[2024-01-24 10:47:06,586] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,596] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,596] [INFO] DQC Reference Directory: /var/lib/cwl/stgdbcc90e4-f4b7-4e7c-be48-bb455906d91c/dqc_reference
[2024-01-24 10:47:12,685] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,814] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,815] [INFO] Running command: gunzip -c /var/lib/cwl/stg59d5c5cc-c170-4a90-9012-b7f0ae0744ff/GCF_006494535.1_ASM649453v1_genomic.fna.gz | prodigal -d GCF_006494535.1_ASM649453v1_genomic.fna/cds.fna -a GCF_006494535.1_ASM649453v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:26,374] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:26,375] [INFO] Task started: HMMsearch
[2024-01-24 10:47:26,375] [INFO] Running command: hmmsearch --tblout GCF_006494535.1_ASM649453v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdbcc90e4-f4b7-4e7c-be48-bb455906d91c/dqc_reference/reference_markers.hmm GCF_006494535.1_ASM649453v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:26,679] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:26,681] [INFO] Found 6/6 markers.
[2024-01-24 10:47:26,713] [INFO] Query marker FASTA was written to GCF_006494535.1_ASM649453v1_genomic.fna/markers.fasta
[2024-01-24 10:47:26,713] [INFO] Task started: Blastn
[2024-01-24 10:47:26,713] [INFO] Running command: blastn -query GCF_006494535.1_ASM649453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbcc90e4-f4b7-4e7c-be48-bb455906d91c/dqc_reference/reference_markers.fasta -out GCF_006494535.1_ASM649453v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:27,402] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:27,405] [INFO] Selected 26 target genomes.
[2024-01-24 10:47:27,406] [INFO] Target genome list was writen to GCF_006494535.1_ASM649453v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:28,393] [INFO] Task started: fastANI
[2024-01-24 10:47:28,393] [INFO] Running command: fastANI --query /var/lib/cwl/stg59d5c5cc-c170-4a90-9012-b7f0ae0744ff/GCF_006494535.1_ASM649453v1_genomic.fna.gz --refList GCF_006494535.1_ASM649453v1_genomic.fna/target_genomes.txt --output GCF_006494535.1_ASM649453v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:45,446] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:45,447] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdbcc90e4-f4b7-4e7c-be48-bb455906d91c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:45,447] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdbcc90e4-f4b7-4e7c-be48-bb455906d91c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:45,467] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:45,467] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:45,467] [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
Paucihalobacter ruber	strain=CWB-1	GCA_006494535.1	2567861	2567861	type	True	100.0	1172	1173	95	conclusive
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.1631	127	1173	95	below_threshold
Psychroserpens mesophilus	strain=JCM 13413	GCA_000826645.1	325473	325473	type	True	76.9633	129	1173	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	76.9328	114	1173	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	76.9155	135	1173	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	76.8877	133	1173	95	below_threshold
Hanstruepera ponticola	strain=MM-14	GCA_012931685.1	2042995	2042995	type	True	76.8727	140	1173	95	below_threshold
Tamlana sedimentorum	strain=JCM 19808	GCA_000943565.1	1435349	1435349	type	True	76.8654	139	1173	95	below_threshold
Winogradskyella ouciana	strain=ZXX205	GCA_009709615.1	2608631	2608631	type	True	76.7824	127	1173	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	76.7501	102	1173	95	below_threshold
Confluentibacter flavum	strain=3B	GCA_002843175.1	1909700	1909700	type	True	76.6634	149	1173	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.6044	108	1173	95	below_threshold
Confluentibacter citreus	strain=XJNY	GCA_002807055.1	2007307	2007307	type	True	76.5887	136	1173	95	below_threshold
Winogradskyella algicola	strain=IMCC33238	GCA_005869935.1	2575815	2575815	type	True	76.5856	148	1173	95	below_threshold
Hyunsoonleella pacifica	strain=CGMCC 1.11009	GCA_014636335.1	1080224	1080224	type	True	76.553	112	1173	95	below_threshold
Hyunsoonleella pacifica	strain=SW033	GCA_004310335.1	1080224	1080224	type	True	76.5345	113	1173	95	below_threshold
Yeosuana aromativorans	strain=JCM 12862	GCA_014646655.1	288019	288019	type	True	76.5234	126	1173	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	76.455	145	1173	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	76.3959	115	1173	95	below_threshold
Seonamhaeicola marinus	strain=B011	GCA_008085455.1	1912246	1912246	type	True	76.3779	94	1173	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	76.233	132	1173	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	76.1582	66	1173	95	below_threshold
Aestuariibaculum sediminum	strain=TT11	GCA_014596945.1	2770637	2770637	type	True	76.0796	119	1173	95	below_threshold
Formosa sediminum	strain=PS13	GCA_007197735.1	2594004	2594004	type	True	76.0521	113	1173	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:45,472] [INFO] DFAST Taxonomy check result was written to GCF_006494535.1_ASM649453v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:45,472] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:45,473] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:45,473] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdbcc90e4-f4b7-4e7c-be48-bb455906d91c/dqc_reference/checkm_data
[2024-01-24 10:47:45,474] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:45,515] [INFO] Task started: CheckM
[2024-01-24 10:47:45,515] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006494535.1_ASM649453v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006494535.1_ASM649453v1_genomic.fna/checkm_input GCF_006494535.1_ASM649453v1_genomic.fna/checkm_result
[2024-01-24 10:48:27,328] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:27,330] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:27,353] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:27,353] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:27,354] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006494535.1_ASM649453v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:27,354] [INFO] Task started: Blastn
[2024-01-24 10:48:27,355] [INFO] Running command: blastn -query GCF_006494535.1_ASM649453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbcc90e4-f4b7-4e7c-be48-bb455906d91c/dqc_reference/reference_markers_gtdb.fasta -out GCF_006494535.1_ASM649453v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:28,376] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:28,379] [INFO] Selected 23 target genomes.
[2024-01-24 10:48:28,379] [INFO] Target genome list was writen to GCF_006494535.1_ASM649453v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:28,395] [INFO] Task started: fastANI
[2024-01-24 10:48:28,396] [INFO] Running command: fastANI --query /var/lib/cwl/stg59d5c5cc-c170-4a90-9012-b7f0ae0744ff/GCF_006494535.1_ASM649453v1_genomic.fna.gz --refList GCF_006494535.1_ASM649453v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006494535.1_ASM649453v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:42,421] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:42,447] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:42,447] [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_006494535.1	s__Paucihalobacter ruber	100.0	1172	1173	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Paucihalobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018402135.1	s__Paucihalobacter sp018402135	79.5139	360	1173	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Paucihalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366715.1	s__Meridianimaribacter flavus	76.9884	159	1173	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Meridianimaribacter	95.0	97.44	97.06	0.91	0.87	3	-
GCF_000826645.1	s__Psychroserpens mesophilus	76.9437	130	1173	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386195.1	s__Seonamhaeicola aphaedonensis	76.9363	109	1173	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141715.1	s__Arenitalea lutea	76.9337	134	1173	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_012931685.1	s__Pseudobizionia ponticola	76.8908	140	1173	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pseudobizionia	95.0	97.35	97.35	0.92	0.92	2	-
GCA_000171875.1	s__Winogradskyella sp000171875	76.8235	122	1173	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008084905.1	s__Xanthomarina maritima	76.7851	128	1173	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004310325.1	s__Jejuia sp004310325	76.7501	102	1173	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002784145.1	s__Yeosuana sp002784145	76.6198	132	1173	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	99.75	99.57	0.88	0.85	11	-
GCA_003712105.1	s__Winogradskyella sp003712105	76.5961	106	1173	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003944795.1	s__Mangrovimonas spongiae	76.5789	146	1173	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mangrovimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997385.1	s__Seonamhaeicola algicola	76.5476	123	1173	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004310335.1	s__Jejuia pacifica	76.5345	113	1173	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014646655.1	s__Yeosuana aromativorans	76.5234	126	1173	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706045.1	s__Winogradskyella sp002706045	76.4505	104	1173	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002682935.1	s__Winogradskyella sp002682935	76.3924	135	1173	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014297365.1	s__Winogradskyella echinorum	76.3908	148	1173	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002831665.1	s__Lacinutrix sp002831665	76.2615	116	1173	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014596945.1	s__Aestuariibaculum sediminum	76.0796	119	1173	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aestuariibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007197735.1	s__Formosa sediminum	76.0521	113	1173	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Formosa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002441545.1	s__Yeosuana sp002441545	75.7383	110	1173	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:42,449] [INFO] GTDB search result was written to GCF_006494535.1_ASM649453v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:42,450] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:42,455] [INFO] DFAST_QC result json was written to GCF_006494535.1_ASM649453v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:42,456] [INFO] DFAST_QC completed!
[2024-01-24 10:48:42,456] [INFO] Total running time: 0h1m36s