[2023-03-15 02:58:41,619] [INFO] DFAST_QC pipeline started.
[2023-03-15 02:58:41,619] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 02:58:41,619] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0bf33de-623b-4597-9778-5238eea456a0/dqc_reference
[2023-03-15 02:58:45,149] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 02:58:45,149] [INFO] Task started: Prodigal
[2023-03-15 02:58:45,150] [INFO] Running command: cat /var/lib/cwl/stged1ac5f3-3370-4b62-8d96-210665d885d3/OceanDNA-b33317.fa | prodigal -d OceanDNA-b33317/cds.fna -a OceanDNA-b33317/protein.faa -g 11 -q > /dev/null
[2023-03-15 02:59:06,313] [INFO] Task succeeded: Prodigal
[2023-03-15 02:59:06,313] [INFO] Task started: HMMsearch
[2023-03-15 02:59:06,314] [INFO] Running command: hmmsearch --tblout OceanDNA-b33317/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0bf33de-623b-4597-9778-5238eea456a0/dqc_reference/reference_markers.hmm OceanDNA-b33317/protein.faa > /dev/null
[2023-03-15 02:59:06,589] [INFO] Task succeeded: HMMsearch
[2023-03-15 02:59:06,590] [INFO] Found 6/6 markers.
[2023-03-15 02:59:06,612] [INFO] Query marker FASTA was written to OceanDNA-b33317/markers.fasta
[2023-03-15 02:59:06,613] [INFO] Task started: Blastn
[2023-03-15 02:59:06,614] [INFO] Running command: blastn -query OceanDNA-b33317/markers.fasta -db /var/lib/cwl/stgf0bf33de-623b-4597-9778-5238eea456a0/dqc_reference/reference_markers.fasta -out OceanDNA-b33317/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 02:59:07,601] [INFO] Task succeeded: Blastn
[2023-03-15 02:59:07,602] [INFO] Selected 23 target genomes.
[2023-03-15 02:59:07,602] [INFO] Target genome list was writen to OceanDNA-b33317/target_genomes.txt
[2023-03-15 02:59:07,614] [INFO] Task started: fastANI
[2023-03-15 02:59:07,614] [INFO] Running command: fastANI --query /var/lib/cwl/stged1ac5f3-3370-4b62-8d96-210665d885d3/OceanDNA-b33317.fa --refList OceanDNA-b33317/target_genomes.txt --output OceanDNA-b33317/fastani_result.tsv --threads 1
[2023-03-15 02:59:31,506] [INFO] Task succeeded: fastANI
[2023-03-15 02:59:31,507] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0bf33de-623b-4597-9778-5238eea456a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 02:59:31,507] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0bf33de-623b-4597-9778-5238eea456a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 02:59:31,521] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 02:59:31,521] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 02:59:31,521] [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
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	81.2197	569	1103	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	81.168	586	1103	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	81.0881	521	1103	95	below_threshold
Hydrogenophaga borbori	strain=LA-38	GCA_003417535.1	2294117	2294117	type	True	80.8998	574	1103	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	80.7857	584	1103	95	below_threshold
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	80.7671	611	1103	95	below_threshold
Ramlibacter rhizophilus	strain=CCTCC AB2015357	GCA_004681965.1	1781167	1781167	type	True	80.5932	523	1103	95	below_threshold
Hydrogenophaga intermedia	strain=DSM 5680	GCA_005938115.1	65786	65786	type	True	80.5774	566	1103	95	below_threshold
Comamonas phosphati	strain=CGMCC 1.12294	GCA_014637085.1	1211803	1211803	type	True	80.5016	487	1103	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	80.3563	533	1103	95	below_threshold
Pseudorhodoferax soli	strain=DSM 21634	GCA_003337555.1	545864	545864	type	True	80.2977	609	1103	95	below_threshold
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	80.283	506	1103	95	below_threshold
Ramlibacter henchirensis	strain=DSM 14656	GCA_004682015.1	204072	204072	type	True	80.2792	485	1103	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	80.2622	570	1103	95	below_threshold
Xylophilus rhododendri	strain=KACC 21265	GCA_009906855.1	2697032	2697032	type	True	80.2314	511	1103	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	80.2127	514	1103	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	80.1998	519	1103	95	below_threshold
Ottowia beijingensis	strain=GCS-AN-3	GCA_013423955.1	1207057	1207057	type	True	80.169	533	1103	95	below_threshold
Acidovorax avenae subsp. avenae	strain=ATCC 19860	GCA_000176855.2	80870	80867	suspected-type	True	80.1069	528	1103	95	below_threshold
Variovorax guangxiensis	strain=DSM 27352	GCA_003952165.1	1775474	1775474	type	True	80.1046	560	1103	95	below_threshold
Acidovorax cattleyae	strain=DSM 17101	GCA_900104515.1	80868	80868	type	True	80.0364	515	1103	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	79.9708	558	1103	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	79.8324	429	1103	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 02:59:31,521] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33317/tc_result.tsv
[2023-03-15 02:59:31,521] [INFO] ===== Taxonomy check completed =====
[2023-03-15 02:59:31,522] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 02:59:31,522] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0bf33de-623b-4597-9778-5238eea456a0/dqc_reference/checkm_data
[2023-03-15 02:59:31,522] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 02:59:31,531] [INFO] Task started: CheckM
[2023-03-15 02:59:31,531] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33317/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33317/checkm_input OceanDNA-b33317/checkm_result
[2023-03-15 03:00:28,291] [INFO] Task succeeded: CheckM
[2023-03-15 03:00:28,292] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 4.69%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:00:28,295] [INFO] ===== Completeness check finished =====
[2023-03-15 03:00:28,295] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:00:28,295] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33317/markers.fasta)
[2023-03-15 03:00:28,297] [INFO] Task started: Blastn
[2023-03-15 03:00:28,297] [INFO] Running command: blastn -query OceanDNA-b33317/markers.fasta -db /var/lib/cwl/stgf0bf33de-623b-4597-9778-5238eea456a0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33317/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:00:30,595] [INFO] Task succeeded: Blastn
[2023-03-15 03:00:30,596] [INFO] Selected 13 target genomes.
[2023-03-15 03:00:30,596] [INFO] Target genome list was writen to OceanDNA-b33317/target_genomes_gtdb.txt
[2023-03-15 03:00:30,680] [INFO] Task started: fastANI
[2023-03-15 03:00:30,681] [INFO] Running command: fastANI --query /var/lib/cwl/stged1ac5f3-3370-4b62-8d96-210665d885d3/OceanDNA-b33317.fa --refList OceanDNA-b33317/target_genomes_gtdb.txt --output OceanDNA-b33317/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:00:42,872] [INFO] Task succeeded: fastANI
[2023-03-15 03:00:42,880] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 03:00:42,880] [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_003500955.1	s__Hylemonella sp003500955	99.6701	857	1103	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013334205.1	s__Hylemonella sp013334205	85.8111	810	1103	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001432305.1	s__Hylemonella sp001432305	85.441	791	1103	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185015.1	s__Hylemonella sp016185015	85.3221	793	1103	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001797315.1	s__Hylemonella sp001797315	82.8707	665	1103	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	99.98	99.98	0.98	0.98	2	-
GCF_001592265.1	s__Hylemonella delicata	82.3404	662	1103	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002633085.1	s__Hylemonella sp002633085	82.2662	634	1103	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	96.79	96.79	0.90	0.90	2	-
GCA_005503335.1	s__SCMQ01 sp005503335	82.1505	576	1103	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCMQ01	95.0	99.99	99.99	1.00	1.00	3	-
GCF_000215705.1	s__Ramlibacter tataouinensis	81.181	573	1103	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422365.1	s__Pseudorhodoferax sp001422365	80.5638	622	1103	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudorhodoferax	95.0	98.81	98.81	0.87	0.87	3	-
GCF_003269065.1	s__Acidovorax_A anthurii	80.1884	521	1103	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001571325.1	s__Comamonas tsuruhatensis	80.153	543	1103	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.4801	98.55	98.21	0.90	0.80	27	-
GCA_009912175.1	s__Comamonas_F wautersii_A	80.1326	418	1103	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas_F	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 03:00:42,880] [INFO] GTDB search result was written to OceanDNA-b33317/result_gtdb.tsv
[2023-03-15 03:00:42,881] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:00:42,883] [INFO] DFAST_QC result json was written to OceanDNA-b33317/dqc_result.json
[2023-03-15 03:00:42,883] [INFO] DFAST_QC completed!
[2023-03-15 03:00:42,884] [INFO] Total running time: 0h2m1s