[2023-06-04 23:25:33,456] [INFO] DFAST_QC pipeline started.
[2023-06-04 23:25:33,459] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 23:25:33,459] [INFO] DQC Reference Directory: /var/lib/cwl/stge9d47296-db85-41e9-8e81-43dce1a60d89/dqc_reference
[2023-06-04 23:25:34,773] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 23:25:34,774] [INFO] Task started: Prodigal
[2023-06-04 23:25:34,774] [INFO] Running command: gunzip -c /var/lib/cwl/stg04d84de7-6b6c-42e8-8c61-240aa663b8a8/GCA_004557455.1_ASM455745v1_genomic.fna.gz | prodigal -d GCA_004557455.1_ASM455745v1_genomic.fna/cds.fna -a GCA_004557455.1_ASM455745v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 23:25:51,290] [INFO] Task succeeded: Prodigal
[2023-06-04 23:25:51,291] [INFO] Task started: HMMsearch
[2023-06-04 23:25:51,291] [INFO] Running command: hmmsearch --tblout GCA_004557455.1_ASM455745v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9d47296-db85-41e9-8e81-43dce1a60d89/dqc_reference/reference_markers.hmm GCA_004557455.1_ASM455745v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 23:25:51,546] [INFO] Task succeeded: HMMsearch
[2023-06-04 23:25:51,547] [INFO] Found 6/6 markers.
[2023-06-04 23:25:51,577] [INFO] Query marker FASTA was written to GCA_004557455.1_ASM455745v1_genomic.fna/markers.fasta
[2023-06-04 23:25:51,578] [INFO] Task started: Blastn
[2023-06-04 23:25:51,578] [INFO] Running command: blastn -query GCA_004557455.1_ASM455745v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9d47296-db85-41e9-8e81-43dce1a60d89/dqc_reference/reference_markers.fasta -out GCA_004557455.1_ASM455745v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 23:25:52,170] [INFO] Task succeeded: Blastn
[2023-06-04 23:25:52,174] [INFO] Selected 18 target genomes.
[2023-06-04 23:25:52,174] [INFO] Target genome list was writen to GCA_004557455.1_ASM455745v1_genomic.fna/target_genomes.txt
[2023-06-04 23:25:52,220] [INFO] Task started: fastANI
[2023-06-04 23:25:52,220] [INFO] Running command: fastANI --query /var/lib/cwl/stg04d84de7-6b6c-42e8-8c61-240aa663b8a8/GCA_004557455.1_ASM455745v1_genomic.fna.gz --refList GCA_004557455.1_ASM455745v1_genomic.fna/target_genomes.txt --output GCA_004557455.1_ASM455745v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 23:26:03,355] [INFO] Task succeeded: fastANI
[2023-06-04 23:26:03,355] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge9d47296-db85-41e9-8e81-43dce1a60d89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 23:26:03,356] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge9d47296-db85-41e9-8e81-43dce1a60d89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 23:26:03,361] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 23:26:03,362] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 23:26:03,362] [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 glycaniphila	strain=Pyt	GCA_001683795.1	1679444	1679444	type	True	76.5209	70	803	95	below_threshold
Akkermansia muciniphila	strain=DSM 22959	GCA_008000975.1	239935	239935	type	True	76.3168	54	803	95	below_threshold
Akkermansia muciniphila	strain=ATCC BAA-835	GCA_017504145.1	239935	239935	type	True	76.3168	54	803	95	below_threshold
Akkermansia muciniphila	strain=ATCC BAA-835	GCA_000020225.1	239935	239935	type	True	76.2983	53	803	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 23:26:03,364] [INFO] DFAST Taxonomy check result was written to GCA_004557455.1_ASM455745v1_genomic.fna/tc_result.tsv
[2023-06-04 23:26:03,364] [INFO] ===== Taxonomy check completed =====
[2023-06-04 23:26:03,365] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 23:26:03,365] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9d47296-db85-41e9-8e81-43dce1a60d89/dqc_reference/checkm_data
[2023-06-04 23:26:03,366] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 23:26:03,403] [INFO] Task started: CheckM
[2023-06-04 23:26:03,404] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004557455.1_ASM455745v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004557455.1_ASM455745v1_genomic.fna/checkm_input GCA_004557455.1_ASM455745v1_genomic.fna/checkm_result
[2023-06-04 23:26:51,380] [INFO] Task succeeded: CheckM
[2023-06-04 23:26:51,382] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 3.93%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 23:26:51,409] [INFO] ===== Completeness check finished =====
[2023-06-04 23:26:51,409] [INFO] ===== Start GTDB Search =====
[2023-06-04 23:26:51,410] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004557455.1_ASM455745v1_genomic.fna/markers.fasta)
[2023-06-04 23:26:51,410] [INFO] Task started: Blastn
[2023-06-04 23:26:51,410] [INFO] Running command: blastn -query GCA_004557455.1_ASM455745v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9d47296-db85-41e9-8e81-43dce1a60d89/dqc_reference/reference_markers_gtdb.fasta -out GCA_004557455.1_ASM455745v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 23:26:52,217] [INFO] Task succeeded: Blastn
[2023-06-04 23:26:52,222] [INFO] Selected 21 target genomes.
[2023-06-04 23:26:52,222] [INFO] Target genome list was writen to GCA_004557455.1_ASM455745v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 23:26:52,454] [INFO] Task started: fastANI
[2023-06-04 23:26:52,454] [INFO] Running command: fastANI --query /var/lib/cwl/stg04d84de7-6b6c-42e8-8c61-240aa663b8a8/GCA_004557455.1_ASM455745v1_genomic.fna.gz --refList GCA_004557455.1_ASM455745v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004557455.1_ASM455745v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 23:27:01,277] [INFO] Task succeeded: fastANI
[2023-06-04 23:27:01,297] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 23:27:01,297] [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
GCA_004557455.1	s__Akkermansia muciniphila_D	100.0	799	803	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	97.02	97.00	0.87	0.87	3	conclusive
GCA_017409465.1	s__Akkermansia sp017409465	79.1299	147	803	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017398765.1	s__Akkermansia sp017398765	78.799	128	803	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017435365.1	s__Akkermansia sp017435365	78.6803	222	803	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548895.1	s__Akkermansia intestinavium	78.551	199	803	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	98.50	98.44	0.87	0.84	5	-
GCA_017937215.1	s__Akkermansia sp017937215	78.5122	197	803	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	97.30	97.14	0.82	0.81	3	-
GCA_015061985.1	s__Akkermansia sp015061985	78.5081	174	803	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	98.01	98.01	0.81	0.81	2	-
GCA_015062005.1	s__Akkermansia sp015062005	78.5057	207	803	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904501955.1	s__Akkermansia sp904501955	78.3808	194	803	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	100.00	100.00	0.99	0.99	2	-
GCA_017517385.1	s__Akkermansia sp017517385	78.1968	139	803	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017555465.1	s__Akkermansia sp017555465	78.1734	142	803	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015062045.1	s__Akkermansia sp015062045	78.1131	119	803	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017472085.1	s__Akkermansia sp017472085	78.0441	168	803	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017379255.1	s__Akkermansia sp017379255	77.8892	158	803	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017546845.1	s__Akkermansia sp017546845	77.5334	149	803	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017504805.1	s__Akkermansia sp017504805	77.4389	150	803	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	98.93	98.93	0.80	0.80	2	-
GCA_015062055.1	s__Akkermansia sp015062055	77.38	120	803	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904501975.1	s__Akkermansia sp904501975	77.2569	124	803	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-04 23:27:01,299] [INFO] GTDB search result was written to GCA_004557455.1_ASM455745v1_genomic.fna/result_gtdb.tsv
[2023-06-04 23:27:01,300] [INFO] ===== GTDB Search completed =====
[2023-06-04 23:27:01,303] [INFO] DFAST_QC result json was written to GCA_004557455.1_ASM455745v1_genomic.fna/dqc_result.json
[2023-06-04 23:27:01,303] [INFO] DFAST_QC completed!
[2023-06-04 23:27:01,304] [INFO] Total running time: 0h1m28s