[2024-01-24 13:16:55,304] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:16:55,305] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:16:55,306] [INFO] DQC Reference Directory: /var/lib/cwl/stg860e92af-b2c2-4228-ba92-bbacdcb45a43/dqc_reference
[2024-01-24 13:16:56,505] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:16:56,506] [INFO] Task started: Prodigal
[2024-01-24 13:16:56,507] [INFO] Running command: gunzip -c /var/lib/cwl/stge1c1b0de-ea6b-4024-be84-32f60604cea7/GCF_001913155.1_ASM191315v1_genomic.fna.gz | prodigal -d GCF_001913155.1_ASM191315v1_genomic.fna/cds.fna -a GCF_001913155.1_ASM191315v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:11,025] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:11,026] [INFO] Task started: HMMsearch
[2024-01-24 13:17:11,026] [INFO] Running command: hmmsearch --tblout GCF_001913155.1_ASM191315v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg860e92af-b2c2-4228-ba92-bbacdcb45a43/dqc_reference/reference_markers.hmm GCF_001913155.1_ASM191315v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:11,324] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:11,326] [INFO] Found 6/6 markers.
[2024-01-24 13:17:11,365] [INFO] Query marker FASTA was written to GCF_001913155.1_ASM191315v1_genomic.fna/markers.fasta
[2024-01-24 13:17:11,365] [INFO] Task started: Blastn
[2024-01-24 13:17:11,365] [INFO] Running command: blastn -query GCF_001913155.1_ASM191315v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg860e92af-b2c2-4228-ba92-bbacdcb45a43/dqc_reference/reference_markers.fasta -out GCF_001913155.1_ASM191315v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:12,035] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:12,039] [INFO] Selected 15 target genomes.
[2024-01-24 13:17:12,039] [INFO] Target genome list was writen to GCF_001913155.1_ASM191315v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:12,044] [INFO] Task started: fastANI
[2024-01-24 13:17:12,045] [INFO] Running command: fastANI --query /var/lib/cwl/stge1c1b0de-ea6b-4024-be84-32f60604cea7/GCF_001913155.1_ASM191315v1_genomic.fna.gz --refList GCF_001913155.1_ASM191315v1_genomic.fna/target_genomes.txt --output GCF_001913155.1_ASM191315v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:24,933] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:24,934] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg860e92af-b2c2-4228-ba92-bbacdcb45a43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:24,934] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg860e92af-b2c2-4228-ba92-bbacdcb45a43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:24,948] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:17:24,949] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:24,949] [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
Maribacter hydrothermalis	strain=T28	GCA_001913155.1	1836467	1836467	type	True	100.0	1422	1423	95	conclusive
Maribacter hydrothermalis	strain=T28	GCA_001673755.1	1836467	1836467	type	True	99.9722	1383	1423	95	conclusive
Maribacter spongiicola	strain=DSM 25233	GCA_004364165.1	1206753	1206753	type	True	81.6156	850	1423	95	below_threshold
Maribacter aquivivus	strain=DSM 16478	GCA_900142175.1	228958	228958	type	True	81.6078	828	1423	95	below_threshold
Maribacter caenipelagi	strain=CECT 8455	GCA_004364175.1	1447781	1447781	type	True	81.2955	807	1423	95	below_threshold
Maribacter ulvicola	strain=DSM 15366	GCA_900155985.1	228959	228959	type	True	81.1435	780	1423	95	below_threshold
Maribacter stanieri	strain=DSM 19891	GCA_900112245.1	440514	440514	type	True	80.9021	825	1423	95	below_threshold
Maribacter arcticus	strain=DSM 23546	GCA_900167935.1	561365	561365	type	True	80.5389	735	1423	95	below_threshold
Maribacter orientalis	strain=DSM 16471	GCA_900109345.1	228957	228957	type	True	80.3605	768	1423	95	below_threshold
Maribacter litoralis	strain=SDRB-Phe2	GCA_003075045.1	2059726	2059726	type	True	80.2374	756	1423	95	below_threshold
Zobellia barbeyronii	strain=KMM 6746	GCA_018603515.1	2748009	2748009	type	True	77.1051	255	1423	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.3205	88	1423	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.2231	102	1423	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	76.1696	80	1423	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	75.9815	83	1423	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:24,950] [INFO] DFAST Taxonomy check result was written to GCF_001913155.1_ASM191315v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:24,951] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:24,951] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:24,951] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg860e92af-b2c2-4228-ba92-bbacdcb45a43/dqc_reference/checkm_data
[2024-01-24 13:17:24,952] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:25,005] [INFO] Task started: CheckM
[2024-01-24 13:17:25,006] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001913155.1_ASM191315v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001913155.1_ASM191315v1_genomic.fna/checkm_input GCF_001913155.1_ASM191315v1_genomic.fna/checkm_result
[2024-01-24 13:18:09,541] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:09,542] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:09,564] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:09,564] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:09,564] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001913155.1_ASM191315v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:09,565] [INFO] Task started: Blastn
[2024-01-24 13:18:09,565] [INFO] Running command: blastn -query GCF_001913155.1_ASM191315v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg860e92af-b2c2-4228-ba92-bbacdcb45a43/dqc_reference/reference_markers_gtdb.fasta -out GCF_001913155.1_ASM191315v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:10,490] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:10,495] [INFO] Selected 14 target genomes.
[2024-01-24 13:18:10,495] [INFO] Target genome list was writen to GCF_001913155.1_ASM191315v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:10,522] [INFO] Task started: fastANI
[2024-01-24 13:18:10,522] [INFO] Running command: fastANI --query /var/lib/cwl/stge1c1b0de-ea6b-4024-be84-32f60604cea7/GCF_001913155.1_ASM191315v1_genomic.fna.gz --refList GCF_001913155.1_ASM191315v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001913155.1_ASM191315v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:23,147] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:23,171] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:23,172] [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_001913155.1	s__Maribacter hydrothermalis	100.0	1422	1423	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_004364165.1	s__Maribacter spongiicola	81.6156	850	1423	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142175.1	s__Maribacter aquivivus	81.5934	830	1423	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744105.1	s__Maribacter forsetii	81.4124	829	1423	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364175.1	s__Maribacter caenipelagi	81.2815	810	1423	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155985.1	s__Maribacter ulvicola	81.1344	779	1423	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112245.1	s__Maribacter stanieri	80.8943	828	1423	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	98.09	98.09	0.92	0.92	2	-
GCA_011050675.1	s__Maribacter sp011050675	80.785	817	1423	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900167935.1	s__Maribacter arcticus	80.5471	734	1423	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109345.1	s__Maribacter orientalis	80.3605	768	1423	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075045.1	s__Maribacter litoralis	80.245	755	1423	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.43	97.43	0.90	0.90	2	-
GCF_001447995.1	s__Maribacter dokdonensis	80.1559	720	1423	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.64	97.51	0.89	0.86	13	-
GCF_005771495.1	s__Maribacter sp005771495	79.3215	604	1423	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000186265.1	s__Cellulophaga algicola	77.3299	273	1423	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	98.35	98.34	0.88	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:23,173] [INFO] GTDB search result was written to GCF_001913155.1_ASM191315v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:23,174] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:23,178] [INFO] DFAST_QC result json was written to GCF_001913155.1_ASM191315v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:23,178] [INFO] DFAST_QC completed!
[2024-01-24 13:18:23,179] [INFO] Total running time: 0h1m28s