[2023-03-15 07:29:11,756] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:29:11,756] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:29:11,756] [INFO] DQC Reference Directory: /var/lib/cwl/stg5408c375-0d49-4b2c-9d11-29e23cdbecb4/dqc_reference
[2023-03-15 07:29:13,589] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:29:13,589] [INFO] Task started: Prodigal
[2023-03-15 07:29:13,589] [INFO] Running command: cat /var/lib/cwl/stg417e4420-1576-4a64-a0f5-2b697c82490b/OceanDNA-b6447.fa | prodigal -d OceanDNA-b6447/cds.fna -a OceanDNA-b6447/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:29:30,125] [INFO] Task succeeded: Prodigal
[2023-03-15 07:29:30,125] [INFO] Task started: HMMsearch
[2023-03-15 07:29:30,125] [INFO] Running command: hmmsearch --tblout OceanDNA-b6447/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5408c375-0d49-4b2c-9d11-29e23cdbecb4/dqc_reference/reference_markers.hmm OceanDNA-b6447/protein.faa > /dev/null
[2023-03-15 07:29:30,339] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:29:30,340] [INFO] Found 6/6 markers.
[2023-03-15 07:29:30,357] [INFO] Query marker FASTA was written to OceanDNA-b6447/markers.fasta
[2023-03-15 07:29:30,359] [INFO] Task started: Blastn
[2023-03-15 07:29:30,359] [INFO] Running command: blastn -query OceanDNA-b6447/markers.fasta -db /var/lib/cwl/stg5408c375-0d49-4b2c-9d11-29e23cdbecb4/dqc_reference/reference_markers.fasta -out OceanDNA-b6447/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:29:30,958] [INFO] Task succeeded: Blastn
[2023-03-15 07:29:30,959] [INFO] Selected 22 target genomes.
[2023-03-15 07:29:30,959] [INFO] Target genome list was writen to OceanDNA-b6447/target_genomes.txt
[2023-03-15 07:29:30,972] [INFO] Task started: fastANI
[2023-03-15 07:29:30,972] [INFO] Running command: fastANI --query /var/lib/cwl/stg417e4420-1576-4a64-a0f5-2b697c82490b/OceanDNA-b6447.fa --refList OceanDNA-b6447/target_genomes.txt --output OceanDNA-b6447/fastani_result.tsv --threads 1
[2023-03-15 07:29:44,351] [INFO] Task succeeded: fastANI
[2023-03-15 07:29:44,352] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5408c375-0d49-4b2c-9d11-29e23cdbecb4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:29:44,352] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5408c375-0d49-4b2c-9d11-29e23cdbecb4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:29:44,365] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:29:44,365] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 07:29:44,365] [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 antarctica	strain=SW49	GCA_007997155.1	153266	153266	type	True	78.4267	320	833	95	below_threshold
Aequorivita soesokkakensis	strain=RSSK-12	GCA_001641085.1	1385699	1385699	type	True	78.3986	315	833	95	below_threshold
Aequorivita sinensis	strain=S1-10	GCA_006346335.1	1382458	1382458	type	True	78.3937	301	833	95	below_threshold
Aequorivita iocasae	strain=KX20305	GCA_016757735.1	2803865	2803865	type	True	78.3192	318	833	95	below_threshold
Aequorivita lipolytica	strain=Y10-2	GCA_007997135.1	153267	153267	type	True	78.303	339	833	95	below_threshold
Aequorivita vladivostokensis	strain=KMM 3516	GCA_000952855.1	171194	171194	type	True	78.2866	312	833	95	below_threshold
Aequorivita aquimaris	strain=D-24	GCA_001573155.1	1548749	1548749	type	True	78.1785	344	833	95	below_threshold
Aequorivita sublithincola	strain=DSM 14238	GCA_000265385.1	101385	101385	type	True	78.1423	321	833	95	below_threshold
Aequorivita viscosa	strain=DSM 26349	GCA_900141955.1	797419	797419	type	True	77.7418	243	833	95	below_threshold
Aequorivita viscosa	strain=CGMCC 1.11023	GCA_900106795.1	797419	797419	type	True	77.6873	241	833	95	below_threshold
Tamlana nanhaiensis	strain=FHC16	GCA_000943555.1	1382798	1382798	type	True	76.7297	101	833	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.7099	71	833	95	below_threshold
Marixanthomonas spongiae	strain=HN-E44	GCA_003095375.1	2174845	2174845	type	True	76.591	118	833	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	76.5334	85	833	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	76.5282	84	833	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	76.4992	74	833	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.1733	81	833	95	below_threshold
Lutibacter oricola	strain=DSM 24956	GCA_900106565.1	762486	762486	type	True	76.1056	68	833	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.1027	88	833	95	below_threshold
Cellulophaga omnivescoria	strain=W5C	GCA_001999725.1	1888890	1888890	type	True	76.0419	80	833	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.0184	100	833	95	below_threshold
Aquimarina aggregata	strain=RZW4-3-2	GCA_001632745.1	1642818	1642818	type	True	75.8444	81	833	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 07:29:44,365] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6447/tc_result.tsv
[2023-03-15 07:29:44,365] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:29:44,365] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:29:44,365] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5408c375-0d49-4b2c-9d11-29e23cdbecb4/dqc_reference/checkm_data
[2023-03-15 07:29:44,366] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:29:44,370] [INFO] Task started: CheckM
[2023-03-15 07:29:44,370] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6447/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6447/checkm_input OceanDNA-b6447/checkm_result
[2023-03-15 07:30:27,452] [INFO] Task succeeded: CheckM
[2023-03-15 07:30:27,452] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 07:30:27,455] [INFO] ===== Completeness check finished =====
[2023-03-15 07:30:27,455] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:30:27,455] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6447/markers.fasta)
[2023-03-15 07:30:27,455] [INFO] Task started: Blastn
[2023-03-15 07:30:27,455] [INFO] Running command: blastn -query OceanDNA-b6447/markers.fasta -db /var/lib/cwl/stg5408c375-0d49-4b2c-9d11-29e23cdbecb4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6447/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:30:28,296] [INFO] Task succeeded: Blastn
[2023-03-15 07:30:28,297] [INFO] Selected 17 target genomes.
[2023-03-15 07:30:28,297] [INFO] Target genome list was writen to OceanDNA-b6447/target_genomes_gtdb.txt
[2023-03-15 07:30:28,309] [INFO] Task started: fastANI
[2023-03-15 07:30:28,309] [INFO] Running command: fastANI --query /var/lib/cwl/stg417e4420-1576-4a64-a0f5-2b697c82490b/OceanDNA-b6447.fa --refList OceanDNA-b6447/target_genomes_gtdb.txt --output OceanDNA-b6447/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:30:37,307] [INFO] Task succeeded: fastANI
[2023-03-15 07:30:37,318] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 07:30:37,318] [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
GCA_002375695.1	s__Aequorivita sp002375695	98.9878	805	833	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_006346335.1	s__Aequorivita sinensis	78.4054	300	833	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.40	96.22	0.90	0.88	3	-
GCF_001641085.1	s__Aequorivita soesokkakensis	78.3986	315	833	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.26	97.26	0.92	0.92	2	-
GCA_002364215.1	s__Aequorivita sp002364215	78.3966	341	833	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.66	98.55	0.97	0.89	12	-
GCF_016757735.1	s__Aequorivita sp016757735	78.3311	317	833	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002715485.1	s__Aequorivita sp002715485	78.3237	318	833	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.49	99.49	0.87	0.87	2	-
GCF_000952855.1	s__Aequorivita vladivostokensis	78.2978	311	833	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	98.24	98.00	0.93	0.90	7	-
GCF_900489465.1	s__Aequorivita sp900489465	78.188	334	833	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001573155.1	s__Aequorivita aquimaris	78.1682	345	833	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733915.1	s__Aequorivita sp002733915	78.1379	313	833	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	78.1307	322	833	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	77.8191	290	833	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733185.1	s__GCA-002733185 sp002733185	77.0107	112	833	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012910715.1	s__Flavivirga sp012910715	76.7099	71	833	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181835.1	s__GCA-002733185 sp905181835	76.502	67	833	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004213605.1	s__GCA-002733185 sp004213605	76.2942	51	833	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	95.79	95.79	0.89	0.89	2	-
GCF_001999725.1	s__Cellulophaga omnivescoria	76.0606	79	833	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 07:30:37,318] [INFO] GTDB search result was written to OceanDNA-b6447/result_gtdb.tsv
[2023-03-15 07:30:37,318] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:30:37,320] [INFO] DFAST_QC result json was written to OceanDNA-b6447/dqc_result.json
[2023-03-15 07:30:37,320] [INFO] DFAST_QC completed!
[2023-03-15 07:30:37,321] [INFO] Total running time: 0h1m26s