[2023-03-18 05:27:36,841] [INFO] DFAST_QC pipeline started.
[2023-03-18 05:27:36,841] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 05:27:36,841] [INFO] DQC Reference Directory: /var/lib/cwl/stg435c0b11-328b-4dcc-aa9f-4b8cb754ec26/dqc_reference
[2023-03-18 05:27:38,000] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 05:27:38,000] [INFO] Task started: Prodigal
[2023-03-18 05:27:38,000] [INFO] Running command: cat /var/lib/cwl/stga235932a-9296-4580-acb1-7b924b93d6a3/OceanDNA-b24961.fa | prodigal -d OceanDNA-b24961/cds.fna -a OceanDNA-b24961/protein.faa -g 11 -q > /dev/null
[2023-03-18 05:27:57,403] [INFO] Task succeeded: Prodigal
[2023-03-18 05:27:57,403] [INFO] Task started: HMMsearch
[2023-03-18 05:27:57,403] [INFO] Running command: hmmsearch --tblout OceanDNA-b24961/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg435c0b11-328b-4dcc-aa9f-4b8cb754ec26/dqc_reference/reference_markers.hmm OceanDNA-b24961/protein.faa > /dev/null
[2023-03-18 05:27:57,612] [INFO] Task succeeded: HMMsearch
[2023-03-18 05:27:57,612] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga235932a-9296-4580-acb1-7b924b93d6a3/OceanDNA-b24961.fa]
[2023-03-18 05:27:57,631] [INFO] Query marker FASTA was written to OceanDNA-b24961/markers.fasta
[2023-03-18 05:27:57,632] [INFO] Task started: Blastn
[2023-03-18 05:27:57,632] [INFO] Running command: blastn -query OceanDNA-b24961/markers.fasta -db /var/lib/cwl/stg435c0b11-328b-4dcc-aa9f-4b8cb754ec26/dqc_reference/reference_markers.fasta -out OceanDNA-b24961/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:27:58,454] [INFO] Task succeeded: Blastn
[2023-03-18 05:27:58,455] [INFO] Selected 19 target genomes.
[2023-03-18 05:27:58,455] [INFO] Target genome list was writen to OceanDNA-b24961/target_genomes.txt
[2023-03-18 05:27:58,467] [INFO] Task started: fastANI
[2023-03-18 05:27:58,467] [INFO] Running command: fastANI --query /var/lib/cwl/stga235932a-9296-4580-acb1-7b924b93d6a3/OceanDNA-b24961.fa --refList OceanDNA-b24961/target_genomes.txt --output OceanDNA-b24961/fastani_result.tsv --threads 1
[2023-03-18 05:28:12,294] [INFO] Task succeeded: fastANI
[2023-03-18 05:28:12,295] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg435c0b11-328b-4dcc-aa9f-4b8cb754ec26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 05:28:12,295] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg435c0b11-328b-4dcc-aa9f-4b8cb754ec26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 05:28:12,305] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 05:28:12,305] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 05:28:12,306] [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
Parvibaculum lavamentivorans	strain=DS-1	GCA_000017565.1	256618	256618	type	True	81.4953	691	1028	95	below_threshold
Parvibaculum sedimenti	strain=HXT-9	GCA_009184905.1	2608632	2608632	type	True	79.0594	430	1028	95	below_threshold
Parvibaculum indicum	strain=DSM 25305	GCA_011762095.1	562969	562969	type	True	79.059	497	1028	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	77.3139	124	1028	95	below_threshold
Tepidicaulis marinus	strain=MA2	GCA_000739695.1	1333998	1333998	type	True	77.1197	282	1028	95	below_threshold
Kaistia granuli	strain=Ko04	GCA_000380505.1	363259	363259	type	True	77.0596	119	1028	95	below_threshold
Afipia carboxidovorans	strain=OM5; ATCC 49405	GCA_000021365.1	40137	40137	type	True	77.0435	119	1028	95	below_threshold
Afipia carboxidovorans	strain=OM5	GCA_000218565.1	40137	40137	type	True	77.0303	120	1028	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	76.7754	100	1028	95	below_threshold
Afipia felis	strain=ATCC 53690	GCA_000314735.2	1035	1035	type	True	76.7494	94	1028	95	below_threshold
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	76.7422	140	1028	95	below_threshold
Pleomorphomonas carboxyditropha	strain=SVCO-16	GCA_002770725.1	2023338	2023338	type	True	76.615	116	1028	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	76.5985	94	1028	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_000178815.2	426	426	type	True	76.5418	105	1028	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_002752655.1	426	426	type	True	76.5039	107	1028	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.471	92	1028	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	76.3626	107	1028	95	below_threshold
Breoghania corrubedonensis	strain=DSM 23382	GCA_003053845.1	665038	665038	type	True	76.3079	138	1028	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.2955	108	1028	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 05:28:12,306] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24961/tc_result.tsv
[2023-03-18 05:28:12,306] [INFO] ===== Taxonomy check completed =====
[2023-03-18 05:28:12,306] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 05:28:12,306] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg435c0b11-328b-4dcc-aa9f-4b8cb754ec26/dqc_reference/checkm_data
[2023-03-18 05:28:12,307] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 05:28:12,311] [INFO] Task started: CheckM
[2023-03-18 05:28:12,311] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24961/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24961/checkm_input OceanDNA-b24961/checkm_result
[2023-03-18 05:29:01,737] [INFO] Task succeeded: CheckM
[2023-03-18 05:29:01,738] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 05:29:01,768] [INFO] ===== Completeness check finished =====
[2023-03-18 05:29:01,769] [INFO] ===== Start GTDB Search =====
[2023-03-18 05:29:01,769] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24961/markers.fasta)
[2023-03-18 05:29:01,771] [INFO] Task started: Blastn
[2023-03-18 05:29:01,771] [INFO] Running command: blastn -query OceanDNA-b24961/markers.fasta -db /var/lib/cwl/stg435c0b11-328b-4dcc-aa9f-4b8cb754ec26/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24961/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:29:03,287] [INFO] Task succeeded: Blastn
[2023-03-18 05:29:03,288] [INFO] Selected 6 target genomes.
[2023-03-18 05:29:03,288] [INFO] Target genome list was writen to OceanDNA-b24961/target_genomes_gtdb.txt
[2023-03-18 05:29:03,293] [INFO] Task started: fastANI
[2023-03-18 05:29:03,293] [INFO] Running command: fastANI --query /var/lib/cwl/stga235932a-9296-4580-acb1-7b924b93d6a3/OceanDNA-b24961.fa --refList OceanDNA-b24961/target_genomes_gtdb.txt --output OceanDNA-b24961/fastani_result_gtdb.tsv --threads 1
[2023-03-18 05:29:07,922] [INFO] Task succeeded: fastANI
[2023-03-18 05:29:07,926] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 05:29:07,926] [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_002694985.1	s__Parvibaculum sp002694985	99.9981	1024	1028	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCA_002480495.1	s__Parvibaculum sp002480495	83.8702	774	1028	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.50	98.87	0.94	0.88	9	-
GCA_002842875.1	s__Parvibaculum sp002842875	83.0859	693	1028	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359855.1	s__Parvibaculum sp014359855	82.7604	479	1028	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642695.1	s__Parvibaculum sp017642695	82.1525	687	1028	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.96	99.92	0.99	0.97	4	-
GCF_000017565.1	s__Parvibaculum lavamentivorans	81.4941	691	1028	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 05:29:07,926] [INFO] GTDB search result was written to OceanDNA-b24961/result_gtdb.tsv
[2023-03-18 05:29:07,926] [INFO] ===== GTDB Search completed =====
[2023-03-18 05:29:07,928] [INFO] DFAST_QC result json was written to OceanDNA-b24961/dqc_result.json
[2023-03-18 05:29:07,928] [INFO] DFAST_QC completed!
[2023-03-18 05:29:07,928] [INFO] Total running time: 0h1m31s