[2023-03-17 02:03:51,361] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:03:51,361] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:03:51,361] [INFO] DQC Reference Directory: /var/lib/cwl/stg539d3fa9-5f30-4cdb-961c-f4cb93ec9d63/dqc_reference
[2023-03-17 02:03:52,471] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:03:52,471] [INFO] Task started: Prodigal
[2023-03-17 02:03:52,471] [INFO] Running command: cat /var/lib/cwl/stg854f27c6-671d-44c5-8df5-fd9a9c1f356e/OceanDNA-b33285.fa | prodigal -d OceanDNA-b33285/cds.fna -a OceanDNA-b33285/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:04:15,742] [INFO] Task succeeded: Prodigal
[2023-03-17 02:04:15,743] [INFO] Task started: HMMsearch
[2023-03-17 02:04:15,743] [INFO] Running command: hmmsearch --tblout OceanDNA-b33285/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg539d3fa9-5f30-4cdb-961c-f4cb93ec9d63/dqc_reference/reference_markers.hmm OceanDNA-b33285/protein.faa > /dev/null
[2023-03-17 02:04:15,960] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:04:15,960] [INFO] Found 6/6 markers.
[2023-03-17 02:04:15,982] [INFO] Query marker FASTA was written to OceanDNA-b33285/markers.fasta
[2023-03-17 02:04:15,982] [INFO] Task started: Blastn
[2023-03-17 02:04:15,982] [INFO] Running command: blastn -query OceanDNA-b33285/markers.fasta -db /var/lib/cwl/stg539d3fa9-5f30-4cdb-961c-f4cb93ec9d63/dqc_reference/reference_markers.fasta -out OceanDNA-b33285/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:04:16,967] [INFO] Task succeeded: Blastn
[2023-03-17 02:04:16,968] [INFO] Selected 19 target genomes.
[2023-03-17 02:04:16,968] [INFO] Target genome list was writen to OceanDNA-b33285/target_genomes.txt
[2023-03-17 02:04:16,979] [INFO] Task started: fastANI
[2023-03-17 02:04:16,979] [INFO] Running command: fastANI --query /var/lib/cwl/stg854f27c6-671d-44c5-8df5-fd9a9c1f356e/OceanDNA-b33285.fa --refList OceanDNA-b33285/target_genomes.txt --output OceanDNA-b33285/fastani_result.tsv --threads 1
[2023-03-17 02:04:36,906] [INFO] Task succeeded: fastANI
[2023-03-17 02:04:36,906] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg539d3fa9-5f30-4cdb-961c-f4cb93ec9d63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:04:36,907] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg539d3fa9-5f30-4cdb-961c-f4cb93ec9d63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:04:36,918] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:04:36,918] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 02:04:36,918] [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
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	94.0288	985	1179	95	below_threshold
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	84.2209	799	1179	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	84.16	782	1179	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	84.0921	764	1179	95	below_threshold
Acidovorax avenae subsp. avenae	strain=ATCC 19860	GCA_000176855.2	80870	80867	suspected-type	True	84.0485	826	1179	95	below_threshold
Acidovorax cattleyae	strain=DSM 17101	GCA_900104515.1	80868	80868	type	True	83.9214	820	1179	95	below_threshold
Acidovorax konjaci	strain=DSM 7481	GCA_900112675.1	32040	32040	type	True	83.4152	777	1179	95	below_threshold
Acidovorax valerianellae	strain=DSM 16619	GCA_900102625.1	187868	187868	type	True	83.321	759	1179	95	below_threshold
Delftia acidovorans	strain=NBRC 14950	GCA_001598795.1	80866	80866	type	True	81.8357	677	1179	95	below_threshold
Delftia acidovorans	strain=FDAARGOS_997	GCA_016127415.1	80866	80866	type	True	81.7922	689	1179	95	below_threshold
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	81.7417	624	1179	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	81.7239	723	1179	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_900116825.1	343013	343013	type	True	81.7158	600	1179	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_001298675.1	343013	343013	type	True	81.5528	596	1179	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	81.061	568	1179	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	80.6541	557	1179	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	80.2474	563	1179	95	below_threshold
Diaphorobacter aerolatus	strain=KACC 16536	GCA_014489535.1	1288495	1288495	type	True	80.2055	552	1179	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	80.1071	607	1179	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 02:04:36,918] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33285/tc_result.tsv
[2023-03-17 02:04:36,918] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:04:36,918] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:04:36,918] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg539d3fa9-5f30-4cdb-961c-f4cb93ec9d63/dqc_reference/checkm_data
[2023-03-17 02:04:36,919] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:04:36,924] [INFO] Task started: CheckM
[2023-03-17 02:04:36,924] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33285/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33285/checkm_input OceanDNA-b33285/checkm_result
[2023-03-17 02:05:38,425] [INFO] Task succeeded: CheckM
[2023-03-17 02:05:38,425] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:05:38,427] [INFO] ===== Completeness check finished =====
[2023-03-17 02:05:38,428] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:05:38,428] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33285/markers.fasta)
[2023-03-17 02:05:38,428] [INFO] Task started: Blastn
[2023-03-17 02:05:38,428] [INFO] Running command: blastn -query OceanDNA-b33285/markers.fasta -db /var/lib/cwl/stg539d3fa9-5f30-4cdb-961c-f4cb93ec9d63/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33285/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:05:40,533] [INFO] Task succeeded: Blastn
[2023-03-17 02:05:40,534] [INFO] Selected 15 target genomes.
[2023-03-17 02:05:40,534] [INFO] Target genome list was writen to OceanDNA-b33285/target_genomes_gtdb.txt
[2023-03-17 02:05:40,689] [INFO] Task started: fastANI
[2023-03-17 02:05:40,689] [INFO] Running command: fastANI --query /var/lib/cwl/stg854f27c6-671d-44c5-8df5-fd9a9c1f356e/OceanDNA-b33285.fa --refList OceanDNA-b33285/target_genomes_gtdb.txt --output OceanDNA-b33285/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:05:56,727] [INFO] Task succeeded: fastANI
[2023-03-17 02:05:56,736] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 02:05:56,736] [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_900113035.1	s__Acidovorax_A wautersii	94.0287	985	1179	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_001424265.1	s__Acidovorax_A sp001424265	86.3957	877	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002397315.1	s__Acidovorax_A sp002397315	84.2394	807	1179	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_000687165.1	s__Acidovorax_A oryzae	84.1787	801	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.2137	98.08	98.08	0.87	0.87	2	-
GCF_900100305.1	s__Acidovorax_A citrulli	84.1289	785	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	99.47	99.27	0.97	0.96	11	-
GCF_003269065.1	s__Acidovorax_A anthurii	84.0788	765	1179	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_900104515.1	s__Acidovorax_A cattleyae	83.9183	820	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	99.69	99.69	0.82	0.82	2	-
GCF_000400995.2	s__MR-S7 sp000400995	83.6099	727	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__MR-S7	95.0	97.31	97.31	0.83	0.83	2	-
GCF_900112675.1	s__Acidovorax_A konjaci	83.384	780	1179	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_014489595.1	s__Acidovorax_F monticola	83.3581	753	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_F	95.0	97.51	97.51	0.93	0.93	2	-
GCF_900102625.1	s__Acidovorax_A valerianellae	83.321	759	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003755025.1	s__Diaphorobacter nitroreducens	82.8566	668	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Diaphorobacter	95.0	98.11	97.62	0.91	0.81	15	-
GCF_001424425.1	s__Acidovorax sp001424425	82.8526	760	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	99.93	99.87	0.98	0.97	3	-
GCF_014207955.1	s__Acidovorax soli_A	82.5579	790	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013363755.1	s__Comamonas antarcticus	81.0887	616	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 02:05:56,736] [INFO] GTDB search result was written to OceanDNA-b33285/result_gtdb.tsv
[2023-03-17 02:05:56,736] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:05:56,738] [INFO] DFAST_QC result json was written to OceanDNA-b33285/dqc_result.json
[2023-03-17 02:05:56,738] [INFO] DFAST_QC completed!
[2023-03-17 02:05:56,738] [INFO] Total running time: 0h2m5s