[2023-03-19 00:15:41,729] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:15:41,730] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:15:41,730] [INFO] DQC Reference Directory: /var/lib/cwl/stg7dffe6d5-62a9-434d-b868-591ee85dbabf/dqc_reference
[2023-03-19 00:15:43,438] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:15:43,439] [INFO] Task started: Prodigal
[2023-03-19 00:15:43,439] [INFO] Running command: cat /var/lib/cwl/stg137b9f7e-e7d7-4206-9a15-1a2cdbc48a9c/OceanDNA-b30095.fa | prodigal -d OceanDNA-b30095/cds.fna -a OceanDNA-b30095/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:16:04,884] [INFO] Task succeeded: Prodigal
[2023-03-19 00:16:04,884] [INFO] Task started: HMMsearch
[2023-03-19 00:16:04,884] [INFO] Running command: hmmsearch --tblout OceanDNA-b30095/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7dffe6d5-62a9-434d-b868-591ee85dbabf/dqc_reference/reference_markers.hmm OceanDNA-b30095/protein.faa > /dev/null
[2023-03-19 00:16:05,093] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:16:05,094] [INFO] Found 6/6 markers.
[2023-03-19 00:16:05,114] [INFO] Query marker FASTA was written to OceanDNA-b30095/markers.fasta
[2023-03-19 00:16:05,116] [INFO] Task started: Blastn
[2023-03-19 00:16:05,116] [INFO] Running command: blastn -query OceanDNA-b30095/markers.fasta -db /var/lib/cwl/stg7dffe6d5-62a9-434d-b868-591ee85dbabf/dqc_reference/reference_markers.fasta -out OceanDNA-b30095/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:16:05,962] [INFO] Task succeeded: Blastn
[2023-03-19 00:16:05,963] [INFO] Selected 16 target genomes.
[2023-03-19 00:16:05,963] [INFO] Target genome list was writen to OceanDNA-b30095/target_genomes.txt
[2023-03-19 00:16:05,975] [INFO] Task started: fastANI
[2023-03-19 00:16:05,975] [INFO] Running command: fastANI --query /var/lib/cwl/stg137b9f7e-e7d7-4206-9a15-1a2cdbc48a9c/OceanDNA-b30095.fa --refList OceanDNA-b30095/target_genomes.txt --output OceanDNA-b30095/fastani_result.tsv --threads 1
[2023-03-19 00:16:18,960] [INFO] Task succeeded: fastANI
[2023-03-19 00:16:18,960] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7dffe6d5-62a9-434d-b868-591ee85dbabf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:16:18,960] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7dffe6d5-62a9-434d-b868-591ee85dbabf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:16:18,970] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2023-03-19 00:16:18,970] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-19 00:16:18,971] [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
Roseovarius halotolerans	strain=CECT 8110	GCA_900172255.1	505353	505353	type	True	99.176	1072	1116	95	conclusive
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	99.1722	1071	1116	95	conclusive
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	82.3281	741	1116	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	81.8696	735	1116	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	81.8691	749	1116	95	below_threshold
Roseovarius bejariae	strain=A21	GCA_009669325.1	2576383	2576383	type	True	79.717	606	1116	95	below_threshold
Roseovarius gahaiensis	strain=GH877	GCA_011601345.1	2716691	2716691	type	True	79.549	556	1116	95	below_threshold
Roseovarius confluentis	strain=SAG6	GCA_002917925.1	1852027	1852027	type	True	79.4823	583	1116	95	below_threshold
Roseovarius nubinhibens	strain=ISM	GCA_000152625.1	314263	314263	type	True	79.0536	553	1116	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.7132	441	1116	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.2747	486	1116	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	78.2491	454	1116	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	78.0847	431	1116	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.8603	363	1116	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	77.5879	381	1116	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	76.9822	276	1116	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:16:18,971] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30095/tc_result.tsv
[2023-03-19 00:16:18,971] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:16:18,971] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:16:18,972] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7dffe6d5-62a9-434d-b868-591ee85dbabf/dqc_reference/checkm_data
[2023-03-19 00:16:18,972] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:16:19,006] [INFO] Task started: CheckM
[2023-03-19 00:16:19,007] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30095/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30095/checkm_input OceanDNA-b30095/checkm_result
[2023-03-19 00:17:15,195] [INFO] Task succeeded: CheckM
[2023-03-19 00:17:15,196] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:17:15,199] [INFO] ===== Completeness check finished =====
[2023-03-19 00:17:15,199] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:17:15,199] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30095/markers.fasta)
[2023-03-19 00:17:15,200] [INFO] Task started: Blastn
[2023-03-19 00:17:15,200] [INFO] Running command: blastn -query OceanDNA-b30095/markers.fasta -db /var/lib/cwl/stg7dffe6d5-62a9-434d-b868-591ee85dbabf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30095/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:17:16,771] [INFO] Task succeeded: Blastn
[2023-03-19 00:17:16,772] [INFO] Selected 15 target genomes.
[2023-03-19 00:17:16,772] [INFO] Target genome list was writen to OceanDNA-b30095/target_genomes_gtdb.txt
[2023-03-19 00:17:16,791] [INFO] Task started: fastANI
[2023-03-19 00:17:16,791] [INFO] Running command: fastANI --query /var/lib/cwl/stg137b9f7e-e7d7-4206-9a15-1a2cdbc48a9c/OceanDNA-b30095.fa --refList OceanDNA-b30095/target_genomes_gtdb.txt --output OceanDNA-b30095/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:17:28,460] [INFO] Task succeeded: fastANI
[2023-03-19 00:17:28,469] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:17:28,469] [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_900172255.1	s__Roseovarius halotolerans	99.176	1072	1116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900142765.1	s__Roseovarius litoreus	82.3176	742	1116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	95.85	95.85	0.86	0.86	2	-
GCF_900142665.1	s__Roseovarius pacificus	81.8595	736	1116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.52	95.05	0.91	0.82	3	-
GCF_008728195.1	s__Roseovarius indicus	79.8851	648	1116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.18	97.54	0.97	0.92	4	-
GCF_900142185.1	s__Lutimaribacter pacificus	79.7011	592	1116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009669325.1	s__Roseovarius bejariae	79.7006	608	1116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011601345.1	s__Roseovarius gahaiensis	79.549	556	1116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002917925.1	s__Roseovarius confluentis	79.4895	584	1116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.93	98.93	0.93	0.93	2	-
GCF_003651245.1	s__Roseovarius spongiae	79.4396	555	1116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002166865.1	s__Roseovarius sp002166865	79.4364	568	1116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	79.1843	509	1116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002834145.1	s__Roseovarius salinarum	79.0552	534	1116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314705.1	s__Aquicoccus sp001314705	78.9342	448	1116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aquicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012395815.1	s__Roseicyclus sp012395815	78.0373	406	1116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401055.1	s__Roseicyclus sp018401055	77.7249	271	1116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:17:28,469] [INFO] GTDB search result was written to OceanDNA-b30095/result_gtdb.tsv
[2023-03-19 00:17:28,469] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:17:28,471] [INFO] DFAST_QC result json was written to OceanDNA-b30095/dqc_result.json
[2023-03-19 00:17:28,471] [INFO] DFAST_QC completed!
[2023-03-19 00:17:28,471] [INFO] Total running time: 0h1m47s