[2023-03-15 04:26:44,426] [INFO] DFAST_QC pipeline started.
[2023-03-15 04:26:44,427] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 04:26:44,427] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a6548c0-a6e7-405b-96c0-d97000a94cac/dqc_reference
[2023-03-15 04:26:45,569] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 04:26:45,569] [INFO] Task started: Prodigal
[2023-03-15 04:26:45,569] [INFO] Running command: cat /var/lib/cwl/stgd1284432-a660-4a86-b711-44deab29f30d/OceanDNA-b33313.fa | prodigal -d OceanDNA-b33313/cds.fna -a OceanDNA-b33313/protein.faa -g 11 -q > /dev/null
[2023-03-15 04:26:59,905] [INFO] Task succeeded: Prodigal
[2023-03-15 04:26:59,905] [INFO] Task started: HMMsearch
[2023-03-15 04:26:59,905] [INFO] Running command: hmmsearch --tblout OceanDNA-b33313/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a6548c0-a6e7-405b-96c0-d97000a94cac/dqc_reference/reference_markers.hmm OceanDNA-b33313/protein.faa > /dev/null
[2023-03-15 04:27:00,129] [INFO] Task succeeded: HMMsearch
[2023-03-15 04:27:00,129] [INFO] Found 6/6 markers.
[2023-03-15 04:27:00,158] [INFO] Query marker FASTA was written to OceanDNA-b33313/markers.fasta
[2023-03-15 04:27:00,158] [INFO] Task started: Blastn
[2023-03-15 04:27:00,158] [INFO] Running command: blastn -query OceanDNA-b33313/markers.fasta -db /var/lib/cwl/stg1a6548c0-a6e7-405b-96c0-d97000a94cac/dqc_reference/reference_markers.fasta -out OceanDNA-b33313/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:27:00,980] [INFO] Task succeeded: Blastn
[2023-03-15 04:27:00,984] [INFO] Selected 19 target genomes.
[2023-03-15 04:27:00,984] [INFO] Target genome list was writen to OceanDNA-b33313/target_genomes.txt
[2023-03-15 04:27:00,996] [INFO] Task started: fastANI
[2023-03-15 04:27:00,996] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1284432-a660-4a86-b711-44deab29f30d/OceanDNA-b33313.fa --refList OceanDNA-b33313/target_genomes.txt --output OceanDNA-b33313/fastani_result.tsv --threads 1
[2023-03-15 04:27:16,926] [INFO] Task succeeded: fastANI
[2023-03-15 04:27:16,926] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a6548c0-a6e7-405b-96c0-d97000a94cac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 04:27:16,927] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a6548c0-a6e7-405b-96c0-d97000a94cac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 04:27:16,938] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 04:27:16,938] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 04:27:16,938] [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
Hydrogenophaga palleronii	strain=NBRC 102513	GCA_001571225.1	65655	65655	type	True	83.4747	455	657	95	below_threshold
Hydrogenophaga taeniospiralis	strain=NBRC 102512	GCA_001592305.1	65656	65656	type	True	82.1406	427	657	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	81.812	457	657	95	below_threshold
Hydrogenophaga aromaticivorans	strain=D2P1	GCA_013387465.1	2610898	2610898	type	True	81.7432	447	657	95	below_threshold
Hydrogenophaga borbori	strain=LA-38	GCA_003417535.1	2294117	2294117	type	True	81.5724	435	657	95	below_threshold
Hydrogenophaga intermedia	strain=S1	GCA_000723405.1	65786	65786	type	True	81.5186	436	657	95	below_threshold
Hydrogenophaga intermedia	strain=DSM 5680	GCA_005938115.1	65786	65786	type	True	81.498	440	657	95	below_threshold
Hydrogenophaga intermedia	strain=NBRC 102510	GCA_001571205.1	65786	65786	type	True	81.4578	434	657	95	below_threshold
Hydrogenophaga flava	strain=NBRC 102514	GCA_001571145.1	65657	65657	type	True	81.2511	409	657	95	below_threshold
Hydrogenophaga pseudoflava	strain=NBRC 102511	GCA_001592285.1	47421	47421	type	True	81.2177	401	657	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	79.3081	303	657	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	79.2669	306	657	95	below_threshold
Ottowia beijingensis	strain=GCS-AN-3	GCA_013423955.1	1207057	1207057	type	True	79.1983	283	657	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	79.1645	295	657	95	below_threshold
Variovorax boronicumulans	strain=NBRC 103145	GCA_001591345.1	436515	436515	type	True	79.0517	341	657	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	78.9226	287	657	95	below_threshold
Curvibacter gracilis	strain=ATCC BAA-807	GCA_000518645.1	230310	230310	type	True	78.7838	312	657	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	78.5597	227	657	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	78.5381	301	657	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 04:27:16,939] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33313/tc_result.tsv
[2023-03-15 04:27:16,939] [INFO] ===== Taxonomy check completed =====
[2023-03-15 04:27:16,939] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 04:27:16,940] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a6548c0-a6e7-405b-96c0-d97000a94cac/dqc_reference/checkm_data
[2023-03-15 04:27:16,940] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 04:27:16,946] [INFO] Task started: CheckM
[2023-03-15 04:27:16,946] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33313/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33313/checkm_input OceanDNA-b33313/checkm_result
[2023-03-15 04:27:56,370] [INFO] Task succeeded: CheckM
[2023-03-15 04:27:56,370] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.36%
Contamintation: 8.85%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-15 04:27:56,409] [INFO] ===== Completeness check finished =====
[2023-03-15 04:27:56,410] [INFO] ===== Start GTDB Search =====
[2023-03-15 04:27:56,410] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33313/markers.fasta)
[2023-03-15 04:27:56,412] [INFO] Task started: Blastn
[2023-03-15 04:27:56,412] [INFO] Running command: blastn -query OceanDNA-b33313/markers.fasta -db /var/lib/cwl/stg1a6548c0-a6e7-405b-96c0-d97000a94cac/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33313/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:27:58,051] [INFO] Task succeeded: Blastn
[2023-03-15 04:27:58,056] [INFO] Selected 13 target genomes.
[2023-03-15 04:27:58,056] [INFO] Target genome list was writen to OceanDNA-b33313/target_genomes_gtdb.txt
[2023-03-15 04:27:58,091] [INFO] Task started: fastANI
[2023-03-15 04:27:58,091] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1284432-a660-4a86-b711-44deab29f30d/OceanDNA-b33313.fa --refList OceanDNA-b33313/target_genomes_gtdb.txt --output OceanDNA-b33313/fastani_result_gtdb.tsv --threads 1
[2023-03-15 04:28:08,648] [INFO] Task succeeded: fastANI
[2023-03-15 04:28:08,657] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 04:28:08,657] [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_002127265.1	s__Hydrogenophaga sp002127265	92.2355	589	657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003599455.1	s__Hydrogenophaga sp003599455	85.3839	484	657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018993155.1	s__Hydrogenophaga sp018993155	83.8262	473	657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001571225.1	s__Hydrogenophaga palleronii	83.4552	456	657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001713375.1	s__Hydrogenophaga sp001713375	83.4359	494	657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428625.1	s__Hydrogenophaga sp001428625	83.3742	483	657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010104355.1	s__Hydrogenophaga sp010104355	83.3407	475	657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005503365.1	s__Hydrogenophaga sp005503365	83.233	485	657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823505.1	s__Hydrogenophaga sp013823505	82.9789	440	657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018780385.1	s__Hydrogenophaga sp018780385	82.8805	479	657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592305.1	s__Hydrogenophaga taeniospiralis	82.1349	427	657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002127215.1	s__Hydrogenophaga sp002127215	81.9053	372	657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790705.1	s__Hydrogenophaga sp016790705	80.4572	311	657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 04:28:08,659] [INFO] GTDB search result was written to OceanDNA-b33313/result_gtdb.tsv
[2023-03-15 04:28:08,660] [INFO] ===== GTDB Search completed =====
[2023-03-15 04:28:08,664] [INFO] DFAST_QC result json was written to OceanDNA-b33313/dqc_result.json
[2023-03-15 04:28:08,664] [INFO] DFAST_QC completed!
[2023-03-15 04:28:08,664] [INFO] Total running time: 0h1m24s