[2023-03-16 07:55:45,202] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:55:45,202] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:55:45,202] [INFO] DQC Reference Directory: /var/lib/cwl/stga3efcec7-c139-47b0-b01e-8f916f8546df/dqc_reference
[2023-03-16 07:55:46,307] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:55:46,308] [INFO] Task started: Prodigal
[2023-03-16 07:55:46,309] [INFO] Running command: cat /var/lib/cwl/stg93f90df5-8913-4632-bc02-23f848476a98/OceanDNA-b31056.fa | prodigal -d OceanDNA-b31056/cds.fna -a OceanDNA-b31056/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:56:15,950] [INFO] Task succeeded: Prodigal
[2023-03-16 07:56:15,950] [INFO] Task started: HMMsearch
[2023-03-16 07:56:15,950] [INFO] Running command: hmmsearch --tblout OceanDNA-b31056/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3efcec7-c139-47b0-b01e-8f916f8546df/dqc_reference/reference_markers.hmm OceanDNA-b31056/protein.faa > /dev/null
[2023-03-16 07:56:16,169] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:56:16,170] [INFO] Found 6/6 markers.
[2023-03-16 07:56:16,198] [INFO] Query marker FASTA was written to OceanDNA-b31056/markers.fasta
[2023-03-16 07:56:16,198] [INFO] Task started: Blastn
[2023-03-16 07:56:16,198] [INFO] Running command: blastn -query OceanDNA-b31056/markers.fasta -db /var/lib/cwl/stga3efcec7-c139-47b0-b01e-8f916f8546df/dqc_reference/reference_markers.fasta -out OceanDNA-b31056/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:56:16,905] [INFO] Task succeeded: Blastn
[2023-03-16 07:56:16,906] [INFO] Selected 30 target genomes.
[2023-03-16 07:56:16,906] [INFO] Target genome list was writen to OceanDNA-b31056/target_genomes.txt
[2023-03-16 07:56:16,923] [INFO] Task started: fastANI
[2023-03-16 07:56:16,923] [INFO] Running command: fastANI --query /var/lib/cwl/stg93f90df5-8913-4632-bc02-23f848476a98/OceanDNA-b31056.fa --refList OceanDNA-b31056/target_genomes.txt --output OceanDNA-b31056/fastani_result.tsv --threads 1
[2023-03-16 07:56:38,000] [INFO] Task succeeded: fastANI
[2023-03-16 07:56:38,000] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3efcec7-c139-47b0-b01e-8f916f8546df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:56:38,000] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3efcec7-c139-47b0-b01e-8f916f8546df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:56:38,014] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:56:38,014] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 07:56:38,014] [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
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_000513295.1	55518	55518	type	True	76.1478	124	1482	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.0845	123	1482	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_002995515.1	55518	55518	type	True	76.0145	124	1482	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	75.9499	125	1482	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	75.7704	81	1482	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	75.755	107	1482	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	75.744	116	1482	95	below_threshold
Ferrovibrio terrae	strain=K5	GCA_007197755.1	2594003	2594003	type	True	75.7347	97	1482	95	below_threshold
Oceanibacterium hippocampi	strain=CECT 7691	GCA_900172325.1	745714	745714	type	True	75.7212	93	1482	95	below_threshold
Magnetospirillum magnetotacticum	strain=MS-1	GCA_000829825.1	188	188	type	True	75.7081	103	1482	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	75.5515	105	1482	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	75.5455	116	1482	95	below_threshold
Devosia equisanguinis	strain=CIP 111628	GCA_900631955.1	2490941	2490941	type	True	75.4436	57	1482	95	below_threshold
Nisaea denitrificans	strain=DSM 18348	GCA_000426505.1	390877	390877	type	True	75.4414	74	1482	95	below_threshold
Niveispirillum irakense	strain=DSM 11586	GCA_000429645.1	34011	34011	type	True	75.4209	76	1482	95	below_threshold
Xanthobacter agilis	strain=LMG 16336	GCA_021730435.1	47492	47492	type	True	75.3962	75	1482	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	75.3494	72	1482	95	below_threshold
Azospirillum melinis	strain=TMCY0552	GCA_013340935.1	328839	328839	type	True	75.3096	135	1482	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	75.2971	136	1482	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	75.2834	57	1482	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	75.2542	93	1482	95	below_threshold
Elstera cyanobacteriorum	strain=TH019	GCA_002251735.1	2022747	2022747	type	True	75.2251	57	1482	95	below_threshold
Elstera cyanobacteriorum	strain=CGMCC 1.15802	GCA_014643715.1	2022747	2022747	type	True	75.2251	57	1482	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	75.2114	74	1482	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:56:38,018] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31056/tc_result.tsv
[2023-03-16 07:56:38,019] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:56:38,019] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:56:38,019] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3efcec7-c139-47b0-b01e-8f916f8546df/dqc_reference/checkm_data
[2023-03-16 07:56:38,019] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:56:38,033] [INFO] Task started: CheckM
[2023-03-16 07:56:38,033] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31056/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31056/checkm_input OceanDNA-b31056/checkm_result
[2023-03-16 07:57:49,377] [INFO] Task succeeded: CheckM
[2023-03-16 07:57:49,377] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:57:49,385] [INFO] ===== Completeness check finished =====
[2023-03-16 07:57:49,386] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:57:49,386] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31056/markers.fasta)
[2023-03-16 07:57:49,387] [INFO] Task started: Blastn
[2023-03-16 07:57:49,387] [INFO] Running command: blastn -query OceanDNA-b31056/markers.fasta -db /var/lib/cwl/stga3efcec7-c139-47b0-b01e-8f916f8546df/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31056/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:57:50,718] [INFO] Task succeeded: Blastn
[2023-03-16 07:57:50,719] [INFO] Selected 27 target genomes.
[2023-03-16 07:57:50,719] [INFO] Target genome list was writen to OceanDNA-b31056/target_genomes_gtdb.txt
[2023-03-16 07:57:51,240] [INFO] Task started: fastANI
[2023-03-16 07:57:51,240] [INFO] Running command: fastANI --query /var/lib/cwl/stg93f90df5-8913-4632-bc02-23f848476a98/OceanDNA-b31056.fa --refList OceanDNA-b31056/target_genomes_gtdb.txt --output OceanDNA-b31056/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:58:08,738] [INFO] Task succeeded: fastANI
[2023-03-16 07:58:08,751] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 07:58:08,751] [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_018674495.1	s__GCA-2687515 sp018674495	99.7835	1411	1482	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UBA2165;g__GCA-2687515	95.0	99.77	99.72	0.95	0.94	13	conclusive
GCA_002687515.1	s__GCA-2687515 sp002687515	79.7697	663	1482	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UBA2165;g__GCA-2687515	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013204125.1	s__JABMOP01 sp013204125	77.2223	283	1482	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UBA2165;g__JABMOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650635.1	s__Magnetospirillum moscoviense	76.0942	122	1482	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	96.81	95.25	0.84	0.84	3	-
GCA_015232485.1	s__JADFZP01 sp015232485	76.0786	92	1482	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	96.70	95.97	0.70	0.69	3	-
GCA_015232025.1	s__JADFZP01 sp015232025	76.0585	86	1482	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015231795.1	s__WMHbin7 sp015231795	76.0583	89	1482	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__WMHbin7;g__WMHbin7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002325375.1	s__UBA1479 sp002325375	75.9939	112	1482	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_002725625.1	s__GCA-2725625 sp002725625	75.9066	96	1482	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UBA2165;g__GCA-2725625	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002105535.1	s__Phaeospirillum sp002105535	75.8949	127	1482	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001511835.1	s__Phaeospirillum sp001511835	75.8814	144	1482	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000968135.1	s__Magnetospira sp000968135	75.8695	101	1482	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospiraceae;g__Magnetospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002696205.1	s__UBA1479 sp002696205	75.8692	95	1482	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	75.8665	102	1482	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_002327565.1	s__UBA2165 sp002327565	75.8506	102	1482	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UBA2165;g__UBA2165	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001618175.1	s__Oceanibaculum pacificum	75.7529	117	1482	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016195145.1	s__JACQAF01 sp016195145	75.7448	70	1482	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__JACQAF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101965.1	s__Rhodospira trueperi	75.6259	81	1482	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018671895.1	s__JABHGV01 sp018671895	75.6091	53	1482	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_016212565.1	s__JACRFY01 sp016212565	75.582	105	1482	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JACRFY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003550065.1	s__Sphingomonas caeni	75.408	67	1482	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826565.1	s__CADEFF01 sp902826565	75.3545	79	1482	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__CADEFF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 07:58:08,758] [INFO] GTDB search result was written to OceanDNA-b31056/result_gtdb.tsv
[2023-03-16 07:58:08,758] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:58:08,761] [INFO] DFAST_QC result json was written to OceanDNA-b31056/dqc_result.json
[2023-03-16 07:58:08,761] [INFO] DFAST_QC completed!
[2023-03-16 07:58:08,761] [INFO] Total running time: 0h2m24s