[2024-01-24 13:24:12,458] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:24:12,472] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:24:12,472] [INFO] DQC Reference Directory: /var/lib/cwl/stgba7bb7d1-4120-4ae5-b0e2-afcef878d666/dqc_reference
[2024-01-24 13:24:13,630] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:24:13,631] [INFO] Task started: Prodigal
[2024-01-24 13:24:13,631] [INFO] Running command: gunzip -c /var/lib/cwl/stg34ee01d2-fa45-47b0-8d1e-66778de2a077/GCF_902499555.1_CECT_9532_genomic.fna.gz | prodigal -d GCF_902499555.1_CECT_9532_genomic.fna/cds.fna -a GCF_902499555.1_CECT_9532_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:24:27,295] [INFO] Task succeeded: Prodigal
[2024-01-24 13:24:27,295] [INFO] Task started: HMMsearch
[2024-01-24 13:24:27,295] [INFO] Running command: hmmsearch --tblout GCF_902499555.1_CECT_9532_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba7bb7d1-4120-4ae5-b0e2-afcef878d666/dqc_reference/reference_markers.hmm GCF_902499555.1_CECT_9532_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:24:27,534] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:24:27,536] [INFO] Found 6/6 markers.
[2024-01-24 13:24:27,573] [INFO] Query marker FASTA was written to GCF_902499555.1_CECT_9532_genomic.fna/markers.fasta
[2024-01-24 13:24:27,574] [INFO] Task started: Blastn
[2024-01-24 13:24:27,574] [INFO] Running command: blastn -query GCF_902499555.1_CECT_9532_genomic.fna/markers.fasta -db /var/lib/cwl/stgba7bb7d1-4120-4ae5-b0e2-afcef878d666/dqc_reference/reference_markers.fasta -out GCF_902499555.1_CECT_9532_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:28,206] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:28,210] [INFO] Selected 16 target genomes.
[2024-01-24 13:24:28,210] [INFO] Target genome list was writen to GCF_902499555.1_CECT_9532_genomic.fna/target_genomes.txt
[2024-01-24 13:24:28,225] [INFO] Task started: fastANI
[2024-01-24 13:24:28,225] [INFO] Running command: fastANI --query /var/lib/cwl/stg34ee01d2-fa45-47b0-8d1e-66778de2a077/GCF_902499555.1_CECT_9532_genomic.fna.gz --refList GCF_902499555.1_CECT_9532_genomic.fna/target_genomes.txt --output GCF_902499555.1_CECT_9532_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:24:37,854] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:37,854] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba7bb7d1-4120-4ae5-b0e2-afcef878d666/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:24:37,855] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba7bb7d1-4120-4ae5-b0e2-afcef878d666/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:24:37,867] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:24:37,867] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:24:37,868] [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
Mesonia oceanica	strain=ISS653	GCA_902499555.1	2687242	2687242	type	True	100.0	1392	1392	95	conclusive
Zunongwangia profunda	strain=SMA-87	GCA_000023465.1	398743	398743	type	True	81.3617	267	1392	95	below_threshold
Mesonia mobilis	strain=KCTC 12708	GCA_014651475.1	369791	369791	type	True	81.2943	700	1392	95	below_threshold
Mesonia mobilis	strain=DSM 19841	GCA_000423405.1	369791	369791	type	True	81.2486	697	1392	95	below_threshold
Mesonia phycicola	strain=DSM 21425	GCA_900141885.1	579105	579105	type	True	79.103	502	1392	95	below_threshold
Zunongwangia atlantica	strain=22II14-10F7	GCA_002094855.1	1502297	1502297	type	True	78.8697	237	1392	95	below_threshold
Mesonia algae	strain=DSM 15361	GCA_003253545.1	213248	213248	type	True	77.4399	286	1392	95	below_threshold
Algibacter alginicilyticus	strain=HZ22	GCA_001310225.1	1736674	1736674	type	True	77.0161	110	1392	95	below_threshold
Pustulibacterium marinum	strain=CGMCC 1.12333	GCA_900116665.1	1224947	1224947	type	True	77.0111	120	1392	95	below_threshold
Gramella lutea	strain=YJ019	GCA_022489035.1	1607951	1607951	type	True	76.7726	95	1392	95	below_threshold
Mesohalobacter halotolerans	strain=WDS2C27	GCA_006120725.1	1883405	1883405	type	True	76.5184	58	1392	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.4752	105	1392	95	below_threshold
Kordia algicida	strain=OT-1	GCA_000154725.1	221066	221066	type	True	76.0716	110	1392	95	below_threshold
Tenacibaculum adriaticum	strain=DSM 18961	GCA_008124875.1	413713	413713	type	True	75.989	97	1392	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:24:37,869] [INFO] DFAST Taxonomy check result was written to GCF_902499555.1_CECT_9532_genomic.fna/tc_result.tsv
[2024-01-24 13:24:37,870] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:24:37,870] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:24:37,871] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba7bb7d1-4120-4ae5-b0e2-afcef878d666/dqc_reference/checkm_data
[2024-01-24 13:24:37,872] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:24:37,914] [INFO] Task started: CheckM
[2024-01-24 13:24:37,914] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902499555.1_CECT_9532_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902499555.1_CECT_9532_genomic.fna/checkm_input GCF_902499555.1_CECT_9532_genomic.fna/checkm_result
[2024-01-24 13:25:18,494] [INFO] Task succeeded: CheckM
[2024-01-24 13:25:18,495] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:25:18,513] [INFO] ===== Completeness check finished =====
[2024-01-24 13:25:18,513] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:25:18,514] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902499555.1_CECT_9532_genomic.fna/markers.fasta)
[2024-01-24 13:25:18,514] [INFO] Task started: Blastn
[2024-01-24 13:25:18,514] [INFO] Running command: blastn -query GCF_902499555.1_CECT_9532_genomic.fna/markers.fasta -db /var/lib/cwl/stgba7bb7d1-4120-4ae5-b0e2-afcef878d666/dqc_reference/reference_markers_gtdb.fasta -out GCF_902499555.1_CECT_9532_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:19,378] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:19,381] [INFO] Selected 7 target genomes.
[2024-01-24 13:25:19,381] [INFO] Target genome list was writen to GCF_902499555.1_CECT_9532_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:25:19,392] [INFO] Task started: fastANI
[2024-01-24 13:25:19,392] [INFO] Running command: fastANI --query /var/lib/cwl/stg34ee01d2-fa45-47b0-8d1e-66778de2a077/GCF_902499555.1_CECT_9532_genomic.fna.gz --refList GCF_902499555.1_CECT_9532_genomic.fna/target_genomes_gtdb.txt --output GCF_902499555.1_CECT_9532_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:25:24,710] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:24,717] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:25:24,718] [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_902499555.1	s__Mesonia oceanica	100.0	1392	1392	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.91	99.87	0.96	0.92	8	conclusive
GCF_008692195.1	s__Mesonia sp008692195	85.2812	931	1392	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423405.1	s__Mesonia mobilis	81.2571	697	1392	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.98	99.98	0.99	0.99	2	-
GCA_012964435.1	s__Mesonia sp012964435	80.9254	656	1392	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.98	99.98	0.99	0.99	2	-
GCF_900141885.1	s__Mesonia phycicola	79.0938	503	1392	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667275.1	s__Mesonia aquimarina	78.5321	368	1392	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002631855.1	s__Marixanthomonas sp002631855	77.1798	152	1392	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:25:24,719] [INFO] GTDB search result was written to GCF_902499555.1_CECT_9532_genomic.fna/result_gtdb.tsv
[2024-01-24 13:25:24,720] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:25:24,723] [INFO] DFAST_QC result json was written to GCF_902499555.1_CECT_9532_genomic.fna/dqc_result.json
[2024-01-24 13:25:24,723] [INFO] DFAST_QC completed!
[2024-01-24 13:25:24,723] [INFO] Total running time: 0h1m12s