[2023-03-18 00:05:54,509] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:05:54,510] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:05:54,510] [INFO] DQC Reference Directory: /var/lib/cwl/stg12cd0e7a-7db6-4e3f-8e22-b09ce92e3430/dqc_reference
[2023-03-18 00:05:55,687] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:05:55,688] [INFO] Task started: Prodigal
[2023-03-18 00:05:55,688] [INFO] Running command: cat /var/lib/cwl/stg06e43c4c-ae8a-4362-8290-d693b6fcf3a0/OceanDNA-b24163.fa | prodigal -d OceanDNA-b24163/cds.fna -a OceanDNA-b24163/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:06:14,639] [INFO] Task succeeded: Prodigal
[2023-03-18 00:06:14,639] [INFO] Task started: HMMsearch
[2023-03-18 00:06:14,639] [INFO] Running command: hmmsearch --tblout OceanDNA-b24163/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg12cd0e7a-7db6-4e3f-8e22-b09ce92e3430/dqc_reference/reference_markers.hmm OceanDNA-b24163/protein.faa > /dev/null
[2023-03-18 00:06:14,842] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:06:14,842] [INFO] Found 6/6 markers.
[2023-03-18 00:06:14,861] [INFO] Query marker FASTA was written to OceanDNA-b24163/markers.fasta
[2023-03-18 00:06:14,862] [INFO] Task started: Blastn
[2023-03-18 00:06:14,862] [INFO] Running command: blastn -query OceanDNA-b24163/markers.fasta -db /var/lib/cwl/stg12cd0e7a-7db6-4e3f-8e22-b09ce92e3430/dqc_reference/reference_markers.fasta -out OceanDNA-b24163/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:06:15,596] [INFO] Task succeeded: Blastn
[2023-03-18 00:06:15,597] [INFO] Selected 35 target genomes.
[2023-03-18 00:06:15,597] [INFO] Target genome list was writen to OceanDNA-b24163/target_genomes.txt
[2023-03-18 00:06:15,618] [INFO] Task started: fastANI
[2023-03-18 00:06:15,618] [INFO] Running command: fastANI --query /var/lib/cwl/stg06e43c4c-ae8a-4362-8290-d693b6fcf3a0/OceanDNA-b24163.fa --refList OceanDNA-b24163/target_genomes.txt --output OceanDNA-b24163/fastani_result.tsv --threads 1
[2023-03-18 00:06:42,163] [INFO] Task succeeded: fastANI
[2023-03-18 00:06:42,164] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg12cd0e7a-7db6-4e3f-8e22-b09ce92e3430/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:06:42,164] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg12cd0e7a-7db6-4e3f-8e22-b09ce92e3430/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:06:42,173] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:06:42,173] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:06:42,173] [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
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.4837	67	1035	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.4143	75	1035	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.2315	51	1035	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.159	75	1035	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	75.9659	58	1035	95	below_threshold
Nisaea nitritireducens	strain=DSM 19540	GCA_014904795.1	568392	568392	type	True	75.9307	55	1035	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	75.9173	63	1035	95	below_threshold
Ferrovibrio terrae	strain=K5	GCA_007197755.1	2594003	2594003	type	True	75.896	61	1035	95	below_threshold
Azospirillum thiophilum	strain=BV-S	GCA_001305595.1	528244	528244	type	True	75.8937	64	1035	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	75.8639	65	1035	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	75.8442	60	1035	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_003119195.2	1064539	1064539	type	True	75.7577	57	1035	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	75.7038	67	1035	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	75.6398	54	1035	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.6276	76	1035	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:06:42,176] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24163/tc_result.tsv
[2023-03-18 00:06:42,178] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:06:42,178] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:06:42,178] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg12cd0e7a-7db6-4e3f-8e22-b09ce92e3430/dqc_reference/checkm_data
[2023-03-18 00:06:42,179] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:06:42,192] [INFO] Task started: CheckM
[2023-03-18 00:06:42,192] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24163/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24163/checkm_input OceanDNA-b24163/checkm_result
[2023-03-18 00:07:30,005] [INFO] Task succeeded: CheckM
[2023-03-18 00:07:30,005] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:07:30,028] [INFO] ===== Completeness check finished =====
[2023-03-18 00:07:30,028] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:07:30,028] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24163/markers.fasta)
[2023-03-18 00:07:30,029] [INFO] Task started: Blastn
[2023-03-18 00:07:30,029] [INFO] Running command: blastn -query OceanDNA-b24163/markers.fasta -db /var/lib/cwl/stg12cd0e7a-7db6-4e3f-8e22-b09ce92e3430/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24163/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:07:31,335] [INFO] Task succeeded: Blastn
[2023-03-18 00:07:31,348] [INFO] Selected 26 target genomes.
[2023-03-18 00:07:31,348] [INFO] Target genome list was writen to OceanDNA-b24163/target_genomes_gtdb.txt
[2023-03-18 00:07:31,368] [INFO] Task started: fastANI
[2023-03-18 00:07:31,368] [INFO] Running command: fastANI --query /var/lib/cwl/stg06e43c4c-ae8a-4362-8290-d693b6fcf3a0/OceanDNA-b24163.fa --refList OceanDNA-b24163/target_genomes_gtdb.txt --output OceanDNA-b24163/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:07:48,302] [INFO] Task succeeded: fastANI
[2023-03-18 00:07:48,309] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:07:48,309] [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_002471575.1	s__UBA830 sp002471575	95.9973	885	1035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	97.90	95.90	0.91	0.84	7	conclusive
GCA_905181725.1	s__UBA830 sp905181725	77.1375	288	1035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479125.1	s__UBA830 sp905479125	76.8255	273	1035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	98.22	98.19	0.84	0.83	3	-
GCA_002689465.1	s__UBA830 sp002689465	76.7247	77	1035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307375.1	s__JAFKFH01 sp017307375	75.882	67	1035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__JAFKFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904705.1	s__Nisaea sp014904705	75.8639	65	1035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018660305.1	s__JABJKO01 sp018660305	75.7604	58	1035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__JABJKO01	95.0	99.60	99.60	0.81	0.81	2	-
GCA_013003675.1	s__JABDIP01 sp013003675	75.7441	50	1035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__JABDIP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002239065.1	s__MPNO01 sp002239065	75.7266	97	1035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__MPNO01;g__MPNO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728835.1	s__Hypericibacter adhaerens	75.7038	67	1035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Hypericibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003349955.1	s__Azospirillum brasilense_B	75.6549	56	1035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	95.36	95.36	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-03-18 00:07:48,313] [INFO] GTDB search result was written to OceanDNA-b24163/result_gtdb.tsv
[2023-03-18 00:07:48,316] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:07:48,320] [INFO] DFAST_QC result json was written to OceanDNA-b24163/dqc_result.json
[2023-03-18 00:07:48,320] [INFO] DFAST_QC completed!
[2023-03-18 00:07:48,320] [INFO] Total running time: 0h1m54s