[2023-03-18 10:41:19,243] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:41:19,244] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:41:19,244] [INFO] DQC Reference Directory: /var/lib/cwl/stgb00fb98e-441e-4c2f-8cf3-2d4b03bb6e5a/dqc_reference
[2023-03-18 10:41:20,434] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:41:20,435] [INFO] Task started: Prodigal
[2023-03-18 10:41:20,435] [INFO] Running command: cat /var/lib/cwl/stgad57da1f-8e7f-4b31-97df-28358b6f6298/OceanDNA-b23481.fa | prodigal -d OceanDNA-b23481/cds.fna -a OceanDNA-b23481/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:41:34,973] [INFO] Task succeeded: Prodigal
[2023-03-18 10:41:34,973] [INFO] Task started: HMMsearch
[2023-03-18 10:41:34,973] [INFO] Running command: hmmsearch --tblout OceanDNA-b23481/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb00fb98e-441e-4c2f-8cf3-2d4b03bb6e5a/dqc_reference/reference_markers.hmm OceanDNA-b23481/protein.faa > /dev/null
[2023-03-18 10:41:35,152] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:41:35,153] [INFO] Found 6/6 markers.
[2023-03-18 10:41:35,173] [INFO] Query marker FASTA was written to OceanDNA-b23481/markers.fasta
[2023-03-18 10:41:35,174] [INFO] Task started: Blastn
[2023-03-18 10:41:35,175] [INFO] Running command: blastn -query OceanDNA-b23481/markers.fasta -db /var/lib/cwl/stgb00fb98e-441e-4c2f-8cf3-2d4b03bb6e5a/dqc_reference/reference_markers.fasta -out OceanDNA-b23481/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:41:35,946] [INFO] Task succeeded: Blastn
[2023-03-18 10:41:35,946] [INFO] Selected 16 target genomes.
[2023-03-18 10:41:35,946] [INFO] Target genome list was writen to OceanDNA-b23481/target_genomes.txt
[2023-03-18 10:41:35,960] [INFO] Task started: fastANI
[2023-03-18 10:41:35,960] [INFO] Running command: fastANI --query /var/lib/cwl/stgad57da1f-8e7f-4b31-97df-28358b6f6298/OceanDNA-b23481.fa --refList OceanDNA-b23481/target_genomes.txt --output OceanDNA-b23481/fastani_result.tsv --threads 1
[2023-03-18 10:41:48,385] [INFO] Task succeeded: fastANI
[2023-03-18 10:41:48,386] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb00fb98e-441e-4c2f-8cf3-2d4b03bb6e5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:41:48,386] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb00fb98e-441e-4c2f-8cf3-2d4b03bb6e5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:41:48,396] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:41:48,396] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 10:41:48,396] [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	80.1515	507	801	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	80.0172	511	801	95	below_threshold
Phenylobacterium hankyongense	strain=HKS-05	GCA_003254505.1	1813876	1813876	type	True	79.8714	429	801	95	below_threshold
Phenylobacterium zucineum	strain=HLK1	GCA_000017265.1	284016	284016	type	True	79.4151	449	801	95	below_threshold
Phenylobacterium soli	strain=LX32	GCA_003254475.1	2170551	2170551	type	True	79.3965	423	801	95	below_threshold
Phenylobacterium haematophilum	strain=DSM 21793	GCA_014196295.1	98513	98513	type	True	79.3772	435	801	95	below_threshold
Phenylobacterium deserti	strain=YIM 73061	GCA_003254705.1	1914756	1914756	type	True	79.1382	346	801	95	below_threshold
Phenylobacterium parvum	strain=HYN0004	GCA_003150835.1	2201350	2201350	type	True	79.0866	329	801	95	below_threshold
Phenylobacterium kunshanense	strain=BUT-10	GCA_003254525.1	1445034	1445034	type	True	78.8902	394	801	95	below_threshold
Caulobacter soli	strain=Ji-3-8	GCA_011045195.1	2708539	2708539	type	True	78.7863	360	801	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	78.7289	358	801	95	below_threshold
Caulobacter hibisci	strain=KACC 18849	GCA_016135805.1	2035993	2035993	type	True	78.6216	370	801	95	below_threshold
Caulobacter zeae	strain=410	GCA_002858925.1	2055137	2055137	type	True	78.5115	378	801	95	below_threshold
Caulobacter endophyticus	strain=774	GCA_003116815.1	2172652	2172652	type	True	78.2271	368	801	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	76.6876	121	801	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	75.8833	97	801	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 10:41:48,398] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23481/tc_result.tsv
[2023-03-18 10:41:48,401] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:41:48,401] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:41:48,401] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb00fb98e-441e-4c2f-8cf3-2d4b03bb6e5a/dqc_reference/checkm_data
[2023-03-18 10:41:48,402] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:41:48,423] [INFO] Task started: CheckM
[2023-03-18 10:41:48,423] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23481/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23481/checkm_input OceanDNA-b23481/checkm_result
[2023-03-18 10:42:27,015] [INFO] Task succeeded: CheckM
[2023-03-18 10:42:27,016] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 10:42:27,022] [INFO] ===== Completeness check finished =====
[2023-03-18 10:42:27,022] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:42:27,022] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23481/markers.fasta)
[2023-03-18 10:42:27,023] [INFO] Task started: Blastn
[2023-03-18 10:42:27,023] [INFO] Running command: blastn -query OceanDNA-b23481/markers.fasta -db /var/lib/cwl/stgb00fb98e-441e-4c2f-8cf3-2d4b03bb6e5a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23481/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:42:28,504] [INFO] Task succeeded: Blastn
[2023-03-18 10:42:28,507] [INFO] Selected 15 target genomes.
[2023-03-18 10:42:28,507] [INFO] Target genome list was writen to OceanDNA-b23481/target_genomes_gtdb.txt
[2023-03-18 10:42:28,534] [INFO] Task started: fastANI
[2023-03-18 10:42:28,534] [INFO] Running command: fastANI --query /var/lib/cwl/stgad57da1f-8e7f-4b31-97df-28358b6f6298/OceanDNA-b23481.fa --refList OceanDNA-b23481/target_genomes_gtdb.txt --output OceanDNA-b23481/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:42:39,070] [INFO] Task succeeded: fastANI
[2023-03-18 10:42:39,080] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 10:42:39,080] [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_002441055.1	s__Phenylobacterium sp002441055	96.87	609	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002363865.1	s__Phenylobacterium sp002363865	89.6262	740	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.98	99.98	0.95	0.91	3	-
GCA_013911965.1	s__Phenylobacterium sp013911965	83.265	608	801	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	80.1013	502	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.74	99.70	0.93	0.91	3	-
GCF_016772415.1	s__Phenylobacterium sp016772415	80.0334	509	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254505.1	s__Phenylobacterium hankyongense	79.8778	428	801	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	79.5797	400	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017265.1	s__Phenylobacterium zucineum	79.4148	449	801	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	79.4015	422	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018135625.1	s__BOG-935 sp018135625	78.922	363	801	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_903842425.1	s__Phenylobacterium sp903842425	78.8311	248	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903930545.1	s__Phenylobacterium sp903930545	78.8163	300	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.53	99.48	0.90	0.90	3	-
GCA_016234625.1	s__Caulobacter sp016234625	78.59	323	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001375595.1	s__Phenylobacterium immobile	78.5092	248	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903909375.1	s__Phenylobacterium sp903909375	78.1982	282	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 10:42:39,081] [INFO] GTDB search result was written to OceanDNA-b23481/result_gtdb.tsv
[2023-03-18 10:42:39,081] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:42:39,083] [INFO] DFAST_QC result json was written to OceanDNA-b23481/dqc_result.json
[2023-03-18 10:42:39,083] [INFO] DFAST_QC completed!
[2023-03-18 10:42:39,083] [INFO] Total running time: 0h1m20s