[2023-03-15 14:37:46,943] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:37:46,947] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:37:46,948] [INFO] DQC Reference Directory: /var/lib/cwl/stg03b172ea-2356-400e-a4a7-ff5aa502d54a/dqc_reference
[2023-03-15 14:37:48,678] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:37:48,679] [INFO] Task started: Prodigal
[2023-03-15 14:37:48,679] [INFO] Running command: cat /var/lib/cwl/stg81b1dd62-1eb6-4a2a-8710-674bef12837e/OceanDNA-b29999.fa | prodigal -d OceanDNA-b29999/cds.fna -a OceanDNA-b29999/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:38:03,542] [INFO] Task succeeded: Prodigal
[2023-03-15 14:38:03,542] [INFO] Task started: HMMsearch
[2023-03-15 14:38:03,542] [INFO] Running command: hmmsearch --tblout OceanDNA-b29999/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03b172ea-2356-400e-a4a7-ff5aa502d54a/dqc_reference/reference_markers.hmm OceanDNA-b29999/protein.faa > /dev/null
[2023-03-15 14:38:03,738] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:38:03,739] [INFO] Found 6/6 markers.
[2023-03-15 14:38:03,783] [INFO] Query marker FASTA was written to OceanDNA-b29999/markers.fasta
[2023-03-15 14:38:03,784] [INFO] Task started: Blastn
[2023-03-15 14:38:03,784] [INFO] Running command: blastn -query OceanDNA-b29999/markers.fasta -db /var/lib/cwl/stg03b172ea-2356-400e-a4a7-ff5aa502d54a/dqc_reference/reference_markers.fasta -out OceanDNA-b29999/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:38:04,438] [INFO] Task succeeded: Blastn
[2023-03-15 14:38:04,456] [INFO] Selected 21 target genomes.
[2023-03-15 14:38:04,456] [INFO] Target genome list was writen to OceanDNA-b29999/target_genomes.txt
[2023-03-15 14:38:04,468] [INFO] Task started: fastANI
[2023-03-15 14:38:04,468] [INFO] Running command: fastANI --query /var/lib/cwl/stg81b1dd62-1eb6-4a2a-8710-674bef12837e/OceanDNA-b29999.fa --refList OceanDNA-b29999/target_genomes.txt --output OceanDNA-b29999/fastani_result.tsv --threads 1
[2023-03-15 14:38:19,148] [INFO] Task succeeded: fastANI
[2023-03-15 14:38:19,148] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03b172ea-2356-400e-a4a7-ff5aa502d54a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:38:19,149] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03b172ea-2356-400e-a4a7-ff5aa502d54a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:38:19,157] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2023-03-15 14:38:19,158] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 14:38:19,158] [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
Planktotalea frisia	strain=DSM 23709	GCA_003254185.1	696762	696762	type	True	99.0855	675	713	95	conclusive
Planktotalea frisia	strain=SH6-1	GCA_001890925.1	696762	696762	type	True	99.0839	667	713	95	conclusive
Planktotalea arctica	strain=IMCC9565	GCA_002105285.1	1481893	1481893	type	True	79.9743	343	713	95	below_threshold
Cognatishimia activa	strain=CECT 5113	GCA_001458335.1	1715691	1715691	type	True	76.9958	64	713	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	76.8768	82	713	95	below_threshold
Shimia thalassica	strain=CECT 7735	GCA_001458215.1	1715693	1715693	type	True	76.8149	75	713	95	below_threshold
Pelagicola litoralis	strain=CL-ES2	GCA_005518135.1	420403	420403	type	True	76.4724	52	713	95	below_threshold
Shimia haliotis	strain=DSM 28453	GCA_900114415.1	1280847	1280847	type	True	76.4493	85	713	95	below_threshold
Yoonia rosea	strain=DSM 29591	GCA_900156505.1	287098	287098	type	True	76.3207	75	713	95	below_threshold
Roseovarius marisflavi	strain=DSM 29327	GCA_900142625.1	1054996	1054996	type	True	76.3177	88	713	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	76.2939	65	713	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	76.2325	59	713	95	below_threshold
Celeribacter litoreus	strain=ASW11-22	GCA_020165855.1	2876714	2876714	type	True	76.0124	50	713	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	75.9253	50	713	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 14:38:19,158] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29999/tc_result.tsv
[2023-03-15 14:38:19,158] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:38:19,158] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:38:19,158] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03b172ea-2356-400e-a4a7-ff5aa502d54a/dqc_reference/checkm_data
[2023-03-15 14:38:19,159] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:38:19,164] [INFO] Task started: CheckM
[2023-03-15 14:38:19,164] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29999/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29999/checkm_input OceanDNA-b29999/checkm_result
[2023-03-15 14:39:00,669] [INFO] Task succeeded: CheckM
[2023-03-15 14:39:00,670] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.44%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 14:39:00,672] [INFO] ===== Completeness check finished =====
[2023-03-15 14:39:00,672] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:39:00,672] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29999/markers.fasta)
[2023-03-15 14:39:00,673] [INFO] Task started: Blastn
[2023-03-15 14:39:00,673] [INFO] Running command: blastn -query OceanDNA-b29999/markers.fasta -db /var/lib/cwl/stg03b172ea-2356-400e-a4a7-ff5aa502d54a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29999/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:39:01,786] [INFO] Task succeeded: Blastn
[2023-03-15 14:39:01,787] [INFO] Selected 10 target genomes.
[2023-03-15 14:39:01,787] [INFO] Target genome list was writen to OceanDNA-b29999/target_genomes_gtdb.txt
[2023-03-15 14:39:01,797] [INFO] Task started: fastANI
[2023-03-15 14:39:01,797] [INFO] Running command: fastANI --query /var/lib/cwl/stg81b1dd62-1eb6-4a2a-8710-674bef12837e/OceanDNA-b29999.fa --refList OceanDNA-b29999/target_genomes_gtdb.txt --output OceanDNA-b29999/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:39:08,078] [INFO] Task succeeded: fastANI
[2023-03-15 14:39:08,085] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 14:39:08,085] [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_001890925.1	s__Planktotalea frisia	99.0839	667	713	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktotalea	95.0	99.35	98.99	0.94	0.89	4	conclusive
GCA_000156115.1	s__Planktotalea sp000156115	80.0231	407	713	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktotalea	95.0	99.77	99.74	0.95	0.90	3	-
GCF_002105285.1	s__Planktotalea arctica	79.9743	343	713	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018607995.1	s__Planktotalea sp018607995	79.7977	368	713	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018607965.1	s__Planktotalea sp018607965	79.2267	304	713	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458335.1	s__Cognatishimia activa	76.9958	64	713	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatishimia	95.0	99.97	99.97	0.99	0.99	2	-
GCF_001292625.1	s__Shimia sp001292625	76.6106	85	713	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156505.1	s__Yoonia rosea	76.3207	75	713	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	96.70	96.70	0.95	0.95	2	-
GCF_011040495.1	s__Roseovarius aestuariivivens_A	76.2533	58	713	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226775.1	s__Marinovum sp006226775	75.7673	52	713	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 14:39:08,085] [INFO] GTDB search result was written to OceanDNA-b29999/result_gtdb.tsv
[2023-03-15 14:39:08,085] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:39:08,087] [INFO] DFAST_QC result json was written to OceanDNA-b29999/dqc_result.json
[2023-03-15 14:39:08,087] [INFO] DFAST_QC completed!
[2023-03-15 14:39:08,087] [INFO] Total running time: 0h1m21s