[2023-03-18 01:18:16,273] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:18:16,282] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:18:16,282] [INFO] DQC Reference Directory: /var/lib/cwl/stg74ed9bf3-0575-4138-b2b6-234a67344e6c/dqc_reference
[2023-03-18 01:18:18,216] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:18:18,217] [INFO] Task started: Prodigal
[2023-03-18 01:18:18,217] [INFO] Running command: cat /var/lib/cwl/stgdf232e4e-194c-47a2-93b6-56fadafa50e7/OceanDNA-b30090.fa | prodigal -d OceanDNA-b30090/cds.fna -a OceanDNA-b30090/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:18:41,203] [INFO] Task succeeded: Prodigal
[2023-03-18 01:18:41,204] [INFO] Task started: HMMsearch
[2023-03-18 01:18:41,204] [INFO] Running command: hmmsearch --tblout OceanDNA-b30090/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74ed9bf3-0575-4138-b2b6-234a67344e6c/dqc_reference/reference_markers.hmm OceanDNA-b30090/protein.faa > /dev/null
[2023-03-18 01:18:41,413] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:18:41,414] [INFO] Found 6/6 markers.
[2023-03-18 01:18:41,436] [INFO] Query marker FASTA was written to OceanDNA-b30090/markers.fasta
[2023-03-18 01:18:41,439] [INFO] Task started: Blastn
[2023-03-18 01:18:41,439] [INFO] Running command: blastn -query OceanDNA-b30090/markers.fasta -db /var/lib/cwl/stg74ed9bf3-0575-4138-b2b6-234a67344e6c/dqc_reference/reference_markers.fasta -out OceanDNA-b30090/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:18:42,384] [INFO] Task succeeded: Blastn
[2023-03-18 01:18:42,385] [INFO] Selected 22 target genomes.
[2023-03-18 01:18:42,385] [INFO] Target genome list was writen to OceanDNA-b30090/target_genomes.txt
[2023-03-18 01:18:42,428] [INFO] Task started: fastANI
[2023-03-18 01:18:42,428] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf232e4e-194c-47a2-93b6-56fadafa50e7/OceanDNA-b30090.fa --refList OceanDNA-b30090/target_genomes.txt --output OceanDNA-b30090/fastani_result.tsv --threads 1
[2023-03-18 01:19:00,776] [INFO] Task succeeded: fastANI
[2023-03-18 01:19:00,776] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74ed9bf3-0575-4138-b2b6-234a67344e6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:19:00,777] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74ed9bf3-0575-4138-b2b6-234a67344e6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:19:00,789] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:19:00,789] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 01:19:00,790] [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 tolerans	strain=DSM 11457	GCA_900109855.1	74031	74031	type	True	92.5913	999	1189	95	below_threshold
Roseovarius nitratireducens	strain=TFZ	GCA_002925845.1	2044597	2044597	type	True	82.3914	726	1189	95	below_threshold
Roseovarius azorensis	strain=DSM 100674	GCA_900109455.1	1287727	1287727	type	True	81.6259	731	1189	95	below_threshold
Roseovarius mucosus	strain=DSM 17069	GCA_000768555.3	215743	215743	type	True	81.2492	775	1189	95	below_threshold
Roseovarius gaetbuli	strain=CECT 8370	GCA_900172365.1	1356575	1356575	type	True	79.859	687	1189	95	below_threshold
Roseovarius marisflavi	strain=DSM 29327	GCA_900142625.1	1054996	1054996	type	True	79.7823	684	1189	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	79.7437	582	1189	95	below_threshold
Roseovarius halotolerans	strain=CECT 8110	GCA_900172255.1	505353	505353	type	True	79.688	589	1189	95	below_threshold
Roseovarius nubinhibens	strain=ISM	GCA_000152625.1	314263	314263	type	True	79.3653	519	1189	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	79.1832	602	1189	95	below_threshold
Roseovarius confluentis	strain=SAG6	GCA_002917925.1	1852027	1852027	type	True	79.0994	551	1189	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	78.9849	483	1189	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	78.757	518	1189	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.5414	431	1189	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.4449	489	1189	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	78.3782	431	1189	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	78.2416	429	1189	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.9694	397	1189	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	77.5829	389	1189	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	77.4703	299	1189	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.2679	278	1189	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.8039	239	1189	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:19:00,790] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30090/tc_result.tsv
[2023-03-18 01:19:00,790] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:19:00,790] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:19:00,790] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74ed9bf3-0575-4138-b2b6-234a67344e6c/dqc_reference/checkm_data
[2023-03-18 01:19:00,791] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:19:00,797] [INFO] Task started: CheckM
[2023-03-18 01:19:00,797] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30090/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30090/checkm_input OceanDNA-b30090/checkm_result
[2023-03-18 01:20:00,131] [INFO] Task succeeded: CheckM
[2023-03-18 01:20:00,131] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:20:00,157] [INFO] ===== Completeness check finished =====
[2023-03-18 01:20:00,157] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:20:00,157] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30090/markers.fasta)
[2023-03-18 01:20:00,159] [INFO] Task started: Blastn
[2023-03-18 01:20:00,159] [INFO] Running command: blastn -query OceanDNA-b30090/markers.fasta -db /var/lib/cwl/stg74ed9bf3-0575-4138-b2b6-234a67344e6c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30090/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:20:01,996] [INFO] Task succeeded: Blastn
[2023-03-18 01:20:02,029] [INFO] Selected 11 target genomes.
[2023-03-18 01:20:02,029] [INFO] Target genome list was writen to OceanDNA-b30090/target_genomes_gtdb.txt
[2023-03-18 01:20:02,044] [INFO] Task started: fastANI
[2023-03-18 01:20:02,044] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf232e4e-194c-47a2-93b6-56fadafa50e7/OceanDNA-b30090.fa --refList OceanDNA-b30090/target_genomes_gtdb.txt --output OceanDNA-b30090/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:20:11,786] [INFO] Task succeeded: fastANI
[2023-03-18 01:20:11,794] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:20:11,794] [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_900109855.1	s__Roseovarius tolerans	92.6095	998	1189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.73	96.73	0.86	0.86	2	-
GCF_002072155.1	s__Roseovarius sp002072155	88.8512	847	1189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002925845.1	s__Roseovarius nitratireducens	82.3817	726	1189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.60	96.60	0.90	0.90	2	-
GCA_016278295.1	s__Roseovarius sp016278295	82.3141	591	1189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842985.1	s__Roseovarius sp002842985	81.8246	733	1189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109455.1	s__Roseovarius azorensis	81.6136	733	1189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002720475.1	s__Roseovarius sp002720475	81.5778	523	1189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.80	99.74	0.82	0.71	3	-
GCA_014359765.1	s__Roseovarius sp014359765	81.3707	581	1189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069895.1	s__Roseovarius sp018069895	81.2744	702	1189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.42	99.42	0.86	0.86	2	-
GCF_002080415.1	s__Roseovarius mucosus_A	80.6191	737	1189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.86	96.11	0.91	0.79	6	-
GCF_003651245.1	s__Roseovarius spongiae	79.2348	545	1189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:20:11,794] [INFO] GTDB search result was written to OceanDNA-b30090/result_gtdb.tsv
[2023-03-18 01:20:11,794] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:20:11,798] [INFO] DFAST_QC result json was written to OceanDNA-b30090/dqc_result.json
[2023-03-18 01:20:11,798] [INFO] DFAST_QC completed!
[2023-03-18 01:20:11,798] [INFO] Total running time: 0h1m56s