[2024-01-24 14:47:07,108] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:07,110] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:07,110] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f01ca56-cfb0-4256-bea2-0b75bf8936c3/dqc_reference
[2024-01-24 14:47:08,392] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:08,397] [INFO] Task started: Prodigal
[2024-01-24 14:47:08,399] [INFO] Running command: gunzip -c /var/lib/cwl/stg1b834526-a27d-422b-aa2c-088235c0e05f/GCF_005885635.1_ASM588563v1_genomic.fna.gz | prodigal -d GCF_005885635.1_ASM588563v1_genomic.fna/cds.fna -a GCF_005885635.1_ASM588563v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:30,224] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:30,224] [INFO] Task started: HMMsearch
[2024-01-24 14:47:30,224] [INFO] Running command: hmmsearch --tblout GCF_005885635.1_ASM588563v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f01ca56-cfb0-4256-bea2-0b75bf8936c3/dqc_reference/reference_markers.hmm GCF_005885635.1_ASM588563v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:30,540] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:30,542] [INFO] Found 6/6 markers.
[2024-01-24 14:47:30,611] [INFO] Query marker FASTA was written to GCF_005885635.1_ASM588563v1_genomic.fna/markers.fasta
[2024-01-24 14:47:30,612] [INFO] Task started: Blastn
[2024-01-24 14:47:30,612] [INFO] Running command: blastn -query GCF_005885635.1_ASM588563v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f01ca56-cfb0-4256-bea2-0b75bf8936c3/dqc_reference/reference_markers.fasta -out GCF_005885635.1_ASM588563v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:31,309] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:31,312] [INFO] Selected 23 target genomes.
[2024-01-24 14:47:31,313] [INFO] Target genome list was writen to GCF_005885635.1_ASM588563v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:31,321] [INFO] Task started: fastANI
[2024-01-24 14:47:31,321] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b834526-a27d-422b-aa2c-088235c0e05f/GCF_005885635.1_ASM588563v1_genomic.fna.gz --refList GCF_005885635.1_ASM588563v1_genomic.fna/target_genomes.txt --output GCF_005885635.1_ASM588563v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:48,609] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:48,609] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f01ca56-cfb0-4256-bea2-0b75bf8936c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:48,609] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f01ca56-cfb0-4256-bea2-0b75bf8936c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:48,627] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:48,627] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:48,627] [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 algarum	strain=RZ26	GCA_005885635.1	2578118	2578118	type	True	100.0	1692	1692	95	conclusive
Maribacter forsetii	strain=DSM 18668	GCA_000744105.1	444515	444515	type	True	77.0914	185	1692	95	below_threshold
Maribacter vaceletii	strain=DSM 25230	GCA_003634105.1	1206816	1206816	type	True	77.0631	189	1692	95	below_threshold
Maribacter caenipelagi	strain=CECT 8455	GCA_004364175.1	1447781	1447781	type	True	77.0247	178	1692	95	below_threshold
Maribacter stanieri	strain=DSM 19891	GCA_900112245.1	440514	440514	type	True	77.01	179	1692	95	below_threshold
Zobellia amurskyensis	strain=KMM 3526	GCA_009725985.1	248905	248905	type	True	76.9444	203	1692	95	below_threshold
Maribacter arcticus	strain=DSM 23546	GCA_900167935.1	561365	561365	type	True	76.9225	182	1692	95	below_threshold
Maribacter aquivivus	strain=DSM 16478	GCA_900142175.1	228958	228958	type	True	76.9213	200	1692	95	below_threshold
Arenibacter arenosicollis	strain=BSSL-BM3	GCA_014397245.1	2762274	2762274	type	True	76.9136	104	1692	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001913155.1	1836467	1836467	type	True	76.8029	167	1692	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001673755.1	1836467	1836467	type	True	76.7694	170	1692	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	76.7194	65	1692	95	below_threshold
Arenibacter echinorum	strain=DSM 23522	GCA_003259375.1	440515	440515	type	True	76.7109	123	1692	95	below_threshold
Arenibacter latericius	strain=DSM 15913	GCA_000424985.1	86104	86104	type	True	76.6068	103	1692	95	below_threshold
Cellulophaga tyrosinoxydans	strain=DSM 21164	GCA_900176415.1	504486	504486	type	True	76.4459	155	1692	95	below_threshold
Muricauda hymeniacidonis	strain=176CP4-71	GCA_004296335.1	2517819	2517819	type	True	76.3659	101	1692	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	76.2182	81	1692	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	76.1654	81	1692	95	below_threshold
Muricauda amphidinii	strain=LMIT004	GCA_013090115.1	2735167	2735167	type	True	76.051	103	1692	95	below_threshold
Hanstruepera ponticola	strain=MM-14	GCA_012931685.1	2042995	2042995	type	True	76.0478	69	1692	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.0358	68	1692	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:48,630] [INFO] DFAST Taxonomy check result was written to GCF_005885635.1_ASM588563v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:48,631] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:48,632] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:48,632] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f01ca56-cfb0-4256-bea2-0b75bf8936c3/dqc_reference/checkm_data
[2024-01-24 14:47:48,636] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:48,688] [INFO] Task started: CheckM
[2024-01-24 14:47:48,689] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005885635.1_ASM588563v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005885635.1_ASM588563v1_genomic.fna/checkm_input GCF_005885635.1_ASM588563v1_genomic.fna/checkm_result
[2024-01-24 14:48:51,180] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:51,181] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:51,218] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:51,218] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:51,219] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005885635.1_ASM588563v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:51,219] [INFO] Task started: Blastn
[2024-01-24 14:48:51,219] [INFO] Running command: blastn -query GCF_005885635.1_ASM588563v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f01ca56-cfb0-4256-bea2-0b75bf8936c3/dqc_reference/reference_markers_gtdb.fasta -out GCF_005885635.1_ASM588563v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:52,226] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:52,230] [INFO] Selected 25 target genomes.
[2024-01-24 14:48:52,230] [INFO] Target genome list was writen to GCF_005885635.1_ASM588563v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:52,268] [INFO] Task started: fastANI
[2024-01-24 14:48:52,268] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b834526-a27d-422b-aa2c-088235c0e05f/GCF_005885635.1_ASM588563v1_genomic.fna.gz --refList GCF_005885635.1_ASM588563v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005885635.1_ASM588563v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:49:11,402] [INFO] Task succeeded: fastANI
[2024-01-24 14:49:11,429] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:49:11,429] [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_005885635.1	s__RZ26 sp005885635	100.0	1692	1692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__RZ26	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003232155.1	s__RZ26 sp003232155	77.8576	193	1692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__RZ26	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970695.1	s__Maribacter sp002742365	77.6641	195	1692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	96.61	96.61	0.86	0.86	2	-
GCF_000744105.1	s__Maribacter forsetii	77.08	186	1692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634105.1	s__Maribacter_B vaceletii	77.0259	192	1692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364175.1	s__Maribacter caenipelagi	77.0092	178	1692	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	77.0082	180	1692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	98.09	98.09	0.92	0.92	2	-
GCF_900142175.1	s__Maribacter aquivivus	76.9337	197	1692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167935.1	s__Maribacter arcticus	76.9277	182	1692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000621125.1	s__Maribacter antarcticus	76.9132	165	1692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001913155.1	s__Maribacter hydrothermalis	76.7892	168	1692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001430825.1	s__Sediminicola sp001430825	76.75	117	1692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Sediminicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004310325.1	s__Jejuia sp004310325	76.7194	65	1692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009797025.1	s__Cellulophaga sp009797025	76.7157	158	1692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014596745.1	s__Maribacter_A sp014596745	76.7085	154	1692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005771495.1	s__Maribacter sp005771495	76.6067	168	1692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019021925.1	s__Cellulophaga sp019021925	76.5932	163	1692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050675.1	s__Maribacter sp011050675	76.501	188	1692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	0.99	0.99	2	-
GCA_003712125.1	s__Muricauda_A sp003712125	76.4667	81	1692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176415.1	s__Cellulophaga tyrosinoxydans	76.4459	155	1692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004296335.1	s__Muricauda sp004296335	76.3659	101	1692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003712105.1	s__Winogradskyella sp003712105	76.2452	64	1692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114265.1	s__Flaviramulus basaltis	76.2232	81	1692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013090115.1	s__Muricauda amphidinii	76.052	103	1692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001005315.1	s__Kordia jejudonensis	75.9607	78	1692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:49:11,431] [INFO] GTDB search result was written to GCF_005885635.1_ASM588563v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:49:11,432] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:49:11,441] [INFO] DFAST_QC result json was written to GCF_005885635.1_ASM588563v1_genomic.fna/dqc_result.json
[2024-01-24 14:49:11,441] [INFO] DFAST_QC completed!
[2024-01-24 14:49:11,441] [INFO] Total running time: 0h2m4s