[2023-03-18 20:40:41,184] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:40:41,184] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:40:41,184] [INFO] DQC Reference Directory: /var/lib/cwl/stg275b5275-0438-4e7d-9630-6b4ae49c2272/dqc_reference
[2023-03-18 20:40:42,273] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:40:42,273] [INFO] Task started: Prodigal
[2023-03-18 20:40:42,273] [INFO] Running command: cat /var/lib/cwl/stg74e4a477-8077-40d6-8cc0-05c2d49b4bfd/OceanDNA-b30807.fa | prodigal -d OceanDNA-b30807/cds.fna -a OceanDNA-b30807/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:40:50,567] [INFO] Task succeeded: Prodigal
[2023-03-18 20:40:50,567] [INFO] Task started: HMMsearch
[2023-03-18 20:40:50,567] [INFO] Running command: hmmsearch --tblout OceanDNA-b30807/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg275b5275-0438-4e7d-9630-6b4ae49c2272/dqc_reference/reference_markers.hmm OceanDNA-b30807/protein.faa > /dev/null
[2023-03-18 20:40:50,810] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:40:50,811] [INFO] Found 6/6 markers.
[2023-03-18 20:40:50,826] [INFO] Query marker FASTA was written to OceanDNA-b30807/markers.fasta
[2023-03-18 20:40:50,826] [INFO] Task started: Blastn
[2023-03-18 20:40:50,826] [INFO] Running command: blastn -query OceanDNA-b30807/markers.fasta -db /var/lib/cwl/stg275b5275-0438-4e7d-9630-6b4ae49c2272/dqc_reference/reference_markers.fasta -out OceanDNA-b30807/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:40:51,568] [INFO] Task succeeded: Blastn
[2023-03-18 20:40:51,569] [INFO] Selected 32 target genomes.
[2023-03-18 20:40:51,569] [INFO] Target genome list was writen to OceanDNA-b30807/target_genomes.txt
[2023-03-18 20:40:51,580] [INFO] Task started: fastANI
[2023-03-18 20:40:51,580] [INFO] Running command: fastANI --query /var/lib/cwl/stg74e4a477-8077-40d6-8cc0-05c2d49b4bfd/OceanDNA-b30807.fa --refList OceanDNA-b30807/target_genomes.txt --output OceanDNA-b30807/fastani_result.tsv --threads 1
[2023-03-18 20:41:18,054] [INFO] Task succeeded: fastANI
[2023-03-18 20:41:18,054] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg275b5275-0438-4e7d-9630-6b4ae49c2272/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:41:18,054] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg275b5275-0438-4e7d-9630-6b4ae49c2272/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:41:18,068] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:41:18,068] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 20:41:18,068] [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
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	76.825	66	380	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.6487	92	380	95	below_threshold
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	76.597	70	380	95	below_threshold
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	76.5653	86	380	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_000513295.1	55518	55518	type	True	76.4873	69	380	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.3924	61	380	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	76.3665	72	380	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.3407	77	380	95	below_threshold
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	76.1863	69	380	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	76.156	90	380	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	76.1429	66	380	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.103	92	380	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.1028	54	380	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	76.0701	71	380	95	below_threshold
Rhodothalassium salexigens	strain=DSM 2132	GCA_016583875.1	1086	1086	type	True	76.0565	56	380	95	below_threshold
Rhodothalassium salexigens	strain=DSM 2132	GCA_004341375.1	1086	1086	type	True	76.0272	57	380	95	below_threshold
Azospirillum melinis	strain=TMCY0552	GCA_013340935.1	328839	328839	type	True	76.0181	86	380	95	below_threshold
Skermanella aerolata	strain=5416T-32	GCA_000936425.1	393310	393310	type	True	76.0179	63	380	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	75.999	61	380	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	75.9504	87	380	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	75.9219	55	380	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	75.9183	58	380	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	75.8747	58	380	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	75.8735	101	380	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	75.6338	52	380	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	75.4952	52	380	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 20:41:18,069] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30807/tc_result.tsv
[2023-03-18 20:41:18,069] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:41:18,069] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:41:18,069] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg275b5275-0438-4e7d-9630-6b4ae49c2272/dqc_reference/checkm_data
[2023-03-18 20:41:18,070] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:41:18,074] [INFO] Task started: CheckM
[2023-03-18 20:41:18,074] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30807/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30807/checkm_input OceanDNA-b30807/checkm_result
[2023-03-18 20:41:43,498] [INFO] Task succeeded: CheckM
[2023-03-18 20:41:43,498] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 4.55%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 20:41:43,500] [INFO] ===== Completeness check finished =====
[2023-03-18 20:41:43,500] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:41:43,501] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30807/markers.fasta)
[2023-03-18 20:41:43,501] [INFO] Task started: Blastn
[2023-03-18 20:41:43,501] [INFO] Running command: blastn -query OceanDNA-b30807/markers.fasta -db /var/lib/cwl/stg275b5275-0438-4e7d-9630-6b4ae49c2272/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30807/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:41:44,882] [INFO] Task succeeded: Blastn
[2023-03-18 20:41:44,883] [INFO] Selected 13 target genomes.
[2023-03-18 20:41:44,883] [INFO] Target genome list was writen to OceanDNA-b30807/target_genomes_gtdb.txt
[2023-03-18 20:41:44,936] [INFO] Task started: fastANI
[2023-03-18 20:41:44,937] [INFO] Running command: fastANI --query /var/lib/cwl/stg74e4a477-8077-40d6-8cc0-05c2d49b4bfd/OceanDNA-b30807.fa --refList OceanDNA-b30807/target_genomes_gtdb.txt --output OceanDNA-b30807/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:41:51,556] [INFO] Task succeeded: fastANI
[2023-03-18 20:41:51,563] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 20:41:51,564] [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_002938075.1	s__Casp-alpha2 sp002938075	97.7337	292	380	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	conclusive
GCA_002686255.1	s__Casp-alpha2 sp002686255	90.8946	306	380	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_016763915.1	s__Casp-alpha2 sp016763915	79.8189	119	380	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_014382345.1	s__Casp-alpha2 sp014382345	78.6806	208	380	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	78.5398	134	380	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_016187325.1	s__JACPJY01 sp016187325	78.5388	190	380	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__JACPJY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002938315.1	s__Casp-alpha2 sp002938315	78.0069	177	380	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	-
GCA_013204265.1	s__Casp-alpha2 sp013204265	77.5225	145	380	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_002781745.1	s__UBA1479 sp002781745	77.0493	129	380	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706405.1	s__UBA1479 sp002706405	76.7822	104	380	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	99.68	99.68	0.89	0.89	2	-
GCA_009694195.1	s__SHVQ01 sp009694195	76.1551	55	380	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-12-FULL-67-15;g__SHVQ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 20:41:51,564] [INFO] GTDB search result was written to OceanDNA-b30807/result_gtdb.tsv
[2023-03-18 20:41:51,564] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:41:51,566] [INFO] DFAST_QC result json was written to OceanDNA-b30807/dqc_result.json
[2023-03-18 20:41:51,566] [INFO] DFAST_QC completed!
[2023-03-18 20:41:51,566] [INFO] Total running time: 0h1m10s