: 50389 hits
g__Sorangium.s__Sorangium_cellulosum: 23206 hits
g__Ralstonia.s__Ralstonia_solanacearum: 130886 hits
g__Streptomyces.s__Streptomyces_chartreusis: 50209 hits
g__Microcoleus.s__Microcoleus_vaginatus: 50897 hits
g__Thermomonospora.s__Thermomonospora_curvata: 7545 hits
g__Oscillatoria.s__Oscillatoria_nigro_viridis: 57072 hits
g__Thiobacillus.s__Thiobacillus_denitrificans: 9660 hits
g__Nitrolancetus.s__Nitrolancetus_hollandicus: 2190 hits
g__Mycobacterium.s__Mycobacterium_phlei: 14061 hits
g__Mesorhizobium.s__Mesorhizobium_loti: 75494 hits
g__Nocardia.s__Nocardia_cyriacigeorgica: 7691 hits
g__Bradyrhizobium.s__Bradyrhizobium_japonicum: 97896 hits
g__Mycobacterium.s__Mycobacterium_thermoresistibile: 11079 hits
g__Sphaerobacter.s__Sphaerobacter_thermophilus: 28213 hits
g__Azospirillum.s__Azospirillum_lipoferum: 16455 hits
g__Ornithinimicrobium.s__Ornithinimicrobium_pekingense: 21767 hits
g__Niastella.s__Niastella_koreensis: 3942 hits
g__Pseudomonas.s__Pseudomonas_mendocina: 66700 hits
g__Rhizobium.s__Rhizobium_etli: 24481 hits
g__Symbiobacterium.s__Symbiobacterium_thermophilum: 2288 hits
g__Methylophilus.s__Methylophilus_methylotrophus: 5095 hits
g__Pseudomonas.s__Pseudomonas_putida: 75837 hits
g__Alcanivorax.s__Alcanivorax_pacificus: 5942 hits
g__Variovorax.s__Variovorax_paradoxus: 149075 hits
g__Bordetella.s__Bordetella_petrii: 22574 hits
g__Paracoccus.s__Paracoccus_denitrificans: 15743 hits
g__Sphingobium.s__Sphingobium_chinhatense: 71054 hits
g__Pseudomonas.s__Pseudomonas_stutzeri: 28769 hits
g__Coprothermobacter.s__Coprothermobacter_proteolyticus: 789 hits
g__Singularimonas.s__Singularimonas_variicoloris: 49225 hits
g__Sporichthya.s__Sporichthya_polymorpha: 36650 hits
g__Phenylobacterium.s__Phenylobacterium_zucineum: 32040 hits
g__Dyadobacter.s__Dyadobacter_fermentans: 7850 hits
g__Rhodopseudomonas.s__Rhodopseudomonas_palustris: 43425 hits
g__Sphingomonas.s__Sphingomonas_wittichii: 110169 hits
g__Achromobacter.s__Achromobacter_piechaudii: 8155 hits
g__Nitrosospira.s__Nitrosospira_multiformis: 2142 hits
g__Rhizobium.s__Rhizobium_leguminosarum: 31950 hits
Total gene families from nucleotide alignment: 89611
Unaligned reads after nucleotide alignment: 99.2044730605 %
Running diamond ........
Aligning to reference database: uniref50_annotated.1.1.dmnd
I have filtered the tomato reads using soap.
(base) [jkyin@c02n12 soap2_solanum]$ 2bwt-builder GCF_000188115.4_SL3.0_genomic.fna
Index building is completed.
Total elapsed time = 743.23 s
get the unmapped reads as clean reads.
(base) [jkyin@c02n12 A57RS1T1]$ soap -a A57RS1T1_1.clean.fq.gz -b A57RS1T1_2.clean.fq.gz -D /public/home/jkyin/biosoft/database/soap2_solanum/GCF_000188115.4_SL3.0_genomic.fna.index -o output -2 unpaired -u A57RS1T1.fa
Using fastq_screen check the tomato contamination, only ~1% reads were considered as host genome.
As you suggested in other threads, I blast ~ 10 reads from the unmapped reads produced by humann2, I almost did not found any hits.
That’'s common to see?
Or is there sth wrong?
Your output is missing the % of reads mapped after the translated search (diamond) step, which is where I’d expect to see the majority of mapping happening for a non-mammalian microbiome. If you’re blasting reads that were unmapped after diamond, especially blastx’ing against a protein database, and not seeing any hits, it’s a pretty good sign that you have a lot of very novel DNA sequence in your sample.
Until now, I got the % of reads mapped after the translated search step. They were reasonable I think. Here is an example of the samples. Thanks for help very much.
Unaligned reads after translated alignment: 42.8833739778 %
Hello I have another question. It seems that humann2 stuck in the step Creating custom ChocoPhlAn database; But the temp dir is updating. Is there sth wrong. By the way, I have run other samples successfully. Thanks for help.
Creating output directory: /public/home/jkyin/yjk/tomato_micro/humann2_uniref50/HG70RS1T2C
Output files will be written to: /public/home/jkyin/yjk/tomato_micro/humann2_uniref50/HG70RS1T2C
Writing temp files to directory: /public/home/jkyin/yjk/tomato_micro/humann2_uniref50/HG70RS1T2C/HG70RS1T2C_humann2_temp_pKbZmH
File ( /public/home/jkyin/yjk/tomato_micro/raw/HG70RS1T2C.fa ) is of format: fasta
Found g__Sphingobium.s__Sphingobium_unclassified : 42.34% of mapped reads
Found g__Caulobacter.s__Caulobacter_unclassified : 11.60% of mapped reads
Found g__Actinoplanes.s__Actinoplanes_unclassified : 6.83% of mapped reads
Found g__Sphingopyxis.s__Sphingopyxis_unclassified : 3.09% of mapped reads
Found g__Caulobacter.s__Caulobacter_vibrioides : 2.62% of mapped reads
Found g__Burkholderia.s__Burkholderia_unclassified : 2.57% of mapped reads
Found g__Massilia.s__Massilia_unclassified : 2.20% of mapped reads
Found g__Sphingomonas.s__Sphingomonas_wittichii : 2.16% of mapped reads
Found g__Ralstonia.s__Ralstonia_unclassified : 1.90% of mapped reads
Found g__Leifsonia.s__Leifsonia_unclassified : 1.78% of mapped reads
Found g__Variovorax.s__Variovorax_unclassified : 1.29% of mapped reads
Found g__Hyphomicrobium.s__Hyphomicrobium_denitrificans : 1.11% of mapped reads
Found g__Mesorhizobium.s__Mesorhizobium_unclassified : 1.05% of mapped reads
Found g__Asticcacaulis.s__Asticcacaulis_unclassified : 1.03% of mapped reads
Found g__Rhodanobacter.s__Rhodanobacter_unclassified : 0.87% of mapped reads
Found g__Rhizobium.s__Rhizobium_etli : 0.86% of mapped reads
Found g__Agromyces.s__Agromyces_unclassified : 0.83% of mapped reads
Found g__Rhodopseudomonas.s__Rhodopseudomonas_palustris : 0.77% of mapped reads
Found g__Nocardioides.s__Nocardioides_unclassified : 0.75% of mapped reads
Found g__Streptomyces.s__Streptomyces_chartreusis : 0.66% of mapped reads
Found g__Bradyrhizobium.s__Bradyrhizobium_japonicum : 0.62% of mapped reads
Found g__Microcoleus.s__Microcoleus_vaginatus : 0.48% of mapped reads
Found g__Pseudonocardia.s__Pseudonocardia_unclassified : 0.46% of mapped reads
Found g__Sorangium.s__Sorangium_cellulosum : 0.46% of mapped reads
Found g__Pseudomonas.s__Pseudomonas_unclassified : 0.42% of mapped reads
Found g__Rhizobium.s__Rhizobium_lupini : 0.41% of mapped reads
Found g__Oscillatoria.s__Oscillatoria_nigro_viridis : 0.41% of mapped reads
Found g__Rhizobium.s__Rhizobium_leguminosarum : 0.40% of mapped reads
Found g__Azospirillum.s__Azospirillum_lipoferum : 0.35% of mapped reads
Found g__Achromobacter.s__Achromobacter_unclassified : 0.34% of mapped reads
Found g__Mesorhizobium.s__Mesorhizobium_loti : 0.33% of mapped reads
Found g__Janthinobacterium.s__Janthinobacterium_unclassified : 0.33% of mapped reads
Found g__Agrobacterium.s__Agrobacterium_unclassified : 0.32% of mapped reads
Found g__Brevundimonas.s__Brevundimonas_unclassified : 0.31% of mapped reads
Found g__Hyphomicrobium.s__Hyphomicrobium_unclassified : 0.31% of mapped reads
Found g__Niastella.s__Niastella_koreensis : 0.30% of mapped reads
Found g__Paracoccus.s__Paracoccus_denitrificans : 0.27% of mapped reads
Found g__Ralstonia.s__Ralstonia_pickettii : 0.27% of mapped reads
Found g__Oscillatoria.s__Oscillatoria_unclassified : 0.25% of mapped reads
Found g__Cellulomonas.s__Cellulomonas_unclassified : 0.25% of mapped reads
Found g__Streptomyces.s__Streptomyces_gancidicus : 0.24% of mapped reads
Found g__Afipia.s__Afipia_unclassified : 0.23% of mapped reads
Found g__Salinispora.s__Salinispora_unclassified : 0.22% of mapped reads
Found g__Micromonospora.s__Micromonospora_unclassified : 0.20% of mapped reads
Found g__Pseudanabaena.s__Pseudanabaena_unclassified : 0.20% of mapped reads
Found g__Alicycliphilus.s__Alicycliphilus_unclassified : 0.19% of mapped reads
Found g__Pedobacter.s__Pedobacter_unclassified : 0.14% of mapped reads
Found g__Terriglobus.s__Terriglobus_unclassified : 0.13% of mapped reads
Found g__Microcoleus.s__Microcoleus_unclassified : 0.13% of mapped reads
Found g__Methylophilus.s__Methylophilus_methylotrophus : 0.12% of mapped reads
Found g__Sphingobacterium.s__Sphingobacterium_unclassified : 0.11% of mapped reads
Found g__Cupriavidus.s__Cupriavidus_unclassified : 0.11% of mapped reads
Found g__Azospirillum.s__Azospirillum_unclassified : 0.11% of mapped reads
Found g__Agrobacterium.s__Agrobacterium_tumefaciens : 0.10% of mapped reads
Found g__Kribbella.s__Kribbella_unclassified : 0.09% of mapped reads
Found g__Methylotenera.s__Methylotenera_unclassified : 0.07% of mapped reads
Found g__Pseudoxanthomonas.s__Pseudoxanthomonas_unclassified : 0.07% of mapped reads
Found g__Bordetella.s__Bordetella_unclassified : 0.07% of mapped reads
Found g__Bradyrhizobium.s__Bradyrhizobium_elkanii : 0.07% of mapped reads
Found g__Cytophaga.s__Cytophaga_unclassified : 0.07% of mapped reads
Found g__Dyadobacter.s__Dyadobacter_unclassified : 0.06% of mapped reads
Found g__Stenotrophomonas.s__Stenotrophomonas_maltophilia : 0.06% of mapped reads
Found g__Polaromonas.s__Polaromonas_unclassified : 0.05% of mapped reads
Found g__Sphingobium.s__Sphingobium_indicum : 0.05% of mapped reads
Found g__Bacillus.s__Bacillus_megaterium : 0.04% of mapped reads
Found g__Cupriavidus.s__Cupriavidus_taiwanensis : 0.03% of mapped reads
Found g__Variovorax.s__Variovorax_paradoxus : 0.03% of mapped reads
Found g__Achromobacter.s__Achromobacter_piechaudii : 0.02% of mapped reads
Found g__Sphingobium.s__Sphingobium_chinhatense : 0.02% of mapped reads
Total species selected from prescreen: 69
Selected species explain 96.66% of predicted community composition
Creating custom ChocoPhlAn database ........
/bin/gunzip -c /public/home/jkyin/biosoft/database/chocophlan/g__Cupriavidus.s__Cupriavidus_taiwanensis.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Achromobacter.s__Achromobacter_piechaudii.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Stenotrophomonas.s__Stenotrophomonas_maltophilia.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Bacillus.s__Bacillus_megaterium.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Variovorax.s__Variovorax_paradoxus.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Rhizobium.s__Rhizobium_etli.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Streptomyces.s__Streptomyces_chartreusis.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Paracoccus.s__Paracoccus_denitrificans.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Sphingobium.s__Sphingobium_indicum.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Caulobacter.s__Caulobacter_vibrioides.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Microcoleus.s__Microcoleus_vaginatus.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Agrobacterium.s__Agrobacterium_tumefaciens.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Bradyrhizobium.s__Bradyrhizobium_elkanii.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Ralstonia.s__Ralstonia_pickettii.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Sphingobium.s__Sphingobium_chinhatense.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Hyphomicrobium.s__Hyphomicrobium_denitrificans.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Streptomyces.s__Streptomyces_gancidicus.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Oscillatoria.s__Oscillatoria_nigro_viridis.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Rhizobium.s__Rhizobium_leguminosarum.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Bradyrhizobium.s__Bradyrhizobium_japonicum.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Methylophilus.s__Methylophilus_methylotrophus.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Rhizobium.s__Rhizobium_lupini.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Mesorhizobium
This is a fairly complex sample (69 species detected) so it might just be taking a long time to index the custom database. As long as the directory is updating that’s a good sign.
However, when 103 species detected, the speed is much faster than this sample. I run them at the same time, 103 species has been completed, this 69 species is still in Creating custom ChocoPhlAn database ........
If no things wrong, I will be more patient.
File ( /public/home/jkyin/yjk/tomato_micro/raw/HG64RS3T1.fa ) is of format: fasta
Found g__Sphingopyxis.s__Sphingopyxis_unclassified : 23.04% of mapped reads
Found g__Bordetella.s__Bordetella_unclassified : 7.60% of mapped reads
Found g__Achromobacter.s__Achromobacter_unclassified : 6.34% of mapped reads
Found g__Arthrobacter.s__Arthrobacter_sp_162MFSha1_1 : 5.92% of mapped reads
Found g__Paracoccus.s__Paracoccus_unclassified : 5.11% of mapped reads
Found g__Actinoplanes.s__Actinoplanes_unclassified : 4.67% of mapped reads
Found g__Pseudomonas.s__Pseudomonas_unclassified : 3.96% of mapped reads
Found g__Gammaretrovirus.s__Spleen_focus_forming_virus : 3.81% of mapped reads
Found g__Pseudomonas.s__Pseudomonas_putida : 3.68% of mapped reads
Found g__Sphingobium.s__Sphingobium_unclassified : 3.60% of mapped reads
Found g__Massilia.s__Massilia_unclassified : 3.57% of mapped reads
Found g__Achromobacter.s__Achromobacter_piechaudii : 2.37% of mapped reads
Found g__Apscaviroid.s__Apple_scar_skin_viroid : 2.11% of mapped reads
Found g__Agromyces.s__Agromyces_unclassified : 2.00% of mapped reads
Found g__Comamonas.s__Comamonas_testosteroni : 1.90% of mapped reads
Found g__Cellulomonas.s__Cellulomonas_unclassified : 1.78% of mapped reads
Found g__Orthohepadnavirus.s__Orthohepadnavirus_unclassified : 1.17% of mapped reads
Found g__Bacillus.s__Bacillus_cereus_thuringiensis : 1.06% of mapped reads
Found g__Respirovirus.s__Sendai_virus : 1.00% of mapped reads
Found g__Shinella.s__Shinella_zoogloeoides : 0.90% of mapped reads
Found g__Burkholderia.s__Burkholderia_unclassified : 0.87% of mapped reads
Found g__Bacillus.s__Bacillus_megaterium : 0.81% of mapped reads
Found g__Brevundimonas.s__Brevundimonas_diminuta : 0.69% of mapped reads
Found g__Sphingobacterium.s__Sphingobacterium_unclassified : 0.63% of mapped reads
Found g__Pseudomonas.s__Pseudomonas_stutzeri : 0.61% of mapped reads
Found g__Mesorhizobium.s__Mesorhizobium_unclassified : 0.54% of mapped reads
Found g__Microbacterium.s__Microbacterium_laevaniformans : 0.51% of mapped reads
Found g__Deinococcus.s__Deinococcus_unclassified : 0.49% of mapped reads
Found g__Leifsonia.s__Leifsonia_unclassified : 0.42% of mapped reads
Found g__Sorangium.s__Sorangium_cellulosum : 0.35% of mapped reads
Found g__Asticcacaulis.s__Asticcacaulis_unclassified : 0.34% of mapped reads
Found g__Caulobacter.s__Caulobacter_unclassified : 0.30% of mapped reads
Found g__Variovorax.s__Variovorax_unclassified : 0.30% of mapped reads
Found g__Sphingomonas.s__Sphingomonas_wittichii : 0.30% of mapped reads
Found g__Rhodopseudomonas.s__Rhodopseudomonas_palustris : 0.28% of mapped reads
Found g__Pseudomonas.s__Pseudomonas_mendocina : 0.26% of mapped reads
Found g__Pseudonocardia.s__Pseudonocardia_unclassified : 0.25% of mapped reads
Found g__Nocardioides.s__Nocardioides_unclassified : 0.24% of mapped reads
Found g__Arthrobacter.s__Arthrobacter_globiformis : 0.24% of mapped reads
Found g__Pusillimonas.s__Pusillimonas_unclassified : 0.22% of mapped reads
Found g__Caulobacter.s__Caulobacter_vibrioides : 0.20% of mapped reads
Found g__Bradyrhizobium.s__Bradyrhizobium_japonicum : 0.19% of mapped reads
Found g__Azospirillum.s__Azospirillum_unclassified : 0.17% of mapped reads
Found g__Mesorhizobium.s__Mesorhizobium_loti : 0.17% of mapped reads
Found g__Methylophilus.s__Methylophilus_methylotrophus : 0.16% of mapped reads
Found g__Cellvibrio.s__Cellvibrio_unclassified : 0.16% of mapped reads
Found g__Rhodanobacter.s__Rhodanobacter_unclassified : 0.15% of mapped reads
Found g__Kribbella.s__Kribbella_unclassified : 0.14% of mapped reads
Found g__Rhizobium.s__Rhizobium_etli : 0.14% of mapped reads
Found g__Cupriavidus.s__Cupriavidus_unclassified : 0.13% of mapped reads
Found g__Pseudoxanthomonas.s__Pseudoxanthomonas_unclassified : 0.12% of mapped reads
Found g__Arthrobacter.s__Arthrobacter_arilaitensis : 0.11% of mapped reads
Found g__Brachybacterium.s__Brachybacterium_unclassified : 0.10% of mapped reads
Found g__Paracoccus.s__Paracoccus_denitrificans : 0.10% of mapped reads
Found g__Sinorhizobium.s__Sinorhizobium_unclassified : 0.09% of mapped reads
Found g__Agrobacterium.s__Agrobacterium_tumefaciens : 0.09% of mapped reads
Found g__Thiomonas.s__Thiomonas_unclassified : 0.09% of mapped reads
Found g__Sphingobium.s__Sphingobium_xenophagum : 0.09% of mapped reads
Found g__Brevundimonas.s__Brevundimonas_unclassified : 0.09% of mapped reads
Found g__Brachybacterium.s__Brachybacterium_paraconglomeratum : 0.08% of mapped reads
Found g__Arthrobacter.s__Arthrobacter_chlorophenolicus : 0.08% of mapped reads
Found g__Alpharetrovirus.s__Avian_myelocytomatosis_virus : 0.08% of mapped reads
Found g__Achromobacter.s__Achromobacter_arsenitoxydans : 0.07% of mapped reads
Found g__Agrobacterium.s__Agrobacterium_unclassified : 0.07% of mapped reads
Found g__Corallococcus.s__Corallococcus_coralloides : 0.07% of mapped reads
Found g__Rhizobium.s__Rhizobium_lupini : 0.07% of mapped reads
Found g__Pedobacter.s__Pedobacter_unclassified : 0.06% of mapped reads
Found g__Rhizobium.s__Rhizobium_leguminosarum : 0.06% of mapped reads
Found g__Acinetobacter.s__Acinetobacter_unclassified : 0.06% of mapped reads
Found g__Agrobacterium.s__Agrobacterium_albertimagni : 0.06% of mapped reads
Found g__Hymenobacter.s__Hymenobacter_unclassified : 0.05% of mapped reads
Found g__Afipia.s__Afipia_unclassified : 0.05% of mapped reads
Found g__Janthinobacterium.s__Janthinobacterium_unclassified : 0.05% of mapped reads
Found g__Dyadobacter.s__Dyadobacter_fermentans : 0.05% of mapped reads
Found g__Mycoplasma.s__Mycoplasma_pulmonis : 0.05% of mapped reads
Found g__Microcoleus.s__Microcoleus_vaginatus : 0.05% of mapped reads
Found g__Microcoleus.s__Microcoleus_unclassified : 0.04% of mapped reads
Found g__Bacillus.s__Bacillus_pumilus : 0.04% of mapped reads
Found g__Granulicella.s__Granulicella_unclassified : 0.04% of mapped reads
Found g__Oscillatoria.s__Oscillatoria_unclassified : 0.04% of mapped reads
Found g__Escherichia.s__Escherichia_unclassified : 0.04% of mapped reads
Found g__Niastella.s__Niastella_koreensis : 0.04% of mapped reads
Found g__Leucobacter.s__Leucobacter_unclassified : 0.04% of mapped reads
Found g__Acinetobacter.s__Acinetobacter_schindleri : 0.03% of mapped reads
Found g__Oscillatoria.s__Oscillatoria_nigro_viridis : 0.03% of mapped reads
Found g__Dietzia.s__Dietzia_unclassified : 0.03% of mapped reads
Found g__Dyadobacter.s__Dyadobacter_unclassified : 0.03% of mapped reads
Found g__Anaeromyxobacter.s__Anaeromyxobacter_unclassified : 0.03% of mapped reads
Found g__Cupriavidus.s__Cupriavidus_taiwanensis : 0.03% of mapped reads
Found g__Streptomyces.s__Streptomyces_chartreusis : 0.03% of mapped reads
Found g__Variovorax.s__Variovorax_paradoxus : 0.03% of mapped reads
Found g__Streptomyces.s__Streptomyces_gancidicus : 0.02% of mapped reads
Found g__Ochrobactrum.s__Ochrobactrum_unclassified : 0.02% of mapped reads
Found g__Massilia.s__Massilia_timonae : 0.02% of mapped reads
Found g__Polaromonas.s__Polaromonas_unclassified : 0.01% of mapped reads
Found g__Stenotrophomonas.s__Stenotrophomonas_unclassified : 0.01% of mapped reads
Found g__Lysinibacillus.s__Lysinibacillus_unclassified : 0.01% of mapped reads
Found g__Paenibacillus.s__Paenibacillus_massiliensis : 0.01% of mapped reads
Found g__Roseomonas.s__Roseomonas_unclassified : 0.01% of mapped reads
Found g__Azospirillum.s__Azospirillum_brasilense : 0.01% of mapped reads
Found g__Pseudomonas.s__Pseudomonas_alcaliphila : 0.01% of mapped reads
Found g__Salinispora.s__Salinispora_unclassified : 0.01% of mapped reads
Found g__Stenotrophomonas.s__Stenotrophomonas_maltophilia : 0.01% of mapped reads
Total species selected from prescreen: 103
Selected species explain 98.47% of predicted community composition
Creating custom ChocoPhlAn database ........
/bin/gunzip -c /public/home/jkyin/biosoft/database/chocophlan/g__Cupriavidus.s__Cupriavidus_taiwanensis.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Arthrobacter.s__Arthrobacter_globiformis.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Achromobacter.s__Achromobacter_piechaudii.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Comamonas.s__Comamonas_testosteroni.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Mycoplasma.s__Mycoplasma_pulmonis.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Pseudomonas.s__Pseudomonas_putida.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Respirovirus.s__Sendai_virus.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Stenotrophomonas.s__Stenotrophomonas_maltophilia.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Acinetobacter.s__Acinetobacter_schindleri.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Bacillus.s__Bacillus_megaterium.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Pseudomonas.s__Pseudomonas_mendocina.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Variovorax.s__Variovorax_paradoxus.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Rhizobium.s__Rhizobium_etli.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Bacillus.s__Bacillus_pumilus.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Streptomyces.s__Streptomyces_chartreusis.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Paracoccus.s__Paracoccus_denitrificans.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Caulobacter.s__Caulobacter_vibrioides.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Microcoleus.s__Microcoleus_vaginatus.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Gammaretrovirus.s__Spleen_focus_forming_virus.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Pseudomonas.s__Pseudomonas_stutzeri.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Arthrobacter.s__Arthrobacter_chlorophenolicus.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Microbacterium.s__Microbacterium_laevaniformans.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Corallococcus.s__Corallococcus_coralloides.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Alpharetrovirus.s__Avian_myelocytomatosis_virus.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Sphingobium.s__Sphingobium_xenophagum.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Azospirillum.s__Azospirillum_brasilense.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Apscaviroid.s__Apple_scar_skin_viroid.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Agrobacterium.s__Agrobacterium_tumefaciens.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Brachybacterium.s__Brachybacterium_paraconglomeratum.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Dyadobacter.s__Dyadobacter_fermentans.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Paenibacillus.s__Paenibacillus_massiliensis.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Bacillus.s__Bacillus_cereus_thuringiensis.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Streptomyces.s__Streptomyces_gancidicus.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Pseudomonas.s__Pseudomonas_alcaliphila.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Oscillatoria.s__Oscillatoria_nigro_viridis.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Shinella.s__Shinella_zoogloeoides.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Arthrobacter.s__Arthrobacter_sp_162MFSha1_1.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Achromobacter.s__Achromobacter_arsenitoxydans.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Rhizobium.s__Rhizobium_leguminosarum.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Massilia.s__Massilia_timonae.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Bradyrhizobium.s__Bradyrhizobium_japonicum.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Arthrobacter.s__Arthrobacter_arilaitensis.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Methylophilus.s__Methylophilus_methylotrophus.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Agrobacterium.s__Agrobacterium_albertimagni.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Rhizobium.s__Rhizobium_lupini.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Brevundimonas.s__Brevundimonas_diminuta.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Mesorhizobium.s__Mesorhizobium_loti.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Rhodopseudomonas.s__Rhodopseudomonas_palustris.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Sorangium.s__Sorangium_cellulosum.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Sphingomonas.s__Sphingomonas_wittichii.centroids.v0.1.1.ffn.gz /public/home/jkyin/biosoft/database/chocophlan/g__Niastella.s__Niastella_koreensis.centroids.v0.1.1.ffn.gz
TIMESTAMP: Completed custom database creation : 67 seconds
Running bowtie2-build ........
/public/home/jkyin/miniconda3/envs/humann2/bin/bowtie2-build -f /public/home/jkyin/yjk/tomato_micro/humann2_uniref50/HG64RS3T1/HG64RS3T1_humann2_temp_WOoSOb/HG64RS3T1_custom_chocophlan_database.ffn /public/home/jkyin/yjk/tomato_micro/humann2_uniref50/HG64RS3T1/HG64RS3T1_humann2_temp_WOoSOb/HG64RS3T1_bowtie2_index
TIMESTAMP: Completed database index : 617 seconds
Running bowtie2 ........
/public/home/jkyin/miniconda3/envs/humann2/bin/bowtie2 -f -x /public/home/jkyin/yjk/tomato_micro/humann2_uniref50/HG64RS3T1/HG64RS3T1_humann2_temp_WOoSOb/HG64RS3T1_bowtie2_index -U /public/home/jkyin/yjk/tomato_micro/raw/HG64RS3T1.fa -S /public/home/jkyin/yjk/tomato_micro/humann2_uniref50/HG64RS3T1/HG64RS3T1_humann2_temp_WOoSOb/HG64RS3T1_bowtie2_aligned.sam -p 16 --very-sensitive
TIMESTAMP: Completed nucleotide alignment : 1245 seconds
TIMESTAMP: Completed nucleotide alignment post-processing : 1252 seconds
It ran completely now. Thanks for help and sorry for needless disturbance.