[2024-01-24 15:27:21,936] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:21,938] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:21,938] [INFO] DQC Reference Directory: /var/lib/cwl/stg6678e9bd-5a3d-489b-b1aa-43fec30763a8/dqc_reference
[2024-01-24 15:27:23,247] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:23,249] [INFO] Task started: Prodigal
[2024-01-24 15:27:23,249] [INFO] Running command: gunzip -c /var/lib/cwl/stg738dfe66-ffc1-4ec0-b1b4-d46388bc8e75/GCF_017504145.1_ASM1750414v1_genomic.fna.gz | prodigal -d GCF_017504145.1_ASM1750414v1_genomic.fna/cds.fna -a GCF_017504145.1_ASM1750414v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:40,597] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:40,597] [INFO] Task started: HMMsearch
[2024-01-24 15:27:40,597] [INFO] Running command: hmmsearch --tblout GCF_017504145.1_ASM1750414v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6678e9bd-5a3d-489b-b1aa-43fec30763a8/dqc_reference/reference_markers.hmm GCF_017504145.1_ASM1750414v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:40,865] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:40,866] [INFO] Found 6/6 markers.
[2024-01-24 15:27:40,889] [INFO] Query marker FASTA was written to GCF_017504145.1_ASM1750414v1_genomic.fna/markers.fasta
[2024-01-24 15:27:40,889] [INFO] Task started: Blastn
[2024-01-24 15:27:40,890] [INFO] Running command: blastn -query GCF_017504145.1_ASM1750414v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6678e9bd-5a3d-489b-b1aa-43fec30763a8/dqc_reference/reference_markers.fasta -out GCF_017504145.1_ASM1750414v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:41,480] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:41,483] [INFO] Selected 9 target genomes.
[2024-01-24 15:27:41,483] [INFO] Target genome list was writen to GCF_017504145.1_ASM1750414v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:41,490] [INFO] Task started: fastANI
[2024-01-24 15:27:41,491] [INFO] Running command: fastANI --query /var/lib/cwl/stg738dfe66-ffc1-4ec0-b1b4-d46388bc8e75/GCF_017504145.1_ASM1750414v1_genomic.fna.gz --refList GCF_017504145.1_ASM1750414v1_genomic.fna/target_genomes.txt --output GCF_017504145.1_ASM1750414v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:48,010] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:48,011] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6678e9bd-5a3d-489b-b1aa-43fec30763a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:48,011] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6678e9bd-5a3d-489b-b1aa-43fec30763a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:48,019] [INFO] Found 4 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 15:27:48,019] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:48,019] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Akkermansia muciniphila	strain=ATCC BAA-835	GCA_017504145.1	239935	239935	type	True	100.0	886	888	95	conclusive
Akkermansia muciniphila	strain=ATCC BAA-835	GCA_000020225.1	239935	239935	type	True	99.9995	884	888	95	conclusive
Akkermansia muciniphila	strain=DSM 22959	GCA_008000975.1	239935	239935	type	True	99.9983	885	888	95	conclusive
Akkermansia glycaniphila	strain=Pyt	GCA_001683795.1	1679444	1679444	type	True	77.0879	102	888	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:48,021] [INFO] DFAST Taxonomy check result was written to GCF_017504145.1_ASM1750414v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:48,022] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:48,022] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:48,023] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6678e9bd-5a3d-489b-b1aa-43fec30763a8/dqc_reference/checkm_data
[2024-01-24 15:27:48,024] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:48,071] [INFO] Task started: CheckM
[2024-01-24 15:27:48,071] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017504145.1_ASM1750414v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017504145.1_ASM1750414v1_genomic.fna/checkm_input GCF_017504145.1_ASM1750414v1_genomic.fna/checkm_result
[2024-01-24 15:28:35,030] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:35,032] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:35,051] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:35,051] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:35,052] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017504145.1_ASM1750414v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:35,052] [INFO] Task started: Blastn
[2024-01-24 15:28:35,053] [INFO] Running command: blastn -query GCF_017504145.1_ASM1750414v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6678e9bd-5a3d-489b-b1aa-43fec30763a8/dqc_reference/reference_markers_gtdb.fasta -out GCF_017504145.1_ASM1750414v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:35,848] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:35,852] [INFO] Selected 6 target genomes.
[2024-01-24 15:28:35,852] [INFO] Target genome list was writen to GCF_017504145.1_ASM1750414v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:35,857] [INFO] Task started: fastANI
[2024-01-24 15:28:35,858] [INFO] Running command: fastANI --query /var/lib/cwl/stg738dfe66-ffc1-4ec0-b1b4-d46388bc8e75/GCF_017504145.1_ASM1750414v1_genomic.fna.gz --refList GCF_017504145.1_ASM1750414v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017504145.1_ASM1750414v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:40,311] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:40,321] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:40,321] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000020225.1	s__Akkermansia muciniphila	99.9995	886	888	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	98.03	97.15	0.94	0.85	200	conclusive
GCA_905200945.1	s__Akkermansia sp905200945	94.5474	793	888	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184965.1	s__Akkermansia muciniphila_A	93.8333	784	888	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	98.74	97.99	0.96	0.93	10	-
GCF_018847375.1	s__Akkermansia muciniphila_B	87.5095	749	888	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	98.85	95.28	0.95	0.86	44	-
GCF_002884975.1	s__Akkermansia muciniphila_C	85.9422	728	888	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	98.91	98.50	0.94	0.90	5	-
GCF_018709685.1	s__Akkermansia muciniphila_E	85.7781	701	888	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:40,324] [INFO] GTDB search result was written to GCF_017504145.1_ASM1750414v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:40,325] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:40,327] [INFO] DFAST_QC result json was written to GCF_017504145.1_ASM1750414v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:40,327] [INFO] DFAST_QC completed!
[2024-01-24 15:28:40,327] [INFO] Total running time: 0h1m18s