[2023-06-05 13:16:17,630] [INFO] DFAST_QC pipeline started.
[2023-06-05 13:16:17,632] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 13:16:17,632] [INFO] DQC Reference Directory: /var/lib/cwl/stg33374313-3205-43dd-8078-07a7f8ec0774/dqc_reference
[2023-06-05 13:16:18,873] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 13:16:18,874] [INFO] Task started: Prodigal
[2023-06-05 13:16:18,874] [INFO] Running command: gunzip -c /var/lib/cwl/stgbca91531-eb8c-4993-ac7e-f13149de31c9/GCA_004563385.1_ASM456338v1_genomic.fna.gz | prodigal -d GCA_004563385.1_ASM456338v1_genomic.fna/cds.fna -a GCA_004563385.1_ASM456338v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 13:16:34,545] [INFO] Task succeeded: Prodigal
[2023-06-05 13:16:34,546] [INFO] Task started: HMMsearch
[2023-06-05 13:16:34,546] [INFO] Running command: hmmsearch --tblout GCA_004563385.1_ASM456338v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33374313-3205-43dd-8078-07a7f8ec0774/dqc_reference/reference_markers.hmm GCA_004563385.1_ASM456338v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 13:16:34,777] [INFO] Task succeeded: HMMsearch
[2023-06-05 13:16:34,779] [INFO] Found 6/6 markers.
[2023-06-05 13:16:34,807] [INFO] Query marker FASTA was written to GCA_004563385.1_ASM456338v1_genomic.fna/markers.fasta
[2023-06-05 13:16:34,807] [INFO] Task started: Blastn
[2023-06-05 13:16:34,807] [INFO] Running command: blastn -query GCA_004563385.1_ASM456338v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33374313-3205-43dd-8078-07a7f8ec0774/dqc_reference/reference_markers.fasta -out GCA_004563385.1_ASM456338v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 13:16:35,418] [INFO] Task succeeded: Blastn
[2023-06-05 13:16:35,424] [INFO] Selected 18 target genomes.
[2023-06-05 13:16:35,425] [INFO] Target genome list was writen to GCA_004563385.1_ASM456338v1_genomic.fna/target_genomes.txt
[2023-06-05 13:16:35,428] [INFO] Task started: fastANI
[2023-06-05 13:16:35,428] [INFO] Running command: fastANI --query /var/lib/cwl/stgbca91531-eb8c-4993-ac7e-f13149de31c9/GCA_004563385.1_ASM456338v1_genomic.fna.gz --refList GCA_004563385.1_ASM456338v1_genomic.fna/target_genomes.txt --output GCA_004563385.1_ASM456338v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 13:16:46,852] [INFO] Task succeeded: fastANI
[2023-06-05 13:16:46,853] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33374313-3205-43dd-8078-07a7f8ec0774/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 13:16:46,854] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33374313-3205-43dd-8078-07a7f8ec0774/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 13:16:46,860] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 13:16:46,860] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 13:16:46,860] [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	76.5265	59	738	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 13:16:46,862] [INFO] DFAST Taxonomy check result was written to GCA_004563385.1_ASM456338v1_genomic.fna/tc_result.tsv
[2023-06-05 13:16:46,863] [INFO] ===== Taxonomy check completed =====
[2023-06-05 13:16:46,864] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 13:16:46,864] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33374313-3205-43dd-8078-07a7f8ec0774/dqc_reference/checkm_data
[2023-06-05 13:16:46,865] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 13:16:46,892] [INFO] Task started: CheckM
[2023-06-05 13:16:46,893] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004563385.1_ASM456338v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004563385.1_ASM456338v1_genomic.fna/checkm_input GCA_004563385.1_ASM456338v1_genomic.fna/checkm_result
[2023-06-05 13:17:33,005] [INFO] Task succeeded: CheckM
[2023-06-05 13:17:33,007] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 14.44%
Strain heterogeneity: 5.56%
--------------------------------------------------------------------------------
[2023-06-05 13:17:33,038] [INFO] ===== Completeness check finished =====
[2023-06-05 13:17:33,039] [INFO] ===== Start GTDB Search =====
[2023-06-05 13:17:33,040] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004563385.1_ASM456338v1_genomic.fna/markers.fasta)
[2023-06-05 13:17:33,041] [INFO] Task started: Blastn
[2023-06-05 13:17:33,041] [INFO] Running command: blastn -query GCA_004563385.1_ASM456338v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33374313-3205-43dd-8078-07a7f8ec0774/dqc_reference/reference_markers_gtdb.fasta -out GCA_004563385.1_ASM456338v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 13:17:33,980] [INFO] Task succeeded: Blastn
[2023-06-05 13:17:33,985] [INFO] Selected 18 target genomes.
[2023-06-05 13:17:33,985] [INFO] Target genome list was writen to GCA_004563385.1_ASM456338v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 13:17:34,019] [INFO] Task started: fastANI
[2023-06-05 13:17:34,019] [INFO] Running command: fastANI --query /var/lib/cwl/stgbca91531-eb8c-4993-ac7e-f13149de31c9/GCA_004563385.1_ASM456338v1_genomic.fna.gz --refList GCA_004563385.1_ASM456338v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004563385.1_ASM456338v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 13:17:41,535] [INFO] Task succeeded: fastANI
[2023-06-05 13:17:41,553] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 13:17:41,553] [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	97.0048	640	738	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_017435365.1	s__Akkermansia sp017435365	78.7174	197	738	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017937215.1	s__Akkermansia sp017937215	78.5933	188	738	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	97.30	97.14	0.82	0.81	3	-
GCA_015062005.1	s__Akkermansia sp015062005	78.5621	188	738	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017409465.1	s__Akkermansia sp017409465	78.3803	146	738	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	78.3225	175	738	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	98.50	98.44	0.87	0.84	5	-
GCA_017471985.1	s__Akkermansia sp017471985	78.2615	141	738	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	78.2565	128	738	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	78.207	170	738	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	100.00	100.00	0.99	0.99	2	-
GCA_015061985.1	s__Akkermansia sp015061985	77.9668	168	738	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	98.01	98.01	0.81	0.81	2	-
GCA_017472085.1	s__Akkermansia sp017472085	77.9279	153	738	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017517805.1	s__Akkermansia sp017517805	77.6801	139	738	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	77.6593	130	738	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	77.4709	101	738	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904502165.1	s__Akkermansia sp904502165	77.0881	104	738	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-05 13:17:41,555] [INFO] GTDB search result was written to GCA_004563385.1_ASM456338v1_genomic.fna/result_gtdb.tsv
[2023-06-05 13:17:41,556] [INFO] ===== GTDB Search completed =====
[2023-06-05 13:17:41,562] [INFO] DFAST_QC result json was written to GCA_004563385.1_ASM456338v1_genomic.fna/dqc_result.json
[2023-06-05 13:17:41,562] [INFO] DFAST_QC completed!
[2023-06-05 13:17:41,562] [INFO] Total running time: 0h1m24s