[2023-06-29 19:13:40,559] [INFO] DFAST_QC pipeline started.
[2023-06-29 19:13:40,562] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 19:13:40,562] [INFO] DQC Reference Directory: /var/lib/cwl/stgefb8887d-c3da-40c7-88d7-583024b5c0fd/dqc_reference
[2023-06-29 19:13:41,980] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 19:13:41,981] [INFO] Task started: Prodigal
[2023-06-29 19:13:41,982] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb209675-0a76-42f5-967b-355f83775568/GCA_021620715.1_ASM2162071v1_genomic.fna.gz | prodigal -d GCA_021620715.1_ASM2162071v1_genomic.fna/cds.fna -a GCA_021620715.1_ASM2162071v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 19:13:56,457] [INFO] Task succeeded: Prodigal
[2023-06-29 19:13:56,457] [INFO] Task started: HMMsearch
[2023-06-29 19:13:56,457] [INFO] Running command: hmmsearch --tblout GCA_021620715.1_ASM2162071v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgefb8887d-c3da-40c7-88d7-583024b5c0fd/dqc_reference/reference_markers.hmm GCA_021620715.1_ASM2162071v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 19:13:56,698] [INFO] Task succeeded: HMMsearch
[2023-06-29 19:13:56,701] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgeb209675-0a76-42f5-967b-355f83775568/GCA_021620715.1_ASM2162071v1_genomic.fna.gz]
[2023-06-29 19:13:56,736] [INFO] Query marker FASTA was written to GCA_021620715.1_ASM2162071v1_genomic.fna/markers.fasta
[2023-06-29 19:13:56,737] [INFO] Task started: Blastn
[2023-06-29 19:13:56,737] [INFO] Running command: blastn -query GCA_021620715.1_ASM2162071v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefb8887d-c3da-40c7-88d7-583024b5c0fd/dqc_reference/reference_markers.fasta -out GCA_021620715.1_ASM2162071v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:13:57,365] [INFO] Task succeeded: Blastn
[2023-06-29 19:13:57,369] [INFO] Selected 11 target genomes.
[2023-06-29 19:13:57,369] [INFO] Target genome list was writen to GCA_021620715.1_ASM2162071v1_genomic.fna/target_genomes.txt
[2023-06-29 19:13:57,371] [INFO] Task started: fastANI
[2023-06-29 19:13:57,371] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb209675-0a76-42f5-967b-355f83775568/GCA_021620715.1_ASM2162071v1_genomic.fna.gz --refList GCA_021620715.1_ASM2162071v1_genomic.fna/target_genomes.txt --output GCA_021620715.1_ASM2162071v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 19:14:06,066] [INFO] Task succeeded: fastANI
[2023-06-29 19:14:06,066] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgefb8887d-c3da-40c7-88d7-583024b5c0fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 19:14:06,067] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgefb8887d-c3da-40c7-88d7-583024b5c0fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 19:14:06,073] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 19:14:06,073] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 19:14:06,074] [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	82.4755	473	661	95	below_threshold
Akkermansia muciniphila	strain=DSM 22959	GCA_008000975.1	239935	239935	type	True	82.4284	476	661	95	below_threshold
Akkermansia muciniphila	strain=ATCC BAA-835	GCA_000020225.1	239935	239935	type	True	82.3839	478	661	95	below_threshold
Akkermansia glycaniphila	strain=Pyt	GCA_001683795.1	1679444	1679444	type	True	77.505	109	661	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 19:14:06,076] [INFO] DFAST Taxonomy check result was written to GCA_021620715.1_ASM2162071v1_genomic.fna/tc_result.tsv
[2023-06-29 19:14:06,077] [INFO] ===== Taxonomy check completed =====
[2023-06-29 19:14:06,077] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 19:14:06,077] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgefb8887d-c3da-40c7-88d7-583024b5c0fd/dqc_reference/checkm_data
[2023-06-29 19:14:06,079] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 19:14:06,106] [INFO] Task started: CheckM
[2023-06-29 19:14:06,107] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021620715.1_ASM2162071v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021620715.1_ASM2162071v1_genomic.fna/checkm_input GCA_021620715.1_ASM2162071v1_genomic.fna/checkm_result
[2023-06-29 19:14:49,239] [INFO] Task succeeded: CheckM
[2023-06-29 19:14:49,241] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 19:14:49,261] [INFO] ===== Completeness check finished =====
[2023-06-29 19:14:49,261] [INFO] ===== Start GTDB Search =====
[2023-06-29 19:14:49,262] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021620715.1_ASM2162071v1_genomic.fna/markers.fasta)
[2023-06-29 19:14:49,262] [INFO] Task started: Blastn
[2023-06-29 19:14:49,262] [INFO] Running command: blastn -query GCA_021620715.1_ASM2162071v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefb8887d-c3da-40c7-88d7-583024b5c0fd/dqc_reference/reference_markers_gtdb.fasta -out GCA_021620715.1_ASM2162071v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:14:50,221] [INFO] Task succeeded: Blastn
[2023-06-29 19:14:50,227] [INFO] Selected 6 target genomes.
[2023-06-29 19:14:50,227] [INFO] Target genome list was writen to GCA_021620715.1_ASM2162071v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 19:14:50,228] [INFO] Task started: fastANI
[2023-06-29 19:14:50,228] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb209675-0a76-42f5-967b-355f83775568/GCA_021620715.1_ASM2162071v1_genomic.fna.gz --refList GCA_021620715.1_ASM2162071v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021620715.1_ASM2162071v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 19:14:54,333] [INFO] Task succeeded: fastANI
[2023-06-29 19:14:54,346] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 19:14:54,346] [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_018847895.1	s__Akkermansia sp001580195	99.9501	660	661	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	99.22	96.77	0.98	0.92	18	conclusive
GCF_004167605.1	s__Akkermansia sp004167605	94.4436	608	661	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	99.95	99.06	0.99	0.93	74	-
GCF_018709685.1	s__Akkermansia muciniphila_E	84.8023	543	661	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018847375.1	s__Akkermansia muciniphila_B	84.7262	554	661	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	84.5895	549	661	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	98.91	98.50	0.94	0.90	5	-
GCA_905200945.1	s__Akkermansia sp905200945	82.3001	470	661	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 19:14:54,348] [INFO] GTDB search result was written to GCA_021620715.1_ASM2162071v1_genomic.fna/result_gtdb.tsv
[2023-06-29 19:14:54,349] [INFO] ===== GTDB Search completed =====
[2023-06-29 19:14:54,351] [INFO] DFAST_QC result json was written to GCA_021620715.1_ASM2162071v1_genomic.fna/dqc_result.json
[2023-06-29 19:14:54,351] [INFO] DFAST_QC completed!
[2023-06-29 19:14:54,352] [INFO] Total running time: 0h1m14s