[2023-03-19 01:35:27,747] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:35:27,747] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:35:27,748] [INFO] DQC Reference Directory: /var/lib/cwl/stg41030ba8-00ef-4b5f-9b06-309d8e965ec2/dqc_reference
[2023-03-19 01:35:29,727] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:35:29,728] [INFO] Task started: Prodigal
[2023-03-19 01:35:29,728] [INFO] Running command: cat /var/lib/cwl/stg031bad28-757b-44a9-9d8f-b4c6a5a60a14/OceanDNA-b30832.fa | prodigal -d OceanDNA-b30832/cds.fna -a OceanDNA-b30832/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:35:43,413] [INFO] Task succeeded: Prodigal
[2023-03-19 01:35:43,413] [INFO] Task started: HMMsearch
[2023-03-19 01:35:43,413] [INFO] Running command: hmmsearch --tblout OceanDNA-b30832/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg41030ba8-00ef-4b5f-9b06-309d8e965ec2/dqc_reference/reference_markers.hmm OceanDNA-b30832/protein.faa > /dev/null
[2023-03-19 01:35:43,590] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:35:43,590] [INFO] Found 6/6 markers.
[2023-03-19 01:35:43,605] [INFO] Query marker FASTA was written to OceanDNA-b30832/markers.fasta
[2023-03-19 01:35:43,606] [INFO] Task started: Blastn
[2023-03-19 01:35:43,606] [INFO] Running command: blastn -query OceanDNA-b30832/markers.fasta -db /var/lib/cwl/stg41030ba8-00ef-4b5f-9b06-309d8e965ec2/dqc_reference/reference_markers.fasta -out OceanDNA-b30832/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:35:44,247] [INFO] Task succeeded: Blastn
[2023-03-19 01:35:44,248] [INFO] Selected 30 target genomes.
[2023-03-19 01:35:44,248] [INFO] Target genome list was writen to OceanDNA-b30832/target_genomes.txt
[2023-03-19 01:35:44,269] [INFO] Task started: fastANI
[2023-03-19 01:35:44,269] [INFO] Running command: fastANI --query /var/lib/cwl/stg031bad28-757b-44a9-9d8f-b4c6a5a60a14/OceanDNA-b30832.fa --refList OceanDNA-b30832/target_genomes.txt --output OceanDNA-b30832/fastani_result.tsv --threads 1
[2023-03-19 01:36:03,385] [INFO] Task succeeded: fastANI
[2023-03-19 01:36:03,385] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg41030ba8-00ef-4b5f-9b06-309d8e965ec2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:36:03,385] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg41030ba8-00ef-4b5f-9b06-309d8e965ec2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:36:03,395] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:36:03,395] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 01:36:03,395] [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
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	76.1658	69	710	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	76.1631	69	710	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	76.0732	73	710	95	below_threshold
Varunaivibrio sulfuroxidans	strain=DSM 101688	GCA_004341725.1	1773489	1773489	type	True	76.0604	50	710	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	76.0548	61	710	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.0126	69	710	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	75.8748	81	710	95	below_threshold
Roseospira goensis	strain=JA135	GCA_014197795.1	391922	391922	type	True	75.8654	58	710	95	below_threshold
Telmatospirillum siberiense	strain=26-4b1	GCA_002845745.1	382514	382514	type	True	75.8169	53	710	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	75.7671	64	710	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_008274945.1	192	192	type	True	75.6913	67	710	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_001315015.1	192	192	type	True	75.68	66	710	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_007827425.1	192	192	type	True	75.6594	67	710	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	75.6266	65	710	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	75.4788	60	710	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 01:36:03,395] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30832/tc_result.tsv
[2023-03-19 01:36:03,395] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:36:03,395] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:36:03,395] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg41030ba8-00ef-4b5f-9b06-309d8e965ec2/dqc_reference/checkm_data
[2023-03-19 01:36:03,396] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:36:03,400] [INFO] Task started: CheckM
[2023-03-19 01:36:03,400] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30832/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30832/checkm_input OceanDNA-b30832/checkm_result
[2023-03-19 01:36:39,510] [INFO] Task succeeded: CheckM
[2023-03-19 01:36:39,510] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:36:39,512] [INFO] ===== Completeness check finished =====
[2023-03-19 01:36:39,512] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:36:39,513] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30832/markers.fasta)
[2023-03-19 01:36:39,514] [INFO] Task started: Blastn
[2023-03-19 01:36:39,514] [INFO] Running command: blastn -query OceanDNA-b30832/markers.fasta -db /var/lib/cwl/stg41030ba8-00ef-4b5f-9b06-309d8e965ec2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30832/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:36:40,632] [INFO] Task succeeded: Blastn
[2023-03-19 01:36:40,633] [INFO] Selected 19 target genomes.
[2023-03-19 01:36:40,633] [INFO] Target genome list was writen to OceanDNA-b30832/target_genomes_gtdb.txt
[2023-03-19 01:36:40,692] [INFO] Task started: fastANI
[2023-03-19 01:36:40,692] [INFO] Running command: fastANI --query /var/lib/cwl/stg031bad28-757b-44a9-9d8f-b4c6a5a60a14/OceanDNA-b30832.fa --refList OceanDNA-b30832/target_genomes_gtdb.txt --output OceanDNA-b30832/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:36:51,233] [INFO] Task succeeded: fastANI
[2023-03-19 01:36:51,241] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 01:36:51,241] [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_002938315.1	s__Casp-alpha2 sp002938315	99.5514	633	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.33	99.24	0.87	0.79	4	conclusive
GCA_016763915.1	s__Casp-alpha2 sp016763915	78.6512	184	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686255.1	s__Casp-alpha2 sp002686255	78.4711	304	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.76	99.74	0.90	0.88	3	-
GCA_002938075.1	s__Casp-alpha2 sp002938075	78.2946	226	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	98.70	98.63	0.78	0.77	3	-
GCA_014382345.1	s__Casp-alpha2 sp014382345	78.2054	331	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.86	99.86	0.92	0.92	2	-
GCA_001510075.1	s__Casp-alpha2 sp001510075	77.9415	204	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013204265.1	s__Casp-alpha2 sp013204265	77.7731	241	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002325375.1	s__UBA1479 sp002325375	76.5325	123	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	99.20	96.43	0.95	0.85	6	-
GCA_016776525.1	s__JADHTD01 sp016776525	76.2901	72	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JADHTD01;g__JADHTD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018671895.1	s__JABHGV01 sp018671895	76.1887	76	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-02-FULL-58-16_A;g__JABHGV01	95.0	99.83	99.79	0.94	0.93	6	-
GCA_014859895.1	s__JACZKS01 sp014859895	75.9057	69	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JACZKS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650715.1	s__Phaeospirillum marisnigri	75.7895	63	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:36:51,241] [INFO] GTDB search result was written to OceanDNA-b30832/result_gtdb.tsv
[2023-03-19 01:36:51,241] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:36:51,243] [INFO] DFAST_QC result json was written to OceanDNA-b30832/dqc_result.json
[2023-03-19 01:36:51,243] [INFO] DFAST_QC completed!
[2023-03-19 01:36:51,243] [INFO] Total running time: 0h1m23s