[2023-03-18 06:02:58,281] [INFO] DFAST_QC pipeline started.
[2023-03-18 06:02:58,281] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 06:02:58,281] [INFO] DQC Reference Directory: /var/lib/cwl/stgb88e4960-45c8-49f6-bd40-415b45af915d/dqc_reference
[2023-03-18 06:03:00,169] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 06:03:00,171] [INFO] Task started: Prodigal
[2023-03-18 06:03:00,171] [INFO] Running command: cat /var/lib/cwl/stg5d373d92-bd40-4afe-af18-0c6d14723f00/OceanDNA-b29498.fa | prodigal -d OceanDNA-b29498/cds.fna -a OceanDNA-b29498/protein.faa -g 11 -q > /dev/null
[2023-03-18 06:03:16,507] [INFO] Task succeeded: Prodigal
[2023-03-18 06:03:16,507] [INFO] Task started: HMMsearch
[2023-03-18 06:03:16,507] [INFO] Running command: hmmsearch --tblout OceanDNA-b29498/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb88e4960-45c8-49f6-bd40-415b45af915d/dqc_reference/reference_markers.hmm OceanDNA-b29498/protein.faa > /dev/null
[2023-03-18 06:03:16,693] [INFO] Task succeeded: HMMsearch
[2023-03-18 06:03:16,694] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5d373d92-bd40-4afe-af18-0c6d14723f00/OceanDNA-b29498.fa]
[2023-03-18 06:03:16,714] [INFO] Query marker FASTA was written to OceanDNA-b29498/markers.fasta
[2023-03-18 06:03:16,715] [INFO] Task started: Blastn
[2023-03-18 06:03:16,715] [INFO] Running command: blastn -query OceanDNA-b29498/markers.fasta -db /var/lib/cwl/stgb88e4960-45c8-49f6-bd40-415b45af915d/dqc_reference/reference_markers.fasta -out OceanDNA-b29498/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:03:17,441] [INFO] Task succeeded: Blastn
[2023-03-18 06:03:17,442] [INFO] Selected 30 target genomes.
[2023-03-18 06:03:17,442] [INFO] Target genome list was writen to OceanDNA-b29498/target_genomes.txt
[2023-03-18 06:03:17,677] [INFO] Task started: fastANI
[2023-03-18 06:03:17,677] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d373d92-bd40-4afe-af18-0c6d14723f00/OceanDNA-b29498.fa --refList OceanDNA-b29498/target_genomes.txt --output OceanDNA-b29498/fastani_result.tsv --threads 1
[2023-03-18 06:03:37,134] [INFO] Task succeeded: fastANI
[2023-03-18 06:03:37,134] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb88e4960-45c8-49f6-bd40-415b45af915d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 06:03:37,134] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb88e4960-45c8-49f6-bd40-415b45af915d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 06:03:37,150] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 06:03:37,150] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 06:03:37,150] [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
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	77.8586	365	805	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	77.4285	299	805	95	below_threshold
Roseovarius marisflavi	strain=DSM 29327	GCA_900142625.1	1054996	1054996	type	True	77.2759	248	805	95	below_threshold
Roseovarius lutimaris	strain=DSM 28463	GCA_900115165.1	1005928	1005928	type	True	77.2042	234	805	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	77.1866	312	805	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.1639	232	805	95	below_threshold
Roseovarius gaetbuli	strain=CECT 8370	GCA_900172365.1	1356575	1356575	type	True	77.1631	258	805	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	77.1348	232	805	95	below_threshold
Antarcticimicrobium sediminis	strain=S4J41	GCA_004348975.1	2546227	2546227	type	True	77.1159	254	805	95	below_threshold
Roseovarius faecimaris	strain=MME-070	GCA_009762325.1	2494550	2494550	type	True	77.0244	245	805	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	76.9865	253	805	95	below_threshold
Pseudodonghicola xiamenensis	strain=DSM 18339	GCA_000429365.1	337702	337702	type	True	76.763	207	805	95	below_threshold
Oceaniglobus trochenteri	strain=G4	GCA_020529025.1	2763260	2763260	type	True	76.7599	197	805	95	below_threshold
Pelagivirga dicentrarchi	strain=YLY04	GCA_003316635.1	2250573	2250573	type	True	76.7032	207	805	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_000520135.2	35806	35806	type	True	76.6871	160	805	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_001633165.1	35806	35806	type	True	76.6845	166	805	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	76.6388	206	805	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	76.6387	208	805	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	76.5841	198	805	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	76.5736	190	805	95	below_threshold
Aliishimia ponticola	strain=MYP11	GCA_004803475.1	2499833	2499833	type	True	76.5471	179	805	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.4485	139	805	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	76.4312	130	805	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	76.4294	149	805	95	below_threshold
Roseovarius aestuarii	strain=KCTC 22174	GCA_019966515.1	475083	475083	type	True	76.4249	166	805	95	below_threshold
Paracoccus subflavus	strain=GY0581	GCA_004310345.1	2528244	2528244	type	True	76.3739	100	805	95	below_threshold
Roseivivax lentus	strain=DSM 29430	GCA_900156805.1	633194	633194	type	True	76.3082	190	805	95	below_threshold
Paracoccus aminophilus	strain=JCM 7686	GCA_000444995.1	34003	34003	type	True	76.305	104	805	95	below_threshold
Paracoccus denitrificans	strain=DSM 413	GCA_900100045.1	266	266	type	True	76.2954	153	805	95	below_threshold
Paracoccus denitrificans	strain=NBRC 102528	GCA_007989485.1	266	266	type	True	76.2651	150	805	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 06:03:37,151] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29498/tc_result.tsv
[2023-03-18 06:03:37,151] [INFO] ===== Taxonomy check completed =====
[2023-03-18 06:03:37,151] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 06:03:37,151] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb88e4960-45c8-49f6-bd40-415b45af915d/dqc_reference/checkm_data
[2023-03-18 06:03:37,152] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 06:03:37,167] [INFO] Task started: CheckM
[2023-03-18 06:03:37,167] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29498/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29498/checkm_input OceanDNA-b29498/checkm_result
[2023-03-18 06:04:19,600] [INFO] Task succeeded: CheckM
[2023-03-18 06:04:19,600] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.52%
Contamintation: 6.25%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-18 06:04:19,603] [INFO] ===== Completeness check finished =====
[2023-03-18 06:04:19,603] [INFO] ===== Start GTDB Search =====
[2023-03-18 06:04:19,603] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29498/markers.fasta)
[2023-03-18 06:04:19,604] [INFO] Task started: Blastn
[2023-03-18 06:04:19,604] [INFO] Running command: blastn -query OceanDNA-b29498/markers.fasta -db /var/lib/cwl/stgb88e4960-45c8-49f6-bd40-415b45af915d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29498/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:04:20,949] [INFO] Task succeeded: Blastn
[2023-03-18 06:04:21,024] [INFO] Selected 23 target genomes.
[2023-03-18 06:04:21,024] [INFO] Target genome list was writen to OceanDNA-b29498/target_genomes_gtdb.txt
[2023-03-18 06:04:21,913] [INFO] Task started: fastANI
[2023-03-18 06:04:21,913] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d373d92-bd40-4afe-af18-0c6d14723f00/OceanDNA-b29498.fa --refList OceanDNA-b29498/target_genomes_gtdb.txt --output OceanDNA-b29498/fastani_result_gtdb.tsv --threads 1
[2023-03-18 06:04:37,025] [INFO] Task succeeded: fastANI
[2023-03-18 06:04:37,038] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 06:04:37,038] [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_009924775.1	s__Lutimaribacter sp009924775	90.159	622	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	78.3509	416	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000526275.1	s__Lutimaribacter sp000526275	77.907	386	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100005.1	s__Lutimaribacter saemankumensis	77.8519	365	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	77.4078	302	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182725.1	s__Thalassobius litoralis	77.3578	287	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002285435.1	s__Actibacterium ureilyticum	77.3166	261	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115165.1	s__Roseovarius lutimaris	77.1942	234	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172365.1	s__Roseovarius gaetbuli	77.1326	260	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744955.1	s__Actibacterium sp000744955	77.1249	237	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348975.1	s__Antarcticimicrobium sediminis	77.0951	256	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002158905.1	s__Yoonia vestfoldensis_B	76.9831	227	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401965.1	s__Roseicyclus sp018401965	76.9623	189	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003316635.1	s__Roseovarius dicentrarchi	76.7116	205	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001482405.1	s__Ponticoccus marisrubri	76.6584	237	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ponticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	76.6277	209	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_018224955.1	s__Aestuariicoccus sp018224955	76.6115	215	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011048875.1	s__Rhodovulum sp011048875	76.5053	139	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342445.1	s__Rhodovulum euryhalinum	76.4294	149	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172285.1	s__Roseovarius aestuarii	76.4264	166	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156805.1	s__Roseivivax lentus	76.318	189	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100045.1	s__Paracoccus denitrificans	76.2921	155	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.78	98.70	0.97	0.88	7	-
GCA_015491895.1	s__WFVA01 sp015491895	76.2441	136	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__WFVA01	95.0	99.60	99.57	0.92	0.91	3	-
--------------------------------------------------------------------------------
[2023-03-18 06:04:37,038] [INFO] GTDB search result was written to OceanDNA-b29498/result_gtdb.tsv
[2023-03-18 06:04:37,039] [INFO] ===== GTDB Search completed =====
[2023-03-18 06:04:37,041] [INFO] DFAST_QC result json was written to OceanDNA-b29498/dqc_result.json
[2023-03-18 06:04:37,041] [INFO] DFAST_QC completed!
[2023-03-18 06:04:37,041] [INFO] Total running time: 0h1m39s