[2023-03-15 17:03:08,025] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:03:08,027] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:03:08,027] [INFO] DQC Reference Directory: /var/lib/cwl/stgf421e937-3956-44ad-9958-1e9330199b22/dqc_reference
[2023-03-15 17:03:14,007] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:03:14,008] [INFO] Task started: Prodigal
[2023-03-15 17:03:14,008] [INFO] Running command: cat /var/lib/cwl/stg2afe188e-dba1-4dbe-b13d-7f8742ea3cf8/OceanDNA-b34122.fa | prodigal -d OceanDNA-b34122/cds.fna -a OceanDNA-b34122/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:03:25,628] [INFO] Task succeeded: Prodigal
[2023-03-15 17:03:25,628] [INFO] Task started: HMMsearch
[2023-03-15 17:03:25,628] [INFO] Running command: hmmsearch --tblout OceanDNA-b34122/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf421e937-3956-44ad-9958-1e9330199b22/dqc_reference/reference_markers.hmm OceanDNA-b34122/protein.faa > /dev/null
[2023-03-15 17:03:25,875] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:03:25,876] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2afe188e-dba1-4dbe-b13d-7f8742ea3cf8/OceanDNA-b34122.fa]
[2023-03-15 17:03:25,902] [INFO] Query marker FASTA was written to OceanDNA-b34122/markers.fasta
[2023-03-15 17:03:25,904] [INFO] Task started: Blastn
[2023-03-15 17:03:25,904] [INFO] Running command: blastn -query OceanDNA-b34122/markers.fasta -db /var/lib/cwl/stgf421e937-3956-44ad-9958-1e9330199b22/dqc_reference/reference_markers.fasta -out OceanDNA-b34122/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:03:29,959] [INFO] Task succeeded: Blastn
[2023-03-15 17:03:29,965] [INFO] Selected 13 target genomes.
[2023-03-15 17:03:29,965] [INFO] Target genome list was writen to OceanDNA-b34122/target_genomes.txt
[2023-03-15 17:03:29,982] [INFO] Task started: fastANI
[2023-03-15 17:03:29,982] [INFO] Running command: fastANI --query /var/lib/cwl/stg2afe188e-dba1-4dbe-b13d-7f8742ea3cf8/OceanDNA-b34122.fa --refList OceanDNA-b34122/target_genomes.txt --output OceanDNA-b34122/fastani_result.tsv --threads 1
[2023-03-15 17:03:38,286] [INFO] Task succeeded: fastANI
[2023-03-15 17:03:38,286] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf421e937-3956-44ad-9958-1e9330199b22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:03:38,287] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf421e937-3956-44ad-9958-1e9330199b22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:03:38,343] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:03:38,343] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 17:03:38,343] [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
Dechloromonas hortensis	strain=MA-1	GCA_009469765.1	337779	337779	type	True	82.2113	355	551	95	below_threshold
Dechloromonas denitrificans	strain=ATCC BAA-841	GCA_001551835.1	281362	281362	type	True	82.1649	351	551	95	below_threshold
Azonexus fungiphilus	strain=DSM 23841	GCA_003634965.1	146940	146940	type	True	81.8422	309	551	95	below_threshold
Azonexus hydrophilus	strain=DSM 23864	GCA_000429605.1	418702	418702	type	True	81.5995	299	551	95	below_threshold
Azospira oryzae	strain=DSM 21223	GCA_004217225.1	146939	146939	type	True	78.8219	188	551	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_009469755.1	1066	1066	type	True	78.5242	168	551	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	78.2946	132	551	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	78.2919	130	551	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	78.2271	161	551	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	78.0196	153	551	95	below_threshold
Rhodocyclus gracilis	strain=DSM 110	GCA_009617575.1	2929842	2929842	type	True	77.989	124	551	95	below_threshold
Thauera phenolivorans	strain=ZV1C	GCA_001696715.1	1792543	1792543	type	True	77.7265	138	551	95	below_threshold
Aromatoleum diolicum	strain=22Lin	GCA_012910955.1	75796	75796	type	True	77.6203	130	551	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 17:03:38,345] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34122/tc_result.tsv
[2023-03-15 17:03:38,348] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:03:38,349] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:03:38,349] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf421e937-3956-44ad-9958-1e9330199b22/dqc_reference/checkm_data
[2023-03-15 17:03:38,349] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:03:38,378] [INFO] Task started: CheckM
[2023-03-15 17:03:38,379] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34122/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34122/checkm_input OceanDNA-b34122/checkm_result
[2023-03-15 17:04:15,121] [INFO] Task succeeded: CheckM
[2023-03-15 17:04:15,122] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.87%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:04:15,146] [INFO] ===== Completeness check finished =====
[2023-03-15 17:04:15,146] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:04:15,146] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34122/markers.fasta)
[2023-03-15 17:04:15,148] [INFO] Task started: Blastn
[2023-03-15 17:04:15,148] [INFO] Running command: blastn -query OceanDNA-b34122/markers.fasta -db /var/lib/cwl/stgf421e937-3956-44ad-9958-1e9330199b22/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34122/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:04:16,389] [INFO] Task succeeded: Blastn
[2023-03-15 17:04:16,404] [INFO] Selected 17 target genomes.
[2023-03-15 17:04:16,404] [INFO] Target genome list was writen to OceanDNA-b34122/target_genomes_gtdb.txt
[2023-03-15 17:04:16,420] [INFO] Task started: fastANI
[2023-03-15 17:04:16,420] [INFO] Running command: fastANI --query /var/lib/cwl/stg2afe188e-dba1-4dbe-b13d-7f8742ea3cf8/OceanDNA-b34122.fa --refList OceanDNA-b34122/target_genomes_gtdb.txt --output OceanDNA-b34122/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:04:27,753] [INFO] Task succeeded: fastANI
[2023-03-15 17:04:27,763] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 17:04:27,764] [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_008711155.1	s__Azonexus sp008711155	97.5014	497	551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	97.59	97.59	0.92	0.92	2	conclusive
GCF_000519045.1	s__Azonexus agitatus	83.6358	378	551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	98.62	98.62	0.86	0.86	2	-
GCA_016790885.1	s__Azonexus sp016790885	83.0079	265	551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009469585.1	s__Azonexus sp009469585	82.7249	352	551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983615.1	s__Azonexus sp017983615	82.4785	316	551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903922075.1	s__Azonexus sp903922075	82.4361	270	551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008933675.1	s__Azonexus sp008933675	82.4143	320	551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009469615.1	s__Azonexus sp009469615	82.3024	320	551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012425.1	s__Azonexus aromaticus_A	81.9502	377	551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	97.34	97.34	0.89	0.89	2	-
GCA_018261895.1	s__Azonexus sp018261895	81.8333	301	551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002470165.1	s__Azonexus sp002470165	81.7437	236	551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002440665.1	s__Azonexus sp002440665	81.686	307	551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018262195.1	s__Azonexus sp018262195	81.6455	343	551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016791065.1	s__Azonexus sp016791065	81.5999	277	551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002425245.1	s__Azonexus sp002425245	81.5203	269	551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001956855.1	s__Azonexus hydrophilus_A	81.3798	305	551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018261905.1	s__Azonexus sp018261905	81.2514	303	551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 17:04:27,765] [INFO] GTDB search result was written to OceanDNA-b34122/result_gtdb.tsv
[2023-03-15 17:04:27,768] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:04:27,771] [INFO] DFAST_QC result json was written to OceanDNA-b34122/dqc_result.json
[2023-03-15 17:04:27,771] [INFO] DFAST_QC completed!
[2023-03-15 17:04:27,771] [INFO] Total running time: 0h1m20s