[2024-01-24 14:06:02,616] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:02,620] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:02,620] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd927208-ec8e-42e2-b932-1e05cba575ee/dqc_reference
[2024-01-24 14:06:03,900] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:03,901] [INFO] Task started: Prodigal
[2024-01-24 14:06:03,901] [INFO] Running command: gunzip -c /var/lib/cwl/stg8864e485-ff4c-42e0-b323-6c847a2f1cc5/GCF_019311235.1_ASM1931123v1_genomic.fna.gz | prodigal -d GCF_019311235.1_ASM1931123v1_genomic.fna/cds.fna -a GCF_019311235.1_ASM1931123v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:13,733] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:13,734] [INFO] Task started: HMMsearch
[2024-01-24 14:06:13,734] [INFO] Running command: hmmsearch --tblout GCF_019311235.1_ASM1931123v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd927208-ec8e-42e2-b932-1e05cba575ee/dqc_reference/reference_markers.hmm GCF_019311235.1_ASM1931123v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:14,095] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:14,096] [INFO] Found 6/6 markers.
[2024-01-24 14:06:14,136] [INFO] Query marker FASTA was written to GCF_019311235.1_ASM1931123v1_genomic.fna/markers.fasta
[2024-01-24 14:06:14,136] [INFO] Task started: Blastn
[2024-01-24 14:06:14,136] [INFO] Running command: blastn -query GCF_019311235.1_ASM1931123v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd927208-ec8e-42e2-b932-1e05cba575ee/dqc_reference/reference_markers.fasta -out GCF_019311235.1_ASM1931123v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:14,967] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:14,971] [INFO] Selected 17 target genomes.
[2024-01-24 14:06:14,971] [INFO] Target genome list was writen to GCF_019311235.1_ASM1931123v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:14,981] [INFO] Task started: fastANI
[2024-01-24 14:06:14,981] [INFO] Running command: fastANI --query /var/lib/cwl/stg8864e485-ff4c-42e0-b323-6c847a2f1cc5/GCF_019311235.1_ASM1931123v1_genomic.fna.gz --refList GCF_019311235.1_ASM1931123v1_genomic.fna/target_genomes.txt --output GCF_019311235.1_ASM1931123v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:27,768] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:27,769] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd927208-ec8e-42e2-b932-1e05cba575ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:27,769] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd927208-ec8e-42e2-b932-1e05cba575ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:27,780] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:06:27,780] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:06:27,780] [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 mobilis	strain=DSM 19841	GCA_000423405.1	369791	369791	type	True	81.3287	629	1078	95	below_threshold
Mesonia mobilis	strain=KCTC 12708	GCA_014651475.1	369791	369791	type	True	81.3121	630	1078	95	below_threshold
Mesonia phycicola	strain=DSM 21425	GCA_900141885.1	579105	579105	type	True	80.3064	566	1078	95	below_threshold
Mesonia oceanica	strain=ISS653	GCA_902499555.1	2687242	2687242	type	True	80.0403	630	1078	95	below_threshold
Mesonia algae	strain=DSM 15361	GCA_003253545.1	213248	213248	type	True	77.92	328	1078	95	below_threshold
Zunongwangia atlantica	strain=22II14-10F7	GCA_002094855.1	1502297	1502297	type	True	77.5079	221	1078	95	below_threshold
Haloflavibacter putidus	strain=PLHSN227	GCA_006546625.1	2576776	2576776	type	True	77.1147	236	1078	95	below_threshold
Cochleicola gelatinilyticus	strain=LPB0005	GCA_001637325.1	1763537	1763537	type	True	77.0545	91	1078	95	below_threshold
Aquimarina spongiae	strain=DSM 22623	GCA_900141785.1	570521	570521	type	True	76.814	96	1078	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	76.5846	115	1078	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	76.4994	119	1078	95	below_threshold
Faecalibacter rhinopitheci	strain=WQ 117	GCA_015234135.1	2779678	2779678	type	True	76.2303	54	1078	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:27,783] [INFO] DFAST Taxonomy check result was written to GCF_019311235.1_ASM1931123v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:27,783] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:27,784] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:27,784] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd927208-ec8e-42e2-b932-1e05cba575ee/dqc_reference/checkm_data
[2024-01-24 14:06:27,785] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:27,832] [INFO] Task started: CheckM
[2024-01-24 14:06:27,832] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019311235.1_ASM1931123v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019311235.1_ASM1931123v1_genomic.fna/checkm_input GCF_019311235.1_ASM1931123v1_genomic.fna/checkm_result
[2024-01-24 14:07:00,890] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:00,891] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:00,914] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:00,915] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:00,915] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019311235.1_ASM1931123v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:00,916] [INFO] Task started: Blastn
[2024-01-24 14:07:00,916] [INFO] Running command: blastn -query GCF_019311235.1_ASM1931123v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd927208-ec8e-42e2-b932-1e05cba575ee/dqc_reference/reference_markers_gtdb.fasta -out GCF_019311235.1_ASM1931123v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:01,885] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:01,889] [INFO] Selected 12 target genomes.
[2024-01-24 14:07:01,889] [INFO] Target genome list was writen to GCF_019311235.1_ASM1931123v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:02,635] [INFO] Task started: fastANI
[2024-01-24 14:07:02,636] [INFO] Running command: fastANI --query /var/lib/cwl/stg8864e485-ff4c-42e0-b323-6c847a2f1cc5/GCF_019311235.1_ASM1931123v1_genomic.fna.gz --refList GCF_019311235.1_ASM1931123v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019311235.1_ASM1931123v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:11,482] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:11,491] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:07:11,492] [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_000423405.1	s__Mesonia mobilis	81.34	627	1078	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	80.8967	586	1078	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	80.306	565	1078	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008692195.1	s__Mesonia sp008692195	80.1219	605	1078	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902499555.1	s__Mesonia oceanica	80.0469	630	1078	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.91	99.87	0.96	0.92	8	-
GCF_003667275.1	s__Mesonia aquimarina	78.135	357	1078	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003253545.1	s__Mesonia algae	77.9325	329	1078	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	95.16	95.16	0.83	0.83	2	-
GCF_900141785.1	s__Aquimarina spongiae	76.814	96	1078	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:11,494] [INFO] GTDB search result was written to GCF_019311235.1_ASM1931123v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:11,494] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:11,505] [INFO] DFAST_QC result json was written to GCF_019311235.1_ASM1931123v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:11,505] [INFO] DFAST_QC completed!
[2024-01-24 14:07:11,505] [INFO] Total running time: 0h1m9s