[2023-03-18 01:03:22,773] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:03:22,773] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:03:22,773] [INFO] DQC Reference Directory: /var/lib/cwl/stg81c813f6-038b-4a0f-b586-87e54edd8ffd/dqc_reference
[2023-03-18 01:03:23,961] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:03:23,961] [INFO] Task started: Prodigal
[2023-03-18 01:03:23,961] [INFO] Running command: cat /var/lib/cwl/stg4725b53e-78aa-4e53-8a24-c9cf762826c2/OceanDNA-b23984.fa | prodigal -d OceanDNA-b23984/cds.fna -a OceanDNA-b23984/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:03:41,031] [INFO] Task succeeded: Prodigal
[2023-03-18 01:03:41,032] [INFO] Task started: HMMsearch
[2023-03-18 01:03:41,032] [INFO] Running command: hmmsearch --tblout OceanDNA-b23984/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81c813f6-038b-4a0f-b586-87e54edd8ffd/dqc_reference/reference_markers.hmm OceanDNA-b23984/protein.faa > /dev/null
[2023-03-18 01:03:41,226] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:03:41,226] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4725b53e-78aa-4e53-8a24-c9cf762826c2/OceanDNA-b23984.fa]
[2023-03-18 01:03:41,246] [INFO] Query marker FASTA was written to OceanDNA-b23984/markers.fasta
[2023-03-18 01:03:41,247] [INFO] Task started: Blastn
[2023-03-18 01:03:41,247] [INFO] Running command: blastn -query OceanDNA-b23984/markers.fasta -db /var/lib/cwl/stg81c813f6-038b-4a0f-b586-87e54edd8ffd/dqc_reference/reference_markers.fasta -out OceanDNA-b23984/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:03:42,030] [INFO] Task succeeded: Blastn
[2023-03-18 01:03:42,030] [INFO] Selected 21 target genomes.
[2023-03-18 01:03:42,031] [INFO] Target genome list was writen to OceanDNA-b23984/target_genomes.txt
[2023-03-18 01:03:42,043] [INFO] Task started: fastANI
[2023-03-18 01:03:42,044] [INFO] Running command: fastANI --query /var/lib/cwl/stg4725b53e-78aa-4e53-8a24-c9cf762826c2/OceanDNA-b23984.fa --refList OceanDNA-b23984/target_genomes.txt --output OceanDNA-b23984/fastani_result.tsv --threads 1
[2023-03-18 01:03:55,600] [INFO] Task succeeded: fastANI
[2023-03-18 01:03:55,601] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81c813f6-038b-4a0f-b586-87e54edd8ffd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:03:55,601] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81c813f6-038b-4a0f-b586-87e54edd8ffd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:03:55,612] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:03:55,612] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 01:03:55,613] [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
Marinicauda pacifica	strain=P-1 km-3	GCA_004793635.1	1133559	1133559	type	True	77.7857	285	916	95	below_threshold
Marinicauda pacifica	strain=CGMCC 1.11031	GCA_014636415.1	1133559	1133559	type	True	77.7818	285	916	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_009806145.1	1133559	1133559	type	True	77.7709	281	916	95	below_threshold
Marinicauda algicola	strain=RMAR8-3	GCA_017161425.1	2029849	2029849	type	True	77.7462	289	916	95	below_threshold
Marinicauda algicola	strain=JCM 31718	GCA_004793685.1	2029849	2029849	type	True	77.7453	292	916	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	77.5617	293	916	95	below_threshold
Glycocaulis alkaliphilus	strain=6B-8	GCA_004000605.1	1434191	1434191	type	True	77.4671	265	916	95	below_threshold
Glycocaulis alkaliphilus	strain=CGMCC 1.12428	GCA_014637625.1	1434191	1434191	type	True	77.3915	266	916	95	below_threshold
Maricaulis salignorans	strain=DSM 16077	GCA_900103475.1	144026	144026	type	True	76.7681	162	916	95	below_threshold
Pedomonas mirosovicensis	strain=A1X5R2	GCA_022569295.1	2908641	2908641	type	True	76.0786	62	916	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	76.0099	96	916	95	below_threshold
Blastochloris viridis	strain=ATCC 19567	GCA_001402875.1	1079	1079	type	True	75.9531	80	916	95	below_threshold
Bradyrhizobium aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	75.8901	94	916	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	75.8873	83	916	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	75.8664	81	916	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	75.8595	61	916	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	75.7825	91	916	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	75.7723	52	916	95	below_threshold
Aureimonas endophytica	strain=CGMCC 1.15367	GCA_014642635.1	2027858	2027858	type	True	75.7376	83	916	95	below_threshold
Alsobacter soli	strain=SH9	GCA_003004785.1	2109933	2109933	type	True	75.6481	88	916	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	75.3892	61	916	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:03:55,613] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23984/tc_result.tsv
[2023-03-18 01:03:55,613] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:03:55,613] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:03:55,613] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81c813f6-038b-4a0f-b586-87e54edd8ffd/dqc_reference/checkm_data
[2023-03-18 01:03:55,614] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:03:55,617] [INFO] Task started: CheckM
[2023-03-18 01:03:55,618] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23984/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23984/checkm_input OceanDNA-b23984/checkm_result
[2023-03-18 01:04:39,307] [INFO] Task succeeded: CheckM
[2023-03-18 01:04:39,307] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:04:39,494] [INFO] ===== Completeness check finished =====
[2023-03-18 01:04:39,494] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:04:39,495] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23984/markers.fasta)
[2023-03-18 01:04:39,496] [INFO] Task started: Blastn
[2023-03-18 01:04:39,496] [INFO] Running command: blastn -query OceanDNA-b23984/markers.fasta -db /var/lib/cwl/stg81c813f6-038b-4a0f-b586-87e54edd8ffd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23984/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:04:40,952] [INFO] Task succeeded: Blastn
[2023-03-18 01:04:40,953] [INFO] Selected 13 target genomes.
[2023-03-18 01:04:40,953] [INFO] Target genome list was writen to OceanDNA-b23984/target_genomes_gtdb.txt
[2023-03-18 01:04:40,961] [INFO] Task started: fastANI
[2023-03-18 01:04:40,961] [INFO] Running command: fastANI --query /var/lib/cwl/stg4725b53e-78aa-4e53-8a24-c9cf762826c2/OceanDNA-b23984.fa --refList OceanDNA-b23984/target_genomes_gtdb.txt --output OceanDNA-b23984/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:04:49,039] [INFO] Task succeeded: fastANI
[2023-03-18 01:04:49,047] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:04:49,047] [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_000420265.1	s__Oceanicaulis alexandrii	97.7866	872	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	97.56	97.05	0.94	0.85	5	conclusive
GCF_003046365.1	s__Oceanicaulis sp003046365	88.7128	809	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	96.56	96.56	0.93	0.93	2	-
GCF_000152745.1	s__Oceanicaulis sp000152745	84.4719	757	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	98.46	98.38	0.90	0.88	7	-
GCF_008630495.1	s__Oceanicaulis satelles	78.7118	372	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124675.1	s__Oceanicaulis sp016124675	78.5181	351	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001657295.1	s__Oceanicaulis sp001657295	78.1772	359	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004793635.1	s__Marinicauda pacifica	77.7857	285	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Marinicauda	95.0	100.00	100.00	1.00	1.00	3	-
GCF_017161425.1	s__Marinicauda algicola	77.7462	289	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Marinicauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004000605.1	s__Glycocaulis alkaliphilus	77.4809	263	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Glycocaulis	95.0	100.00	100.00	0.99	0.99	2	-
GCA_007571185.1	s__Oceanicaulis sp007571185	77.0162	139	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	99.03	99.03	0.79	0.79	2	-
GCF_004358185.1	s__Antarcticimicrobium luteum	75.8539	82	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003646465.1	s__Chachezhania antarctica	75.4768	62	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Chachezhania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004335005.1	s__Paracoccus sp004335005	75.3892	61	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:04:49,164] [INFO] GTDB search result was written to OceanDNA-b23984/result_gtdb.tsv
[2023-03-18 01:04:49,168] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:04:49,171] [INFO] DFAST_QC result json was written to OceanDNA-b23984/dqc_result.json
[2023-03-18 01:04:49,171] [INFO] DFAST_QC completed!
[2023-03-18 01:04:49,171] [INFO] Total running time: 0h1m26s