[2023-06-29 04:41:39,184] [INFO] DFAST_QC pipeline started.
[2023-06-29 04:41:39,190] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 04:41:39,191] [INFO] DQC Reference Directory: /var/lib/cwl/stg768ff44f-c431-4071-803d-cddfddb5c618/dqc_reference
[2023-06-29 04:41:42,376] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 04:41:42,377] [INFO] Task started: Prodigal
[2023-06-29 04:41:42,377] [INFO] Running command: gunzip -c /var/lib/cwl/stgc96d2834-ef3c-43c6-9cbe-a93da83b0966/GCA_027593175.1_ASM2759317v1_genomic.fna.gz | prodigal -d GCA_027593175.1_ASM2759317v1_genomic.fna/cds.fna -a GCA_027593175.1_ASM2759317v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 04:41:54,046] [INFO] Task succeeded: Prodigal
[2023-06-29 04:41:54,047] [INFO] Task started: HMMsearch
[2023-06-29 04:41:54,047] [INFO] Running command: hmmsearch --tblout GCA_027593175.1_ASM2759317v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg768ff44f-c431-4071-803d-cddfddb5c618/dqc_reference/reference_markers.hmm GCA_027593175.1_ASM2759317v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 04:41:54,310] [INFO] Task succeeded: HMMsearch
[2023-06-29 04:41:54,312] [INFO] Found 6/6 markers.
[2023-06-29 04:41:54,342] [INFO] Query marker FASTA was written to GCA_027593175.1_ASM2759317v1_genomic.fna/markers.fasta
[2023-06-29 04:41:54,343] [INFO] Task started: Blastn
[2023-06-29 04:41:54,344] [INFO] Running command: blastn -query GCA_027593175.1_ASM2759317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg768ff44f-c431-4071-803d-cddfddb5c618/dqc_reference/reference_markers.fasta -out GCA_027593175.1_ASM2759317v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:41:54,944] [INFO] Task succeeded: Blastn
[2023-06-29 04:41:54,948] [INFO] Selected 24 target genomes.
[2023-06-29 04:41:54,949] [INFO] Target genome list was writen to GCA_027593175.1_ASM2759317v1_genomic.fna/target_genomes.txt
[2023-06-29 04:41:54,956] [INFO] Task started: fastANI
[2023-06-29 04:41:54,956] [INFO] Running command: fastANI --query /var/lib/cwl/stgc96d2834-ef3c-43c6-9cbe-a93da83b0966/GCA_027593175.1_ASM2759317v1_genomic.fna.gz --refList GCA_027593175.1_ASM2759317v1_genomic.fna/target_genomes.txt --output GCA_027593175.1_ASM2759317v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 04:42:12,713] [INFO] Task succeeded: fastANI
[2023-06-29 04:42:12,714] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg768ff44f-c431-4071-803d-cddfddb5c618/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 04:42:12,715] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg768ff44f-c431-4071-803d-cddfddb5c618/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 04:42:12,734] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 04:42:12,734] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 04:42:12,734] [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
Algoriphagus sanaruensis	strain=M8-2	GCA_001593605.1	1727163	1727163	type	True	77.1837	118	766	95	below_threshold
Algoriphagus litoralis	strain=DSL-12	GCA_003259255.1	2202829	2202829	type	True	77.1428	122	766	95	below_threshold
Algoriphagus boseongensis	strain=CECT 8446	GCA_004362805.1	1442587	1442587	type	True	77.1225	150	766	95	below_threshold
Algoriphagus aestuariicola	strain=JCM 31546	GCA_017254835.1	1852016	1852016	type	True	77.0704	105	766	95	below_threshold
Algoriphagus mannitolivorans	strain=DSM 15301	GCA_000429425.1	226504	226504	type	True	76.9364	141	766	95	below_threshold
Algoriphagus aquaeductus	strain=T4	GCA_003253485.1	475299	475299	type	True	76.8967	174	766	95	below_threshold
Algoriphagus lacus	strain=N3	GCA_003583985.1	2056311	2056311	type	True	76.8738	158	766	95	below_threshold
Algoriphagus boritolerans	strain=DSM 17298	GCA_900108085.1	308111	308111	type	True	76.8411	121	766	95	below_threshold
Algoriphagus ornithinivorans	strain=DSM 15282	GCA_900115305.1	226506	226506	type	True	76.8057	84	766	95	below_threshold
Algoriphagus algorifonticola	strain=hg1	GCA_007655305.1	2593007	2593007	type	True	76.8003	87	766	95	below_threshold
Algoriphagus halophilus	strain=DSM 15292	GCA_900129785.1	226505	226505	type	True	76.778	87	766	95	below_threshold
Algoriphagus kandeliae	strain=XY-J91	GCA_004571135.1	2562278	2562278	type	True	76.5772	80	766	95	below_threshold
Algoriphagus zhangzhouensis	strain=CGMCC 1.11027	GCA_004366575.1	1073327	1073327	type	True	76.5537	90	766	95	below_threshold
Algoriphagus zhangzhouensis	strain=DSM 25035	GCA_900148515.1	1073327	1073327	type	True	76.4504	86	766	95	below_threshold
Rhodonellum psychrophilum	strain=GCM71	GCA_000473765.1	336828	336828	type	True	76.1272	56	766	95	below_threshold
Rhodonellum psychrophilum	strain=DSM 17998	GCA_000381545.1	336828	336828	type	True	76.0577	60	766	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 04:42:12,737] [INFO] DFAST Taxonomy check result was written to GCA_027593175.1_ASM2759317v1_genomic.fna/tc_result.tsv
[2023-06-29 04:42:12,737] [INFO] ===== Taxonomy check completed =====
[2023-06-29 04:42:12,738] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 04:42:12,738] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg768ff44f-c431-4071-803d-cddfddb5c618/dqc_reference/checkm_data
[2023-06-29 04:42:12,739] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 04:42:12,767] [INFO] Task started: CheckM
[2023-06-29 04:42:12,767] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027593175.1_ASM2759317v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027593175.1_ASM2759317v1_genomic.fna/checkm_input GCA_027593175.1_ASM2759317v1_genomic.fna/checkm_result
[2023-06-29 04:42:51,797] [INFO] Task succeeded: CheckM
[2023-06-29 04:42:51,799] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 04:42:51,816] [INFO] ===== Completeness check finished =====
[2023-06-29 04:42:51,817] [INFO] ===== Start GTDB Search =====
[2023-06-29 04:42:51,818] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027593175.1_ASM2759317v1_genomic.fna/markers.fasta)
[2023-06-29 04:42:51,818] [INFO] Task started: Blastn
[2023-06-29 04:42:51,818] [INFO] Running command: blastn -query GCA_027593175.1_ASM2759317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg768ff44f-c431-4071-803d-cddfddb5c618/dqc_reference/reference_markers_gtdb.fasta -out GCA_027593175.1_ASM2759317v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:42:52,582] [INFO] Task succeeded: Blastn
[2023-06-29 04:42:52,587] [INFO] Selected 20 target genomes.
[2023-06-29 04:42:52,588] [INFO] Target genome list was writen to GCA_027593175.1_ASM2759317v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 04:42:52,629] [INFO] Task started: fastANI
[2023-06-29 04:42:52,630] [INFO] Running command: fastANI --query /var/lib/cwl/stgc96d2834-ef3c-43c6-9cbe-a93da83b0966/GCA_027593175.1_ASM2759317v1_genomic.fna.gz --refList GCA_027593175.1_ASM2759317v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027593175.1_ASM2759317v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 04:43:06,407] [INFO] Task succeeded: fastANI
[2023-06-29 04:43:06,425] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 04:43:06,426] [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_005788235.1	s__Algoriphagus sp005788235	82.6521	474	766	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903952135.1	s__Algoriphagus sp903952135	80.8793	498	766	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.47	99.47	0.91	0.91	2	-
GCA_016866385.1	s__Algoriphagus sp016866385	78.6852	268	766	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018336015.1	s__Algoriphagus sp018336015	77.1972	149	766	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001593605.1	s__Algoriphagus sanaruensis	77.1875	117	766	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259255.1	s__Algoriphagus litoralis	77.1428	122	766	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362805.1	s__Algoriphagus boseongensis	77.1396	149	766	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014324365.1	s__Algoriphagus sp014324365	77.0426	174	766	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429425.1	s__Algoriphagus mannitolivorans	76.9378	140	766	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002002735.1	s__Algoriphagus sp002002735	76.9111	135	766	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997215.1	s__Algoriphagus aquimarinus_A	76.7175	82	766	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004571135.1	s__Algoriphagus kandeliae	76.5772	80	766	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429405.1	s__Algoriphagus marincola	76.3585	84	766	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	97.35	97.35	0.90	0.90	2	-
GCA_013373065.1	s__Algoriphagus sp013373065	76.3103	74	766	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381545.1	s__Rhodonellum psychrophilum	76.0577	60	766	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Rhodonellum	95.0	99.99	99.99	1.00	0.99	3	-
--------------------------------------------------------------------------------
[2023-06-29 04:43:06,428] [INFO] GTDB search result was written to GCA_027593175.1_ASM2759317v1_genomic.fna/result_gtdb.tsv
[2023-06-29 04:43:06,428] [INFO] ===== GTDB Search completed =====
[2023-06-29 04:43:06,432] [INFO] DFAST_QC result json was written to GCA_027593175.1_ASM2759317v1_genomic.fna/dqc_result.json
[2023-06-29 04:43:06,432] [INFO] DFAST_QC completed!
[2023-06-29 04:43:06,432] [INFO] Total running time: 0h1m27s