[2023-03-18 02:27:37,208] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:27:37,208] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:27:37,208] [INFO] DQC Reference Directory: /var/lib/cwl/stge67dd140-71a2-4f67-bda9-15d7d56df5f8/dqc_reference
[2023-03-18 02:27:38,463] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:27:38,463] [INFO] Task started: Prodigal
[2023-03-18 02:27:38,463] [INFO] Running command: cat /var/lib/cwl/stg830a6785-d53b-42fb-becf-70aaca69cdae/OceanDNA-b33522.fa | prodigal -d OceanDNA-b33522/cds.fna -a OceanDNA-b33522/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:28:12,439] [INFO] Task succeeded: Prodigal
[2023-03-18 02:28:12,440] [INFO] Task started: HMMsearch
[2023-03-18 02:28:12,440] [INFO] Running command: hmmsearch --tblout OceanDNA-b33522/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge67dd140-71a2-4f67-bda9-15d7d56df5f8/dqc_reference/reference_markers.hmm OceanDNA-b33522/protein.faa > /dev/null
[2023-03-18 02:28:12,769] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:28:12,769] [INFO] Found 6/6 markers.
[2023-03-18 02:28:12,804] [INFO] Query marker FASTA was written to OceanDNA-b33522/markers.fasta
[2023-03-18 02:28:12,804] [INFO] Task started: Blastn
[2023-03-18 02:28:12,804] [INFO] Running command: blastn -query OceanDNA-b33522/markers.fasta -db /var/lib/cwl/stge67dd140-71a2-4f67-bda9-15d7d56df5f8/dqc_reference/reference_markers.fasta -out OceanDNA-b33522/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:28:13,673] [INFO] Task succeeded: Blastn
[2023-03-18 02:28:13,674] [INFO] Selected 29 target genomes.
[2023-03-18 02:28:13,674] [INFO] Target genome list was writen to OceanDNA-b33522/target_genomes.txt
[2023-03-18 02:28:13,687] [INFO] Task started: fastANI
[2023-03-18 02:28:13,687] [INFO] Running command: fastANI --query /var/lib/cwl/stg830a6785-d53b-42fb-becf-70aaca69cdae/OceanDNA-b33522.fa --refList OceanDNA-b33522/target_genomes.txt --output OceanDNA-b33522/fastani_result.tsv --threads 1
[2023-03-18 02:28:39,051] [INFO] Task succeeded: fastANI
[2023-03-18 02:28:39,052] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge67dd140-71a2-4f67-bda9-15d7d56df5f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:28:39,052] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge67dd140-71a2-4f67-bda9-15d7d56df5f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:28:39,067] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:28:39,067] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 02:28:39,067] [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	79.3798	525	1674	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	79.3387	482	1674	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.2807	505	1674	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	79.2294	566	1674	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	79.2289	583	1674	95	below_threshold
Variovorax beijingensis	strain=502	GCA_003951285.1	2496117	2496117	type	True	79.127	568	1674	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	79.0873	520	1674	95	below_threshold
Variovorax soli	strain=NBRC 106424	GCA_001591385.1	376815	376815	type	True	79.0207	529	1674	95	below_threshold
Ottowia beijingensis	strain=GCS-AN-3	GCA_013423955.1	1207057	1207057	type	True	78.9063	472	1674	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	78.8837	416	1674	95	below_threshold
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	78.8002	609	1674	95	below_threshold
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	78.7281	441	1674	95	below_threshold
Pseudorhodoferax soli	strain=DSM 21634	GCA_003337555.1	545864	545864	type	True	78.7188	622	1674	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	78.6976	581	1674	95	below_threshold
Hydrogenophaga intermedia	strain=NBRC 102510	GCA_001571205.1	65786	65786	type	True	78.6971	491	1674	95	below_threshold
Hydrogenophaga intermedia	strain=DSM 5680	GCA_005938115.1	65786	65786	type	True	78.6579	501	1674	95	below_threshold
Hydrogenophaga intermedia	strain=S1	GCA_000723405.1	65786	65786	type	True	78.6413	503	1674	95	below_threshold
Acidovorax avenae subsp. avenae	strain=ATCC 19860	GCA_000176855.2	80870	80867	suspected-type	True	78.5879	452	1674	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	78.4449	394	1674	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	78.3538	412	1674	95	below_threshold
Tepidimonas alkaliphilus	strain=YIM 72238	GCA_007556595.1	2588942	2588942	type	True	78.1639	287	1674	95	below_threshold
Extensimonas vulgaris	strain=S4	GCA_007996985.1	1031594	1031594	type	True	78.0337	308	1674	95	below_threshold
Ideonella azotifigens	strain=DSM 21438	GCA_006519715.1	513160	513160	type	True	78.0302	333	1674	95	below_threshold
Extensimonas vulgaris	strain=CGMCC 1.10977	GCA_007830535.1	1031594	1031594	type	True	78.0177	309	1674	95	below_threshold
Extensimonas vulgaris	strain=DSM 100911	GCA_003337425.1	1031594	1031594	type	True	78.0094	316	1674	95	below_threshold
Mitsuaria chitinivorans	strain=HWN-4	GCA_002761755.1	2917965	2917965	type	True	77.8344	412	1674	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	77.823	388	1674	95	below_threshold
Paucibacter toxinivorans	strain=DSM 16998	GCA_004362525.1	270368	270368	type	True	77.7998	438	1674	95	below_threshold
Pelomonas saccharophila	strain=DSM 654	GCA_004342485.1	304	304	type	True	77.6082	443	1674	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 02:28:39,067] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33522/tc_result.tsv
[2023-03-18 02:28:39,068] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:28:39,068] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:28:39,068] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge67dd140-71a2-4f67-bda9-15d7d56df5f8/dqc_reference/checkm_data
[2023-03-18 02:28:39,068] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:28:39,075] [INFO] Task started: CheckM
[2023-03-18 02:28:39,075] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33522/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33522/checkm_input OceanDNA-b33522/checkm_result
[2023-03-18 02:30:38,389] [INFO] Task succeeded: CheckM
[2023-03-18 02:30:38,389] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 4.69%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-18 02:30:38,393] [INFO] ===== Completeness check finished =====
[2023-03-18 02:30:38,393] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:30:38,393] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33522/markers.fasta)
[2023-03-18 02:30:38,393] [INFO] Task started: Blastn
[2023-03-18 02:30:38,394] [INFO] Running command: blastn -query OceanDNA-b33522/markers.fasta -db /var/lib/cwl/stge67dd140-71a2-4f67-bda9-15d7d56df5f8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33522/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:30:39,985] [INFO] Task succeeded: Blastn
[2023-03-18 02:30:39,986] [INFO] Selected 27 target genomes.
[2023-03-18 02:30:39,986] [INFO] Target genome list was writen to OceanDNA-b33522/target_genomes_gtdb.txt
[2023-03-18 02:30:40,035] [INFO] Task started: fastANI
[2023-03-18 02:30:40,035] [INFO] Running command: fastANI --query /var/lib/cwl/stg830a6785-d53b-42fb-becf-70aaca69cdae/OceanDNA-b33522.fa --refList OceanDNA-b33522/target_genomes_gtdb.txt --output OceanDNA-b33522/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:31:03,239] [INFO] Task succeeded: fastANI
[2023-03-18 02:31:03,254] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 02:31:03,254] [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_018063505.1	s__CAISIP01 sp018063505	81.8046	702	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAISIP01	95.0	99.51	99.51	0.88	0.88	2	-
GCA_016790475.1	s__CAISIP01 sp016790475	80.576	625	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAISIP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005503335.1	s__SCMQ01 sp005503335	80.1419	550	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCMQ01	95.0	99.99	99.99	1.00	1.00	3	-
GCA_001797315.1	s__Hylemonella sp001797315	79.5836	467	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	99.98	99.98	0.98	0.98	2	-
GCA_002842205.1	s__PHCI01 sp002842205	79.446	449	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__PHCI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592265.1	s__Hylemonella delicata	79.2715	454	1674	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	79.2232	412	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	96.79	96.79	0.90	0.90	2	-
GCA_016713005.1	s__Ramlibacter sp016713005	79.0712	428	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382045.1	s__Variovorax paradoxus_A	79.0238	569	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	98.57	98.47	0.92	0.91	6	-
GCA_006227825.1	s__Hydrogenophaga sp006227825	78.9973	354	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011391155.1	s__JAABQG01 sp011391155	78.9729	343	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAABQG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053685.1	s__Variovorax sp003053685	78.942	640	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	100.00	100.00	1.00	1.00	5	-
GCA_016721925.1	s__JAABQG01 sp016721925	78.9364	475	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAABQG01	95.0	98.62	98.32	0.93	0.90	9	-
GCF_001422365.1	s__Pseudorhodoferax sp001422365	78.9069	607	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudorhodoferax	95.0	98.81	98.81	0.87	0.87	3	-
GCA_013423955.1	s__Ottowia beijingensis	78.9052	472	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	97.71	97.71	0.88	0.88	2	-
GCA_013693755.1	s__Tibeticola sp013693755	78.868	443	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tibeticola	95.0	96.98	96.98	0.89	0.89	2	-
GCF_002754375.1	s__Variovorax sp002754375	78.8528	559	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	95.39	95.37	0.86	0.85	3	-
GCF_003337555.1	s__Pseudorhodoferax soli	78.6683	630	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudorhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207955.1	s__Acidovorax soli_A	78.6644	544	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113035.1	s__Acidovorax_A wautersii	78.6396	507	1674	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_018240985.1	s__Alicycliphilus sp018240985	78.156	399	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	99.65	99.65	0.85	0.85	2	-
GCF_007556595.1	s__Tepidimonas alkaliphilus	78.1454	289	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016191995.1	s__Rubrivivax sp016191995	78.0208	419	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013266755.1	s__Aquabacterium_A terrae	77.6854	573	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018780805.1	s__Rubrivivax sp018780805	77.5769	433	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879745.1	s__CAIKUF01 sp014879745	77.3736	316	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAIKUF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790635.1	s__JAEUOS01 sp016790635	76.8322	256	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__JAEUOS01;g__JAEUOS01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 02:31:03,254] [INFO] GTDB search result was written to OceanDNA-b33522/result_gtdb.tsv
[2023-03-18 02:31:03,254] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:31:03,257] [INFO] DFAST_QC result json was written to OceanDNA-b33522/dqc_result.json
[2023-03-18 02:31:03,257] [INFO] DFAST_QC completed!
[2023-03-18 02:31:03,257] [INFO] Total running time: 0h3m26s