[2023-03-16 04:24:46,334] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:24:46,334] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:24:46,334] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d0f7625-93ff-428f-80b0-53c58ccac19f/dqc_reference
[2023-03-16 04:24:48,115] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:24:48,115] [INFO] Task started: Prodigal
[2023-03-16 04:24:48,115] [INFO] Running command: cat /var/lib/cwl/stgd6a46f58-a7a2-4bbd-a597-4a095e91a320/OceanDNA-b33301.fa | prodigal -d OceanDNA-b33301/cds.fna -a OceanDNA-b33301/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:25:09,709] [INFO] Task succeeded: Prodigal
[2023-03-16 04:25:09,709] [INFO] Task started: HMMsearch
[2023-03-16 04:25:09,709] [INFO] Running command: hmmsearch --tblout OceanDNA-b33301/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d0f7625-93ff-428f-80b0-53c58ccac19f/dqc_reference/reference_markers.hmm OceanDNA-b33301/protein.faa > /dev/null
[2023-03-16 04:25:09,967] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:25:09,967] [INFO] Found 6/6 markers.
[2023-03-16 04:25:10,001] [INFO] Query marker FASTA was written to OceanDNA-b33301/markers.fasta
[2023-03-16 04:25:10,002] [INFO] Task started: Blastn
[2023-03-16 04:25:10,002] [INFO] Running command: blastn -query OceanDNA-b33301/markers.fasta -db /var/lib/cwl/stg6d0f7625-93ff-428f-80b0-53c58ccac19f/dqc_reference/reference_markers.fasta -out OceanDNA-b33301/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:25:10,975] [INFO] Task succeeded: Blastn
[2023-03-16 04:25:10,975] [INFO] Selected 12 target genomes.
[2023-03-16 04:25:10,976] [INFO] Target genome list was writen to OceanDNA-b33301/target_genomes.txt
[2023-03-16 04:25:10,985] [INFO] Task started: fastANI
[2023-03-16 04:25:10,985] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6a46f58-a7a2-4bbd-a597-4a095e91a320/OceanDNA-b33301.fa --refList OceanDNA-b33301/target_genomes.txt --output OceanDNA-b33301/fastani_result.tsv --threads 1
[2023-03-16 04:25:23,321] [INFO] Task succeeded: fastANI
[2023-03-16 04:25:23,322] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d0f7625-93ff-428f-80b0-53c58ccac19f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:25:23,322] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d0f7625-93ff-428f-80b0-53c58ccac19f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:25:23,330] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 04:25:23,330] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 04:25:23,331] [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
Herbaspirillum aquaticum	strain=IEH 4430	GCA_002213425.1	568783	568783	type	True	98.5663	970	1043	95	conclusive
Herbaspirillum huttiense subsp. putei	strain=IAM 15032	GCA_000478365.1	230311	863372	type	True	92.8366	936	1043	95	below_threshold
Herbaspirillum rubrisubalbicans	strain=NBRC 102523	GCA_001591225.1	80842	80842	type	True	88.3484	863	1043	95	below_threshold
Herbaspirillum rubrisubalbicans	strain=DSM 11543	GCA_003719195.1	80842	80842	type	True	88.3471	872	1043	95	below_threshold
Herbaspirillum seropedicae	strain=Z67	GCA_001040945.1	964	964	type	True	88.3409	864	1043	95	below_threshold
Herbaspirillum seropedicae	strain=Z67	GCA_013180375.1	964	964	type	True	88.3339	855	1043	95	below_threshold
Herbaspirillum camelliae	strain=WT00C	GCA_001929405.1	1892903	1892903	type	True	88.2702	853	1043	95	below_threshold
Herbaspirillum frisingense	strain=GSF30	GCA_000300975.2	92645	92645	type	True	87.9084	870	1043	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	81.5442	527	1043	95	below_threshold
Noviherbaspirillum aridicola	strain=NCCP-691	GCA_019656455.1	2849687	2849687	type	True	79.8198	333	1043	95	below_threshold
Massilia agilis	strain=JCM 31605	GCA_024756255.1	1811226	1811226	type	True	79.1869	325	1043	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	79.0298	304	1043	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:25:23,331] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33301/tc_result.tsv
[2023-03-16 04:25:23,331] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:25:23,331] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:25:23,331] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d0f7625-93ff-428f-80b0-53c58ccac19f/dqc_reference/checkm_data
[2023-03-16 04:25:23,332] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:25:23,338] [INFO] Task started: CheckM
[2023-03-16 04:25:23,338] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33301/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33301/checkm_input OceanDNA-b33301/checkm_result
[2023-03-16 04:26:17,580] [INFO] Task succeeded: CheckM
[2023-03-16 04:26:17,581] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:26:17,584] [INFO] ===== Completeness check finished =====
[2023-03-16 04:26:17,584] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:26:17,584] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33301/markers.fasta)
[2023-03-16 04:26:17,584] [INFO] Task started: Blastn
[2023-03-16 04:26:17,584] [INFO] Running command: blastn -query OceanDNA-b33301/markers.fasta -db /var/lib/cwl/stg6d0f7625-93ff-428f-80b0-53c58ccac19f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33301/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:26:19,473] [INFO] Task succeeded: Blastn
[2023-03-16 04:26:19,474] [INFO] Selected 8 target genomes.
[2023-03-16 04:26:19,474] [INFO] Target genome list was writen to OceanDNA-b33301/target_genomes_gtdb.txt
[2023-03-16 04:26:19,482] [INFO] Task started: fastANI
[2023-03-16 04:26:19,483] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6a46f58-a7a2-4bbd-a597-4a095e91a320/OceanDNA-b33301.fa --refList OceanDNA-b33301/target_genomes_gtdb.txt --output OceanDNA-b33301/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:26:28,166] [INFO] Task succeeded: fastANI
[2023-03-16 04:26:28,171] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 04:26:28,171] [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_002213425.1	s__Herbaspirillum aquaticum	98.5663	970	1043	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	97.01	95.53	0.89	0.85	3	conclusive
GCF_004367745.1	s__Herbaspirillum huttiense	93.0721	958	1043	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	97.45	97.06	0.87	0.86	14	-
GCF_000261365.1	s__Herbaspirillum sp000261365	90.6374	913	1043	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	98.65	98.65	0.93	0.93	2	-
GCF_003719195.1	s__Herbaspirillum rubrisubalbicans	88.3627	871	1043	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	97.49	96.58	0.87	0.83	8	-
GCF_001040945.1	s__Herbaspirillum seropedicae	88.3514	863	1043	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	98.53	96.09	0.94	0.89	6	-
GCF_000300975.2	s__Herbaspirillum frisingense	87.8981	871	1043	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	97.59	97.42	0.92	0.89	5	-
GCA_019233085.1	s__Herbaspirillum sp019233085	86.952	700	1043	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009914615.1	s__Herbaspirillum frisingense_B	85.6243	670	1043	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:26:28,172] [INFO] GTDB search result was written to OceanDNA-b33301/result_gtdb.tsv
[2023-03-16 04:26:28,172] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:26:28,173] [INFO] DFAST_QC result json was written to OceanDNA-b33301/dqc_result.json
[2023-03-16 04:26:28,173] [INFO] DFAST_QC completed!
[2023-03-16 04:26:28,173] [INFO] Total running time: 0h1m42s