[2023-03-16 08:22:25,420] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:22:25,421] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:22:25,421] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b245b46-c264-4ba8-afcb-6075e9420694/dqc_reference
[2023-03-16 08:22:27,102] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:22:27,103] [INFO] Task started: Prodigal
[2023-03-16 08:22:27,103] [INFO] Running command: cat /var/lib/cwl/stg9f321ab9-6a74-4688-aed0-82ed9c897d3b/OceanDNA-b27597.fa | prodigal -d OceanDNA-b27597/cds.fna -a OceanDNA-b27597/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:22:45,895] [INFO] Task succeeded: Prodigal
[2023-03-16 08:22:45,896] [INFO] Task started: HMMsearch
[2023-03-16 08:22:45,896] [INFO] Running command: hmmsearch --tblout OceanDNA-b27597/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b245b46-c264-4ba8-afcb-6075e9420694/dqc_reference/reference_markers.hmm OceanDNA-b27597/protein.faa > /dev/null
[2023-03-16 08:22:46,086] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:22:46,087] [INFO] Found 6/6 markers.
[2023-03-16 08:22:46,117] [INFO] Query marker FASTA was written to OceanDNA-b27597/markers.fasta
[2023-03-16 08:22:46,118] [INFO] Task started: Blastn
[2023-03-16 08:22:46,118] [INFO] Running command: blastn -query OceanDNA-b27597/markers.fasta -db /var/lib/cwl/stg2b245b46-c264-4ba8-afcb-6075e9420694/dqc_reference/reference_markers.fasta -out OceanDNA-b27597/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:22:46,709] [INFO] Task succeeded: Blastn
[2023-03-16 08:22:46,712] [INFO] Selected 26 target genomes.
[2023-03-16 08:22:46,712] [INFO] Target genome list was writen to OceanDNA-b27597/target_genomes.txt
[2023-03-16 08:22:46,729] [INFO] Task started: fastANI
[2023-03-16 08:22:46,729] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f321ab9-6a74-4688-aed0-82ed9c897d3b/OceanDNA-b27597.fa --refList OceanDNA-b27597/target_genomes.txt --output OceanDNA-b27597/fastani_result.tsv --threads 1
[2023-03-16 08:23:02,587] [INFO] Task succeeded: fastANI
[2023-03-16 08:23:02,587] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b245b46-c264-4ba8-afcb-6075e9420694/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:23:02,587] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b245b46-c264-4ba8-afcb-6075e9420694/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:23:02,601] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:23:02,601] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 08:23:02,602] [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
Nioella ostreopsis	strain=Z7-4	GCA_004000255.1	2448479	2448479	type	True	76.3786	140	977	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	76.3373	85	977	95	below_threshold
Rhodophyticola porphyridii	strain=MA-7-27	GCA_003688285.1	1852017	1852017	type	True	76.2819	150	977	95	below_threshold
Litoreibacter halocynthiae	strain=DSM 29467	GCA_004365635.1	1242689	1242689	type	True	76.2642	84	977	95	below_threshold
Pelagivirga dicentrarchi	strain=YLY04	GCA_003316635.1	2250573	2250573	type	True	76.2421	83	977	95	below_threshold
Nioella nitratireducens	strain=SSW136	GCA_001879715.1	1287720	1287720	type	True	76.2063	121	977	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.2009	71	977	95	below_threshold
Nioella sediminis	strain=JS7-11	GCA_001879695.1	1912092	1912092	type	True	76.1959	134	977	95	below_threshold
Aliishimia ponticola	strain=MYP11	GCA_004803475.1	2499833	2499833	type	True	76.1911	85	977	95	below_threshold
Litoreibacter ponti	strain=DSM 100977	GCA_003054285.1	1510457	1510457	type	True	76.1746	83	977	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	76.1654	92	977	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	76.153	87	977	95	below_threshold
Ruegeria meonggei	strain=CECT 8411	GCA_900172215.1	1446476	1446476	type	True	76.1139	80	977	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	76.1095	92	977	95	below_threshold
Pacificitalea manganoxidans	strain=DY25	GCA_002504165.1	1411902	1411902	type	True	76.1084	72	977	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	76.0732	93	977	95	below_threshold
Pelagicola litoralis	strain=CL-ES2	GCA_005518135.1	420403	420403	type	True	76.0134	54	977	95	below_threshold
Ruegeria profundi	strain=ZGT108	GCA_001507545.1	1685378	1685378	type	True	75.9333	67	977	95	below_threshold
Profundibacter amoris	strain=BAR1	GCA_003544895.1	2171755	2171755	type	True	75.9299	87	977	95	below_threshold
Pseudophaeobacter arcticus	strain=DSM 23566	GCA_000473205.1	385492	385492	type	True	75.9177	100	977	95	below_threshold
Litoreibacter albidus	strain=DSM 26922	GCA_900107015.1	670155	670155	type	True	75.904	77	977	95	below_threshold
Roseovarius tolerans	strain=DSM 11457	GCA_900109855.1	74031	74031	type	True	75.8778	74	977	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	75.8743	66	977	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	75.7635	82	977	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	75.6872	74	977	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 08:23:02,612] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27597/tc_result.tsv
[2023-03-16 08:23:02,628] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:23:02,628] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:23:02,628] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b245b46-c264-4ba8-afcb-6075e9420694/dqc_reference/checkm_data
[2023-03-16 08:23:02,629] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:23:02,660] [INFO] Task started: CheckM
[2023-03-16 08:23:02,660] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27597/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27597/checkm_input OceanDNA-b27597/checkm_result
[2023-03-16 08:23:51,280] [INFO] Task succeeded: CheckM
[2023-03-16 08:23:51,281] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 08:23:51,284] [INFO] ===== Completeness check finished =====
[2023-03-16 08:23:51,284] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:23:51,284] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27597/markers.fasta)
[2023-03-16 08:23:51,285] [INFO] Task started: Blastn
[2023-03-16 08:23:51,285] [INFO] Running command: blastn -query OceanDNA-b27597/markers.fasta -db /var/lib/cwl/stg2b245b46-c264-4ba8-afcb-6075e9420694/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27597/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:23:52,147] [INFO] Task succeeded: Blastn
[2023-03-16 08:23:52,149] [INFO] Selected 28 target genomes.
[2023-03-16 08:23:52,149] [INFO] Target genome list was writen to OceanDNA-b27597/target_genomes_gtdb.txt
[2023-03-16 08:23:52,175] [INFO] Task started: fastANI
[2023-03-16 08:23:52,175] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f321ab9-6a74-4688-aed0-82ed9c897d3b/OceanDNA-b27597.fa --refList OceanDNA-b27597/target_genomes_gtdb.txt --output OceanDNA-b27597/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:24:08,637] [INFO] Task succeeded: fastANI
[2023-03-16 08:24:08,651] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 08:24:08,651] [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_900172365.1	s__Roseovarius gaetbuli	76.5059	106	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017644125.1	s__Rhodophyticola sp017644125	76.396	156	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodophyticola	95.0	99.99	99.99	0.99	0.98	3	-
GCF_004000255.1	s__Nioella ostreopsis	76.3786	140	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017854585.1	s__JAFMHK01 sp017854585	76.3532	126	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAFMHK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007827395.1	s__Rhodophyticola sp007827395	76.3158	155	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodophyticola	95.0	95.40	95.35	0.93	0.92	216	-
GCF_003688285.1	s__Rhodophyticola porphyridii	76.2819	150	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodophyticola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001879715.1	s__Nioella nitratireducens	76.2063	121	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004000435.1	s__Flavimaricola sp004000435	76.2009	71	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Flavimaricola	95.0	99.99	99.97	0.99	0.98	36	-
GCF_001879695.1	s__Nioella sediminis	76.1959	134	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_009857745.1	s__Thalassobius mangrovi	76.1654	92	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018219815.1	s__Thalassobius aquimarinus	76.153	87	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069895.1	s__Roseovarius sp018069895	76.1474	53	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.42	99.42	0.86	0.86	2	-
GCF_004358185.1	s__Antarcticimicrobium luteum	76.1279	91	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032455.1	s__Ruegeria atlantica_B	76.0954	77	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	98.37	96.74	0.95	0.90	3	-
GCF_013155465.1	s__Alterinioella nitratireducens	76.0276	135	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Alterinioella	95.0	97.91	97.83	0.91	0.91	3	-
GCF_013032095.1	s__Ruegeria atlantica_E	76.0079	88	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003428585.1	s__Nioella sp003428585	75.9802	98	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743995.1	s__Ruegeria sp017743995	75.9479	89	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003544895.1	s__Profundibacter amoris	75.9299	87	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109855.1	s__Roseovarius tolerans	75.8778	74	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.73	96.73	0.86	0.86	2	-
GCF_001294455.1	s__Pseudophaeobacter sp001294455	75.656	76	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	98.13	98.13	0.97	0.97	2	-
GCF_003651245.1	s__Roseovarius spongiae	75.5482	63	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689705.1	s__HKCCE3408 sp015689705	75.5471	79	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HKCCE3408	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842985.1	s__Roseovarius sp002842985	75.4649	66	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014323785.1	s__Rhodophyticola sp014323785	75.4368	71	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodophyticola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 08:24:08,651] [INFO] GTDB search result was written to OceanDNA-b27597/result_gtdb.tsv
[2023-03-16 08:24:08,652] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:24:08,654] [INFO] DFAST_QC result json was written to OceanDNA-b27597/dqc_result.json
[2023-03-16 08:24:08,654] [INFO] DFAST_QC completed!
[2023-03-16 08:24:08,654] [INFO] Total running time: 0h1m43s