[2023-03-15 09:25:29,060] [INFO] DFAST_QC pipeline started.
[2023-03-15 09:25:29,060] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 09:25:29,060] [INFO] DQC Reference Directory: /var/lib/cwl/stgab28470e-b1eb-410a-b81b-428e92341015/dqc_reference
[2023-03-15 09:25:30,383] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 09:25:30,383] [INFO] Task started: Prodigal
[2023-03-15 09:25:30,383] [INFO] Running command: cat /var/lib/cwl/stg722d623c-5729-4464-a8b9-06d2612af6bf/OceanDNA-b28228.fa | prodigal -d OceanDNA-b28228/cds.fna -a OceanDNA-b28228/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:25:54,290] [INFO] Task succeeded: Prodigal
[2023-03-15 09:25:54,290] [INFO] Task started: HMMsearch
[2023-03-15 09:25:54,290] [INFO] Running command: hmmsearch --tblout OceanDNA-b28228/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab28470e-b1eb-410a-b81b-428e92341015/dqc_reference/reference_markers.hmm OceanDNA-b28228/protein.faa > /dev/null
[2023-03-15 09:25:54,499] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:25:54,500] [INFO] Found 6/6 markers.
[2023-03-15 09:25:54,523] [INFO] Query marker FASTA was written to OceanDNA-b28228/markers.fasta
[2023-03-15 09:25:54,524] [INFO] Task started: Blastn
[2023-03-15 09:25:54,524] [INFO] Running command: blastn -query OceanDNA-b28228/markers.fasta -db /var/lib/cwl/stgab28470e-b1eb-410a-b81b-428e92341015/dqc_reference/reference_markers.fasta -out OceanDNA-b28228/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:25:55,338] [INFO] Task succeeded: Blastn
[2023-03-15 09:25:55,339] [INFO] Selected 30 target genomes.
[2023-03-15 09:25:55,339] [INFO] Target genome list was writen to OceanDNA-b28228/target_genomes.txt
[2023-03-15 09:25:55,355] [INFO] Task started: fastANI
[2023-03-15 09:25:55,355] [INFO] Running command: fastANI --query /var/lib/cwl/stg722d623c-5729-4464-a8b9-06d2612af6bf/OceanDNA-b28228.fa --refList OceanDNA-b28228/target_genomes.txt --output OceanDNA-b28228/fastani_result.tsv --threads 1
[2023-03-15 09:26:17,228] [INFO] Task succeeded: fastANI
[2023-03-15 09:26:17,228] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab28470e-b1eb-410a-b81b-428e92341015/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:26:17,229] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab28470e-b1eb-410a-b81b-428e92341015/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:26:17,244] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 09:26:17,244] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 09:26:17,245] [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
Puniceibacterium antarcticum	strain=SM1211	GCA_002760615.1	1206336	1206336	type	True	78.4115	347	1230	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	78.3409	363	1230	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	78.0858	371	1230	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	78.0668	330	1230	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	78.0467	378	1230	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	77.9907	428	1230	95	below_threshold
Yoonia vestfoldensis	strain=DSM 16212	GCA_000382265.1	245188	245188	type	True	77.9234	355	1230	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.8781	406	1230	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	77.8671	329	1230	95	below_threshold
Pacificitalea manganoxidans	strain=DY25	GCA_002504165.1	1411902	1411902	type	True	77.8435	265	1230	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	77.8035	341	1230	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.7864	252	1230	95	below_threshold
Roseovarius lutimaris	strain=DSM 28463	GCA_900115165.1	1005928	1005928	type	True	77.7786	365	1230	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	77.7337	357	1230	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	77.7152	401	1230	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.7095	281	1230	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	77.7036	397	1230	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	77.6711	370	1230	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	77.6305	400	1230	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	77.6125	341	1230	95	below_threshold
Roseovarius tolerans	strain=DSM 11457	GCA_900109855.1	74031	74031	type	True	77.6056	368	1230	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_900112725.1	540747	540747	type	True	77.5955	339	1230	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	77.5562	342	1230	95	below_threshold
Roseovarius gaetbuli	strain=CECT 8370	GCA_900172365.1	1356575	1356575	type	True	77.5526	335	1230	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.5015	311	1230	95	below_threshold
Roseovarius marisflavi	strain=DSM 29327	GCA_900142625.1	1054996	1054996	type	True	77.4755	350	1230	95	below_threshold
Roseovarius faecimaris	strain=MME-070	GCA_009762325.1	2494550	2494550	type	True	77.4326	327	1230	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.3932	283	1230	95	below_threshold
Puniceibacterium confluentis	strain=JSSK-17	GCA_007923445.1	1958944	1958944	type	True	77.2484	310	1230	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	77.0029	268	1230	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 09:26:17,245] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28228/tc_result.tsv
[2023-03-15 09:26:17,245] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:26:17,245] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:26:17,245] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab28470e-b1eb-410a-b81b-428e92341015/dqc_reference/checkm_data
[2023-03-15 09:26:17,246] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:26:17,268] [INFO] Task started: CheckM
[2023-03-15 09:26:17,268] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28228/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28228/checkm_input OceanDNA-b28228/checkm_result
[2023-03-15 09:27:17,452] [INFO] Task succeeded: CheckM
[2023-03-15 09:27:17,452] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 09:27:17,455] [INFO] ===== Completeness check finished =====
[2023-03-15 09:27:17,455] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:27:17,455] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28228/markers.fasta)
[2023-03-15 09:27:17,456] [INFO] Task started: Blastn
[2023-03-15 09:27:17,456] [INFO] Running command: blastn -query OceanDNA-b28228/markers.fasta -db /var/lib/cwl/stgab28470e-b1eb-410a-b81b-428e92341015/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28228/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:27:19,013] [INFO] Task succeeded: Blastn
[2023-03-15 09:27:19,049] [INFO] Selected 24 target genomes.
[2023-03-15 09:27:19,049] [INFO] Target genome list was writen to OceanDNA-b28228/target_genomes_gtdb.txt
[2023-03-15 09:27:19,465] [INFO] Task started: fastANI
[2023-03-15 09:27:19,465] [INFO] Running command: fastANI --query /var/lib/cwl/stg722d623c-5729-4464-a8b9-06d2612af6bf/OceanDNA-b28228.fa --refList OceanDNA-b28228/target_genomes_gtdb.txt --output OceanDNA-b28228/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:27:37,494] [INFO] Task succeeded: fastANI
[2023-03-15 09:27:37,507] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 09:27:37,507] [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_002282555.1	s__EhC02 sp002282555	82.1101	379	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__EhC02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001650895.1	s__EhC02 sp001650895	81.9765	807	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__EhC02	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	78.6351	489	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002366795.1	s__UBA3069 sp002366795	78.0763	393	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3069	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016758075.1	s__CAU-1492 sp016758075	78.0323	305	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1492	95.0	99.98	99.98	0.95	0.95	2	-
GCF_009857745.1	s__Thalassobius mangrovi	77.9803	430	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002158905.1	s__Yoonia vestfoldensis_B	77.9152	350	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382265.1	s__Yoonia vestfoldensis	77.906	356	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100085.1	s__Salipiger marinus	77.8767	404	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.13	98.13	0.95	0.95	2	-
GCF_900129345.1	s__Ruegeria intermedia	77.833	331	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507595.1	s__Ruegeria marisrubri	77.8049	340	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402175.1	s__Yoonia sp018402175	77.7581	326	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	95.02	95.02	0.81	0.81	2	-
GCF_018219815.1	s__Thalassobius aquimarinus	77.7149	401	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	77.7103	396	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	-
GCF_002210105.1	s__Pseudooceanicola sp002210105	77.7099	330	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	77.6932	319	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	77.6385	399	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000161775.1	s__Ruegeria lacuscaerulensis	77.6276	326	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_008728195.1	s__Roseovarius indicus	77.6125	341	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.18	97.54	0.97	0.92	4	-
GCF_900142625.1	s__Roseovarius marisflavi	77.4849	348	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018224955.1	s__Aestuariicoccus sp018224955	77.4417	379	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352045.1	s__JL08 sp003352045	77.3377	273	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JL08	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032025.1	s__Ruegeria atlantica_C	77.105	226	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	100.00	100.00	0.99	0.99	2	-
GCF_009827095.1	s__Pseudooceanicola sp009827095	76.9837	271	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2023-03-15 09:27:37,508] [INFO] GTDB search result was written to OceanDNA-b28228/result_gtdb.tsv
[2023-03-15 09:27:37,508] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:27:37,510] [INFO] DFAST_QC result json was written to OceanDNA-b28228/dqc_result.json
[2023-03-15 09:27:37,511] [INFO] DFAST_QC completed!
[2023-03-15 09:27:37,511] [INFO] Total running time: 0h2m8s