[2023-03-18 10:10:14,121] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:10:14,121] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:10:14,121] [INFO] DQC Reference Directory: /var/lib/cwl/stge132353b-b7a8-4807-a45f-396ecf7c99ec/dqc_reference
[2023-03-18 10:10:15,255] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:10:15,273] [INFO] Task started: Prodigal
[2023-03-18 10:10:15,273] [INFO] Running command: cat /var/lib/cwl/stge30d03d2-e417-4034-a105-73686b2c8ef6/OceanDNA-b23468.fa | prodigal -d OceanDNA-b23468/cds.fna -a OceanDNA-b23468/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:10:36,414] [INFO] Task succeeded: Prodigal
[2023-03-18 10:10:36,414] [INFO] Task started: HMMsearch
[2023-03-18 10:10:36,414] [INFO] Running command: hmmsearch --tblout OceanDNA-b23468/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge132353b-b7a8-4807-a45f-396ecf7c99ec/dqc_reference/reference_markers.hmm OceanDNA-b23468/protein.faa > /dev/null
[2023-03-18 10:10:36,616] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:10:36,617] [INFO] Found 6/6 markers.
[2023-03-18 10:10:36,638] [INFO] Query marker FASTA was written to OceanDNA-b23468/markers.fasta
[2023-03-18 10:10:36,640] [INFO] Task started: Blastn
[2023-03-18 10:10:36,640] [INFO] Running command: blastn -query OceanDNA-b23468/markers.fasta -db /var/lib/cwl/stge132353b-b7a8-4807-a45f-396ecf7c99ec/dqc_reference/reference_markers.fasta -out OceanDNA-b23468/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:10:37,504] [INFO] Task succeeded: Blastn
[2023-03-18 10:10:37,506] [INFO] Selected 17 target genomes.
[2023-03-18 10:10:37,506] [INFO] Target genome list was writen to OceanDNA-b23468/target_genomes.txt
[2023-03-18 10:10:37,553] [INFO] Task started: fastANI
[2023-03-18 10:10:37,553] [INFO] Running command: fastANI --query /var/lib/cwl/stge30d03d2-e417-4034-a105-73686b2c8ef6/OceanDNA-b23468.fa --refList OceanDNA-b23468/target_genomes.txt --output OceanDNA-b23468/fastani_result.tsv --threads 1
[2023-03-18 10:10:51,338] [INFO] Task succeeded: fastANI
[2023-03-18 10:10:51,338] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge132353b-b7a8-4807-a45f-396ecf7c99ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:10:51,338] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge132353b-b7a8-4807-a45f-396ecf7c99ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:10:51,349] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:10:51,349] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 10:10:51,349] [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
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	80.8126	700	1156	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	80.6016	664	1156	95	below_threshold
Phenylobacterium hankyongense	strain=HKS-05	GCA_003254505.1	1813876	1813876	type	True	80.5734	569	1156	95	below_threshold
Phenylobacterium zucineum	strain=HLK1	GCA_000017265.1	284016	284016	type	True	79.9049	598	1156	95	below_threshold
Phenylobacterium soli	strain=LX32	GCA_003254475.1	2170551	2170551	type	True	79.8823	584	1156	95	below_threshold
Phenylobacterium haematophilum	strain=DSM 21793	GCA_014196295.1	98513	98513	type	True	79.6845	596	1156	95	below_threshold
Phenylobacterium deserti	strain=YIM 73061	GCA_003254705.1	1914756	1914756	type	True	79.5857	455	1156	95	below_threshold
Phenylobacterium parvum	strain=HYN0004	GCA_003150835.1	2201350	2201350	type	True	79.4122	448	1156	95	below_threshold
Phenylobacterium kunshanense	strain=BUT-10	GCA_003254525.1	1445034	1445034	type	True	79.3978	522	1156	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	79.0276	527	1156	95	below_threshold
Caulobacter hibisci	strain=KACC 18849	GCA_016135805.1	2035993	2035993	type	True	78.9502	530	1156	95	below_threshold
Caulobacter flavus	strain=RHGG3	GCA_003722335.1	1679497	1679497	type	True	78.9321	530	1156	95	below_threshold
Caulobacter flavus	strain=CGMCC1 15093	GCA_002858845.1	1679497	1679497	type	True	78.9259	520	1156	95	below_threshold
Caulobacter mirabilis	strain=FWC 38	GCA_002749615.1	69666	69666	type	True	78.8641	493	1156	95	below_threshold
Brevundimonas subvibrioides	strain=ATCC 15264	GCA_000144605.1	74313	74313	type	True	78.1108	308	1156	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	76.9624	168	1156	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	75.9968	168	1156	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 10:10:51,350] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23468/tc_result.tsv
[2023-03-18 10:10:51,350] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:10:51,350] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:10:51,350] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge132353b-b7a8-4807-a45f-396ecf7c99ec/dqc_reference/checkm_data
[2023-03-18 10:10:51,351] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:10:51,356] [INFO] Task started: CheckM
[2023-03-18 10:10:51,356] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23468/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23468/checkm_input OceanDNA-b23468/checkm_result
[2023-03-18 10:11:44,076] [INFO] Task succeeded: CheckM
[2023-03-18 10:11:44,077] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 10:11:44,081] [INFO] ===== Completeness check finished =====
[2023-03-18 10:11:44,081] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:11:44,082] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23468/markers.fasta)
[2023-03-18 10:11:44,083] [INFO] Task started: Blastn
[2023-03-18 10:11:44,083] [INFO] Running command: blastn -query OceanDNA-b23468/markers.fasta -db /var/lib/cwl/stge132353b-b7a8-4807-a45f-396ecf7c99ec/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23468/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:11:46,306] [INFO] Task succeeded: Blastn
[2023-03-18 10:11:46,309] [INFO] Selected 15 target genomes.
[2023-03-18 10:11:46,309] [INFO] Target genome list was writen to OceanDNA-b23468/target_genomes_gtdb.txt
[2023-03-18 10:11:46,321] [INFO] Task started: fastANI
[2023-03-18 10:11:46,321] [INFO] Running command: fastANI --query /var/lib/cwl/stge30d03d2-e417-4034-a105-73686b2c8ef6/OceanDNA-b23468.fa --refList OceanDNA-b23468/target_genomes_gtdb.txt --output OceanDNA-b23468/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:11:58,646] [INFO] Task succeeded: fastANI
[2023-03-18 10:11:58,658] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 10:11:58,658] [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_002363865.1	s__Phenylobacterium sp002363865	96.6271	1053	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.98	99.98	0.95	0.91	3	conclusive
GCA_002441055.1	s__Phenylobacterium sp002441055	89.3736	706	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911965.1	s__Phenylobacterium sp013911965	83.8165	867	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	98.20	98.20	0.93	0.93	2	-
GCA_018001015.1	s__Phenylobacterium sp018001015	80.6423	686	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.74	99.70	0.93	0.91	3	-
GCF_003254505.1	s__Phenylobacterium hankyongense	80.5492	572	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004799515.1	s__Phenylobacterium sp004799515	79.9724	562	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425305.1	s__Phenylobacterium sp001425305	79.9041	624	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCF_000017265.1	s__Phenylobacterium zucineum	79.8996	598	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.11	99.11	0.98	0.98	2	-
GCF_003254475.1	s__Phenylobacterium soli	79.8713	586	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003136395.1	s__Phenylobacterium sp003136395	79.5001	494	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017418605.1	s__CAISGS01 sp017418605	79.4797	513	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAISGS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018135625.1	s__BOG-935 sp018135625	79.1359	489	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__BOG-935	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903930545.1	s__Phenylobacterium sp903930545	79.1327	399	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.53	99.48	0.90	0.90	3	-
GCF_000426025.1	s__Caulobacter sp000426025	79.1271	529	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016234625.1	s__Caulobacter sp016234625	78.6847	454	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 10:11:58,659] [INFO] GTDB search result was written to OceanDNA-b23468/result_gtdb.tsv
[2023-03-18 10:11:58,660] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:11:58,663] [INFO] DFAST_QC result json was written to OceanDNA-b23468/dqc_result.json
[2023-03-18 10:11:58,663] [INFO] DFAST_QC completed!
[2023-03-18 10:11:58,663] [INFO] Total running time: 0h1m45s