[2024-01-24 13:21:47,067] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:47,069] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:47,069] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b88d83b-ad7c-412e-b7b9-7e855eb0b586/dqc_reference
[2024-01-24 13:21:48,420] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:48,421] [INFO] Task started: Prodigal
[2024-01-24 13:21:48,422] [INFO] Running command: gunzip -c /var/lib/cwl/stgd3739f59-def7-4e8b-809d-31b3f5b49f88/GCF_006346335.1_ASM634633v1_genomic.fna.gz | prodigal -d GCF_006346335.1_ASM634633v1_genomic.fna/cds.fna -a GCF_006346335.1_ASM634633v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:21:58,984] [INFO] Task succeeded: Prodigal
[2024-01-24 13:21:58,985] [INFO] Task started: HMMsearch
[2024-01-24 13:21:58,985] [INFO] Running command: hmmsearch --tblout GCF_006346335.1_ASM634633v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b88d83b-ad7c-412e-b7b9-7e855eb0b586/dqc_reference/reference_markers.hmm GCF_006346335.1_ASM634633v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:21:59,252] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:21:59,253] [INFO] Found 6/6 markers.
[2024-01-24 13:21:59,281] [INFO] Query marker FASTA was written to GCF_006346335.1_ASM634633v1_genomic.fna/markers.fasta
[2024-01-24 13:21:59,281] [INFO] Task started: Blastn
[2024-01-24 13:21:59,281] [INFO] Running command: blastn -query GCF_006346335.1_ASM634633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b88d83b-ad7c-412e-b7b9-7e855eb0b586/dqc_reference/reference_markers.fasta -out GCF_006346335.1_ASM634633v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:59,970] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:59,973] [INFO] Selected 21 target genomes.
[2024-01-24 13:21:59,974] [INFO] Target genome list was writen to GCF_006346335.1_ASM634633v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:00,005] [INFO] Task started: fastANI
[2024-01-24 13:22:00,006] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3739f59-def7-4e8b-809d-31b3f5b49f88/GCF_006346335.1_ASM634633v1_genomic.fna.gz --refList GCF_006346335.1_ASM634633v1_genomic.fna/target_genomes.txt --output GCF_006346335.1_ASM634633v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:15,018] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:15,018] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b88d83b-ad7c-412e-b7b9-7e855eb0b586/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:15,019] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b88d83b-ad7c-412e-b7b9-7e855eb0b586/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:15,035] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:15,036] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:15,036] [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
Aequorivita sinensis	strain=S1-10	GCA_006346335.1	1382458	1382458	type	True	100.0	1021	1024	95	conclusive
Aequorivita viscosa	strain=CGMCC 1.11023	GCA_900106795.1	797419	797419	type	True	79.2991	327	1024	95	below_threshold
Aequorivita viscosa	strain=DSM 26349	GCA_900141955.1	797419	797419	type	True	79.2748	327	1024	95	below_threshold
Aequorivita antarctica	strain=SW49	GCA_007997155.1	153266	153266	type	True	78.4252	350	1024	95	below_threshold
Aequorivita soesokkakensis	strain=RSSK-12	GCA_001641085.1	1385699	1385699	type	True	78.3638	341	1024	95	below_threshold
Aequorivita vladivostokensis	strain=KMM 3516	GCA_000952855.1	171194	171194	type	True	78.2586	275	1024	95	below_threshold
Aequorivita capsosiphonis	strain=DSM 23843	GCA_000429125.1	487317	487317	type	True	78.2361	392	1024	95	below_threshold
Aequorivita lipolytica	strain=Y10-2	GCA_007997135.1	153267	153267	type	True	78.18	347	1024	95	below_threshold
Aequorivita sublithincola	strain=DSM 14238	GCA_000265385.1	101385	101385	type	True	78.0918	399	1024	95	below_threshold
Aequorivita iocasae	strain=KX20305	GCA_016757735.1	2803865	2803865	type	True	78.0612	305	1024	95	below_threshold
Marixanthomonas ophiurae	strain=KMM 3046	GCA_003413745.1	387659	387659	type	True	77.0662	183	1024	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	76.6132	78	1024	95	below_threshold
Tamlana haliotis	strain=B1N29	GCA_008806375.1	2614804	2614804	type	True	76.5679	91	1024	95	below_threshold
Formosa algae	strain=KMM 3553	GCA_001439665.1	225843	225843	type	True	76.4213	101	1024	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.4007	106	1024	95	below_threshold
Cellulophaga omnivescoria	strain=W5C	GCA_001999725.1	1888890	1888890	type	True	76.3074	89	1024	95	below_threshold
Cellulophaga lytica	strain=DSM 7489	GCA_000190595.1	979	979	type	True	76.2017	105	1024	95	below_threshold
Zobellia barbeyronii	strain=KMM 6746	GCA_018603515.1	2748009	2748009	type	True	76.1928	71	1024	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	76.1322	70	1024	95	below_threshold
Aureibaculum flavum	strain=A20	GCA_016406085.1	2795986	2795986	type	True	75.8622	72	1024	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:15,038] [INFO] DFAST Taxonomy check result was written to GCF_006346335.1_ASM634633v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:15,038] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:15,038] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:15,039] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b88d83b-ad7c-412e-b7b9-7e855eb0b586/dqc_reference/checkm_data
[2024-01-24 13:22:15,046] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:15,082] [INFO] Task started: CheckM
[2024-01-24 13:22:15,082] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006346335.1_ASM634633v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006346335.1_ASM634633v1_genomic.fna/checkm_input GCF_006346335.1_ASM634633v1_genomic.fna/checkm_result
[2024-01-24 13:22:50,708] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:50,710] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:50,741] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:50,741] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:50,742] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006346335.1_ASM634633v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:50,742] [INFO] Task started: Blastn
[2024-01-24 13:22:50,743] [INFO] Running command: blastn -query GCF_006346335.1_ASM634633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b88d83b-ad7c-412e-b7b9-7e855eb0b586/dqc_reference/reference_markers_gtdb.fasta -out GCF_006346335.1_ASM634633v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:51,712] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:51,716] [INFO] Selected 16 target genomes.
[2024-01-24 13:22:51,716] [INFO] Target genome list was writen to GCF_006346335.1_ASM634633v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:51,786] [INFO] Task started: fastANI
[2024-01-24 13:22:51,786] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3739f59-def7-4e8b-809d-31b3f5b49f88/GCF_006346335.1_ASM634633v1_genomic.fna.gz --refList GCF_006346335.1_ASM634633v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006346335.1_ASM634633v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:01,710] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:01,723] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:01,723] [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_006346335.1	s__Aequorivita sinensis	100.0	1021	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.40	96.22	0.90	0.88	3	conclusive
GCF_900106795.1	s__Aequorivita viscosa	79.2991	327	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.99	99.99	0.99	0.99	2	-
GCA_002375695.1	s__Aequorivita sp002375695	78.4496	325	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.99	99.99	0.99	0.99	2	-
GCF_007997155.1	s__Aequorivita antarctica	78.3999	352	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.98	99.98	0.99	0.99	2	-
GCF_001641085.1	s__Aequorivita soesokkakensis	78.3638	341	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.26	97.26	0.92	0.92	2	-
GCF_000952855.1	s__Aequorivita vladivostokensis	78.2599	275	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	98.24	98.00	0.93	0.90	7	-
GCF_000429125.1	s__Aequorivita capsosiphonis	78.2332	391	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364215.1	s__Aequorivita sp002364215	78.195	332	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.66	98.55	0.97	0.89	12	-
GCF_007997135.1	s__Aequorivita lipolytica	78.1845	346	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900489465.1	s__Aequorivita sp900489465	78.1738	363	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265385.1	s__Aequorivita sublithincola	78.0918	399	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016649715.1	s__Aequorivita sp016649715	78.0782	291	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016757735.1	s__Aequorivita sp016757735	78.0613	305	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008806375.1	s__Tamlana_A haliotis	76.5679	91	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008033385.1	s__Algibacter pacificus	76.3867	107	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001999725.1	s__Cellulophaga omnivescoria	76.2917	90	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:01,725] [INFO] GTDB search result was written to GCF_006346335.1_ASM634633v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:01,725] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:01,729] [INFO] DFAST_QC result json was written to GCF_006346335.1_ASM634633v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:01,729] [INFO] DFAST_QC completed!
[2024-01-24 13:23:01,729] [INFO] Total running time: 0h1m15s