[2023-03-18 23:27:53,078] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:27:53,078] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:27:53,078] [INFO] DQC Reference Directory: /var/lib/cwl/stgffb71b3d-c1cd-43b0-b4e2-752b54e318db/dqc_reference
[2023-03-18 23:27:54,275] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:27:54,276] [INFO] Task started: Prodigal
[2023-03-18 23:27:54,276] [INFO] Running command: cat /var/lib/cwl/stg9cc18fcd-321e-4a69-958d-b87128769fd7/OceanDNA-b23973.fa | prodigal -d OceanDNA-b23973/cds.fna -a OceanDNA-b23973/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:28:07,165] [INFO] Task succeeded: Prodigal
[2023-03-18 23:28:07,166] [INFO] Task started: HMMsearch
[2023-03-18 23:28:07,166] [INFO] Running command: hmmsearch --tblout OceanDNA-b23973/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgffb71b3d-c1cd-43b0-b4e2-752b54e318db/dqc_reference/reference_markers.hmm OceanDNA-b23973/protein.faa > /dev/null
[2023-03-18 23:28:07,342] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:28:07,342] [INFO] Found 6/6 markers.
[2023-03-18 23:28:07,360] [INFO] Query marker FASTA was written to OceanDNA-b23973/markers.fasta
[2023-03-18 23:28:07,361] [INFO] Task started: Blastn
[2023-03-18 23:28:07,361] [INFO] Running command: blastn -query OceanDNA-b23973/markers.fasta -db /var/lib/cwl/stgffb71b3d-c1cd-43b0-b4e2-752b54e318db/dqc_reference/reference_markers.fasta -out OceanDNA-b23973/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:28:08,126] [INFO] Task succeeded: Blastn
[2023-03-18 23:28:08,127] [INFO] Selected 17 target genomes.
[2023-03-18 23:28:08,127] [INFO] Target genome list was writen to OceanDNA-b23973/target_genomes.txt
[2023-03-18 23:28:08,138] [INFO] Task started: fastANI
[2023-03-18 23:28:08,138] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cc18fcd-321e-4a69-958d-b87128769fd7/OceanDNA-b23973.fa --refList OceanDNA-b23973/target_genomes.txt --output OceanDNA-b23973/fastani_result.tsv --threads 1
[2023-03-18 23:28:18,293] [INFO] Task succeeded: fastANI
[2023-03-18 23:28:18,293] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgffb71b3d-c1cd-43b0-b4e2-752b54e318db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:28:18,293] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgffb71b3d-c1cd-43b0-b4e2-752b54e318db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:28:18,309] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 23:28:18,310] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 23:28:18,310] [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
Glycocaulis albus	strain=CGMCC 1.12766	GCA_014639075.1	1382801	1382801	type	True	98.7289	648	679	95	conclusive
Glycocaulis alkaliphilus	strain=6B-8	GCA_004000605.1	1434191	1434191	type	True	86.2983	598	679	95	below_threshold
Glycocaulis alkaliphilus	strain=CGMCC 1.12428	GCA_014637625.1	1434191	1434191	type	True	86.2904	597	679	95	below_threshold
Marinicauda algicola	strain=JCM 31718	GCA_004793685.1	2029849	2029849	type	True	77.7561	249	679	95	below_threshold
Marinicauda algicola	strain=RMAR8-3	GCA_017161425.1	2029849	2029849	type	True	77.7547	249	679	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_004793635.1	1133559	1133559	type	True	77.7531	214	679	95	below_threshold
Marinicauda pacifica	strain=CGMCC 1.11031	GCA_014636415.1	1133559	1133559	type	True	77.7531	214	679	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	77.5183	211	679	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	75.7413	67	679	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	75.6899	50	679	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	75.6899	50	679	95	below_threshold
Sphingobium sufflavum	strain=HL-25	GCA_021403115.1	1129547	1129547	type	True	75.4825	50	679	95	below_threshold
Sphingomonas leidyi	strain=DSM 4733	GCA_011761945.1	68569	68569	type	True	75.3956	51	679	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:28:18,310] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23973/tc_result.tsv
[2023-03-18 23:28:18,310] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:28:18,310] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:28:18,310] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgffb71b3d-c1cd-43b0-b4e2-752b54e318db/dqc_reference/checkm_data
[2023-03-18 23:28:18,311] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:28:18,315] [INFO] Task started: CheckM
[2023-03-18 23:28:18,315] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23973/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23973/checkm_input OceanDNA-b23973/checkm_result
[2023-03-18 23:28:53,701] [INFO] Task succeeded: CheckM
[2023-03-18 23:28:53,701] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:28:53,703] [INFO] ===== Completeness check finished =====
[2023-03-18 23:28:53,703] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:28:53,704] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23973/markers.fasta)
[2023-03-18 23:28:53,705] [INFO] Task started: Blastn
[2023-03-18 23:28:53,705] [INFO] Running command: blastn -query OceanDNA-b23973/markers.fasta -db /var/lib/cwl/stgffb71b3d-c1cd-43b0-b4e2-752b54e318db/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23973/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:28:55,148] [INFO] Task succeeded: Blastn
[2023-03-18 23:28:55,149] [INFO] Selected 14 target genomes.
[2023-03-18 23:28:55,149] [INFO] Target genome list was writen to OceanDNA-b23973/target_genomes_gtdb.txt
[2023-03-18 23:28:55,155] [INFO] Task started: fastANI
[2023-03-18 23:28:55,155] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cc18fcd-321e-4a69-958d-b87128769fd7/OceanDNA-b23973.fa --refList OceanDNA-b23973/target_genomes_gtdb.txt --output OceanDNA-b23973/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:29:03,555] [INFO] Task succeeded: fastANI
[2023-03-18 23:29:03,563] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:29:03,563] [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_014639075.1	s__Glycocaulis albus	98.7625	647	679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Glycocaulis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004000605.1	s__Glycocaulis alkaliphilus	86.2983	598	679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Glycocaulis	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000744995.1	s__Glycocaulis sp000744995	82.7422	534	679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Glycocaulis	95.0	98.48	98.48	0.95	0.95	2	-
GCF_007050995.1	s__Glycocaulis profundi	78.8597	290	679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Glycocaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630495.1	s__Oceanicaulis satelles	78.2783	271	679	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	78.2752	252	679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152745.1	s__Oceanicaulis sp000152745	77.8286	225	679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	98.46	98.38	0.90	0.88	7	-
GCF_017161425.1	s__Marinicauda algicola	77.7671	248	679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Marinicauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004793635.1	s__Marinicauda pacifica	77.7378	215	679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Marinicauda	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003046365.1	s__Oceanicaulis sp003046365	77.0232	169	679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	96.56	96.56	0.93	0.93	2	-
GCA_001510895.1	s__Mesorhizobium loti_A	75.8403	67	679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101865.1	s__Paracoccus isoporae	75.3977	50	679	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 23:29:03,563] [INFO] GTDB search result was written to OceanDNA-b23973/result_gtdb.tsv
[2023-03-18 23:29:03,563] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:29:03,564] [INFO] DFAST_QC result json was written to OceanDNA-b23973/dqc_result.json
[2023-03-18 23:29:03,565] [INFO] DFAST_QC completed!
[2023-03-18 23:29:03,565] [INFO] Total running time: 0h1m10s