[2023-03-19 04:11:06,926] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:11:06,927] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:11:06,927] [INFO] DQC Reference Directory: /var/lib/cwl/stg62791356-83e9-4a08-a1bc-5c63eb83d30f/dqc_reference
[2023-03-19 04:11:08,644] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:11:08,645] [INFO] Task started: Prodigal
[2023-03-19 04:11:08,645] [INFO] Running command: cat /var/lib/cwl/stg71f72c7b-9d2e-4486-8786-bed0ed216193/OceanDNA-b30086.fa | prodigal -d OceanDNA-b30086/cds.fna -a OceanDNA-b30086/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:11:25,497] [INFO] Task succeeded: Prodigal
[2023-03-19 04:11:25,497] [INFO] Task started: HMMsearch
[2023-03-19 04:11:25,497] [INFO] Running command: hmmsearch --tblout OceanDNA-b30086/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg62791356-83e9-4a08-a1bc-5c63eb83d30f/dqc_reference/reference_markers.hmm OceanDNA-b30086/protein.faa > /dev/null
[2023-03-19 04:11:25,682] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:11:25,682] [INFO] Found 6/6 markers.
[2023-03-19 04:11:25,702] [INFO] Query marker FASTA was written to OceanDNA-b30086/markers.fasta
[2023-03-19 04:11:25,703] [INFO] Task started: Blastn
[2023-03-19 04:11:25,703] [INFO] Running command: blastn -query OceanDNA-b30086/markers.fasta -db /var/lib/cwl/stg62791356-83e9-4a08-a1bc-5c63eb83d30f/dqc_reference/reference_markers.fasta -out OceanDNA-b30086/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:11:26,511] [INFO] Task succeeded: Blastn
[2023-03-19 04:11:26,512] [INFO] Selected 20 target genomes.
[2023-03-19 04:11:26,512] [INFO] Target genome list was writen to OceanDNA-b30086/target_genomes.txt
[2023-03-19 04:11:26,525] [INFO] Task started: fastANI
[2023-03-19 04:11:26,525] [INFO] Running command: fastANI --query /var/lib/cwl/stg71f72c7b-9d2e-4486-8786-bed0ed216193/OceanDNA-b30086.fa --refList OceanDNA-b30086/target_genomes.txt --output OceanDNA-b30086/fastani_result.tsv --threads 1
[2023-03-19 04:11:42,005] [INFO] Task succeeded: fastANI
[2023-03-19 04:11:42,005] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg62791356-83e9-4a08-a1bc-5c63eb83d30f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:11:42,006] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg62791356-83e9-4a08-a1bc-5c63eb83d30f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:11:42,017] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:11:42,017] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:11:42,017] [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 azorensis	strain=DSM 100674	GCA_900109455.1	1287727	1287727	type	True	93.2377	813	890	95	below_threshold
Roseovarius tolerans	strain=DSM 11457	GCA_900109855.1	74031	74031	type	True	81.4819	631	890	95	below_threshold
Roseovarius mucosus	strain=DSM 17069	GCA_000768555.3	215743	215743	type	True	81.4625	621	890	95	below_threshold
Roseovarius nitratireducens	strain=TFZ	GCA_002925845.1	2044597	2044597	type	True	80.1742	570	890	95	below_threshold
Roseovarius marisflavi	strain=DSM 29327	GCA_900142625.1	1054996	1054996	type	True	79.7449	548	890	95	below_threshold
Roseovarius gaetbuli	strain=CECT 8370	GCA_900172365.1	1356575	1356575	type	True	79.7181	570	890	95	below_threshold
Roseovarius lutimaris	strain=DSM 28463	GCA_900115165.1	1005928	1005928	type	True	79.6261	567	890	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	79.168	468	890	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	79.1159	473	890	95	below_threshold
Roseovarius faecimaris	strain=MME-070	GCA_009762325.1	2494550	2494550	type	True	78.8159	428	890	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	78.6852	398	890	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.2956	348	890	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.2909	392	890	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	78.2851	340	890	95	below_threshold
Pelagivirga dicentrarchi	strain=YLY04	GCA_003316635.1	2250573	2250573	type	True	78.1232	346	890	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	78.0524	333	890	95	below_threshold
Pseudopuniceibacterium sediminis	strain=CY03	GCA_003575965.1	2211117	2211117	type	True	77.6268	244	890	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.4648	238	890	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.0466	225	890	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	76.9133	264	890	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:11:42,017] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30086/tc_result.tsv
[2023-03-19 04:11:42,017] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:11:42,018] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:11:42,018] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg62791356-83e9-4a08-a1bc-5c63eb83d30f/dqc_reference/checkm_data
[2023-03-19 04:11:42,019] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:11:42,023] [INFO] Task started: CheckM
[2023-03-19 04:11:42,024] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30086/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30086/checkm_input OceanDNA-b30086/checkm_result
[2023-03-19 04:12:26,312] [INFO] Task succeeded: CheckM
[2023-03-19 04:12:26,312] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.94%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:12:26,315] [INFO] ===== Completeness check finished =====
[2023-03-19 04:12:26,315] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:12:26,315] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30086/markers.fasta)
[2023-03-19 04:12:26,315] [INFO] Task started: Blastn
[2023-03-19 04:12:26,316] [INFO] Running command: blastn -query OceanDNA-b30086/markers.fasta -db /var/lib/cwl/stg62791356-83e9-4a08-a1bc-5c63eb83d30f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30086/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:12:27,796] [INFO] Task succeeded: Blastn
[2023-03-19 04:12:27,797] [INFO] Selected 15 target genomes.
[2023-03-19 04:12:27,797] [INFO] Target genome list was writen to OceanDNA-b30086/target_genomes_gtdb.txt
[2023-03-19 04:12:27,845] [INFO] Task started: fastANI
[2023-03-19 04:12:27,846] [INFO] Running command: fastANI --query /var/lib/cwl/stg71f72c7b-9d2e-4486-8786-bed0ed216193/OceanDNA-b30086.fa --refList OceanDNA-b30086/target_genomes_gtdb.txt --output OceanDNA-b30086/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:12:39,623] [INFO] Task succeeded: fastANI
[2023-03-19 04:12:39,632] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:12:39,632] [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_900109455.1	s__Roseovarius azorensis	93.2377	813	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002783205.1	s__Roseovarius sp002783205	82.5106	634	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.90	99.90	0.93	0.93	2	-
GCA_018066915.1	s__Roseovarius sp018066915	81.6943	568	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.88	99.88	0.93	0.93	2	-
GCF_000744325.1	s__Roseovarius sp000744325	81.5082	622	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768555.3	s__Roseovarius mucosus	81.4625	621	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.95	96.93	0.91	0.89	3	-
GCF_900109855.1	s__Roseovarius tolerans	81.4599	633	890	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	81.3806	611	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152845.1	s__Roseovarius sp000152845	81.2774	608	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.99	97.99	0.83	0.83	2	-
GCF_002080415.1	s__Roseovarius mucosus_A	80.8192	598	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.86	96.11	0.91	0.79	6	-
GCF_018069895.1	s__Roseovarius sp018069895	80.7397	559	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.42	99.42	0.86	0.86	2	-
GCA_016278295.1	s__Roseovarius sp016278295	80.2665	475	890	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	80.1715	571	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.60	96.60	0.90	0.90	2	-
GCF_900142665.1	s__Roseovarius pacificus	79.1585	469	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.52	95.05	0.91	0.82	3	-
GCF_003651245.1	s__Roseovarius spongiae	78.6992	418	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003072125.1	s__Roseovarius sediminicola	78.659	399	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:12:39,632] [INFO] GTDB search result was written to OceanDNA-b30086/result_gtdb.tsv
[2023-03-19 04:12:39,632] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:12:39,634] [INFO] DFAST_QC result json was written to OceanDNA-b30086/dqc_result.json
[2023-03-19 04:12:39,634] [INFO] DFAST_QC completed!
[2023-03-19 04:12:39,634] [INFO] Total running time: 0h1m33s