[2023-03-15 18:39:12,216] [INFO] DFAST_QC pipeline started.
[2023-03-15 18:39:12,217] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 18:39:12,217] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e70c17c-b8c1-44ee-b0d9-424232bea3a4/dqc_reference
[2023-03-15 18:39:13,657] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 18:39:13,657] [INFO] Task started: Prodigal
[2023-03-15 18:39:13,657] [INFO] Running command: cat /var/lib/cwl/stg4f94ae89-e76b-4ccb-b560-69652dd53737/OceanDNA-b24024.fa | prodigal -d OceanDNA-b24024/cds.fna -a OceanDNA-b24024/protein.faa -g 11 -q > /dev/null
[2023-03-15 18:39:39,198] [INFO] Task succeeded: Prodigal
[2023-03-15 18:39:39,198] [INFO] Task started: HMMsearch
[2023-03-15 18:39:39,198] [INFO] Running command: hmmsearch --tblout OceanDNA-b24024/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e70c17c-b8c1-44ee-b0d9-424232bea3a4/dqc_reference/reference_markers.hmm OceanDNA-b24024/protein.faa > /dev/null
[2023-03-15 18:39:39,421] [INFO] Task succeeded: HMMsearch
[2023-03-15 18:39:39,421] [INFO] Found 6/6 markers.
[2023-03-15 18:39:39,447] [INFO] Query marker FASTA was written to OceanDNA-b24024/markers.fasta
[2023-03-15 18:39:39,447] [INFO] Task started: Blastn
[2023-03-15 18:39:39,447] [INFO] Running command: blastn -query OceanDNA-b24024/markers.fasta -db /var/lib/cwl/stg5e70c17c-b8c1-44ee-b0d9-424232bea3a4/dqc_reference/reference_markers.fasta -out OceanDNA-b24024/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:39:40,329] [INFO] Task succeeded: Blastn
[2023-03-15 18:39:40,330] [INFO] Selected 22 target genomes.
[2023-03-15 18:39:40,330] [INFO] Target genome list was writen to OceanDNA-b24024/target_genomes.txt
[2023-03-15 18:39:40,343] [INFO] Task started: fastANI
[2023-03-15 18:39:40,343] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f94ae89-e76b-4ccb-b560-69652dd53737/OceanDNA-b24024.fa --refList OceanDNA-b24024/target_genomes.txt --output OceanDNA-b24024/fastani_result.tsv --threads 1
[2023-03-15 18:39:55,690] [INFO] Task succeeded: fastANI
[2023-03-15 18:39:55,690] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e70c17c-b8c1-44ee-b0d9-424232bea3a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 18:39:55,690] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e70c17c-b8c1-44ee-b0d9-424232bea3a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 18:39:55,703] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 18:39:55,703] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 18:39:55,703] [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
Marinicaulis flavus	strain=SY-3-19	GCA_002943565.1	2058213	2058213	type	True	80.6643	814	1405	95	below_threshold
Amphiplicatus metriothermophilus	strain=DSM 105738	GCA_014199495.1	1519374	1519374	type	True	77.8037	409	1405	95	below_threshold
Amphiplicatus metriothermophilus	strain=CGMCC 1.12710	GCA_900199215.1	1519374	1519374	type	True	77.7454	414	1405	95	below_threshold
Aquisalinus flavus	strain=CGMCC 1.12921	GCA_014640095.1	1526572	1526572	type	True	77.0931	195	1405	95	below_threshold
Aquisalinus flavus	strain=D11M-2	GCA_014534785.1	1526572	1526572	type	True	77.0505	200	1405	95	below_threshold
Aquisalinus flavus	strain=D11M-2	GCA_022559625.1	1526572	1526572	type	True	77.0314	190	1405	95	below_threshold
Aquisalinus luteolus	strain=CGMCC 1.14984	GCA_014640455.1	1566827	1566827	type	True	76.7993	166	1405	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	76.4946	147	1405	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	76.3458	176	1405	95	below_threshold
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	76.3185	162	1405	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	76.2972	150	1405	95	below_threshold
Pyruvatibacter mobilis	strain=CGMCC 1.15125	GCA_014640905.1	1712261	1712261	type	True	76.2037	105	1405	95	below_threshold
Parvularcula marina	strain=SM1705	GCA_003399445.1	2292771	2292771	type	True	76.1671	107	1405	95	below_threshold
Pyruvatibacter mobilis	strain=GYP-11	GCA_009910475.1	1712261	1712261	type	True	76.1582	107	1405	95	below_threshold
Hyphomonas oceanitis	strain=SCH89	GCA_000685295.1	81033	81033	type	True	76.12	75	1405	95	below_threshold
Rhodoblastus acidophilus	strain=DSM 137	GCA_002937135.1	1074	1074	suspected-type	True	76.0484	156	1405	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	75.8984	88	1405	95	below_threshold
Hyphomonas chukchiensis	strain=BH-BN04-4	GCA_000682695.1	1280947	1280947	type	True	75.8975	84	1405	95	below_threshold
Xanthobacter agilis	strain=LMG 16336	GCA_021730435.1	47492	47492	type	True	75.7026	105	1405	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009881095.1	1465486	1465486	type	True	75.6956	95	1405	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	75.5664	72	1405	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	75.475	102	1405	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 18:39:55,704] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24024/tc_result.tsv
[2023-03-15 18:39:55,704] [INFO] ===== Taxonomy check completed =====
[2023-03-15 18:39:55,704] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 18:39:55,704] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e70c17c-b8c1-44ee-b0d9-424232bea3a4/dqc_reference/checkm_data
[2023-03-15 18:39:55,705] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 18:39:55,710] [INFO] Task started: CheckM
[2023-03-15 18:39:55,710] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24024/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24024/checkm_input OceanDNA-b24024/checkm_result
[2023-03-15 18:40:59,031] [INFO] Task succeeded: CheckM
[2023-03-15 18:40:59,032] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 18:40:59,035] [INFO] ===== Completeness check finished =====
[2023-03-15 18:40:59,035] [INFO] ===== Start GTDB Search =====
[2023-03-15 18:40:59,035] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24024/markers.fasta)
[2023-03-15 18:40:59,036] [INFO] Task started: Blastn
[2023-03-15 18:40:59,036] [INFO] Running command: blastn -query OceanDNA-b24024/markers.fasta -db /var/lib/cwl/stg5e70c17c-b8c1-44ee-b0d9-424232bea3a4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24024/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:41:00,801] [INFO] Task succeeded: Blastn
[2023-03-15 18:41:00,802] [INFO] Selected 11 target genomes.
[2023-03-15 18:41:00,802] [INFO] Target genome list was writen to OceanDNA-b24024/target_genomes_gtdb.txt
[2023-03-15 18:41:01,196] [INFO] Task started: fastANI
[2023-03-15 18:41:01,196] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f94ae89-e76b-4ccb-b560-69652dd53737/OceanDNA-b24024.fa --refList OceanDNA-b24024/target_genomes_gtdb.txt --output OceanDNA-b24024/fastani_result_gtdb.tsv --threads 1
[2023-03-15 18:41:08,622] [INFO] Task succeeded: fastANI
[2023-03-15 18:41:08,630] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 18:41:08,630] [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_002943565.1	s__Marinicaulis flavus	80.6466	817	1405	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002704915.1	s__Marinicaulis sp002704915	79.7301	650	1405	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002388885.1	s__Marinicaulis sp002388885	78.3244	438	1405	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001657385.1	s__Marinicaulis sp001657385	78.1577	458	1405	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900199215.1	s__Amphiplicatus metriothermophilus	77.7612	412	1405	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Amphiplicatus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902826095.1	s__CV81 sp902826095	77.3215	342	1405	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__CV81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125425.1	s__Amphiplicatus sp016125425	77.3182	291	1405	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Amphiplicatus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001767925.1	s__CV81 sp001767925	77.3178	335	1405	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__CV81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013389105.1	s__JACADZ01 sp013389105	77.0341	265	1405	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__JACADZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002535.1	s__Marinicaulis sp013002535	76.5717	157	1405	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	99.52	99.49	0.97	0.96	3	-
GCA_009694135.1	s__SHVS01 sp009694135	75.4662	53	1405	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__SHVS01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 18:41:08,630] [INFO] GTDB search result was written to OceanDNA-b24024/result_gtdb.tsv
[2023-03-15 18:41:08,630] [INFO] ===== GTDB Search completed =====
[2023-03-15 18:41:08,632] [INFO] DFAST_QC result json was written to OceanDNA-b24024/dqc_result.json
[2023-03-15 18:41:08,632] [INFO] DFAST_QC completed!
[2023-03-15 18:41:08,632] [INFO] Total running time: 0h1m56s