[2023-03-17 11:19:47,572] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:19:47,572] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:19:47,572] [INFO] DQC Reference Directory: /var/lib/cwl/stga266cba5-2f63-43e7-b4ba-91b885737814/dqc_reference
[2023-03-17 11:19:48,710] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:19:48,710] [INFO] Task started: Prodigal
[2023-03-17 11:19:48,710] [INFO] Running command: cat /var/lib/cwl/stgd0e6d791-90b6-4e38-b253-dc7ba036d402/OceanDNA-b23966.fa | prodigal -d OceanDNA-b23966/cds.fna -a OceanDNA-b23966/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:20:08,514] [INFO] Task succeeded: Prodigal
[2023-03-17 11:20:08,515] [INFO] Task started: HMMsearch
[2023-03-17 11:20:08,515] [INFO] Running command: hmmsearch --tblout OceanDNA-b23966/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga266cba5-2f63-43e7-b4ba-91b885737814/dqc_reference/reference_markers.hmm OceanDNA-b23966/protein.faa > /dev/null
[2023-03-17 11:20:08,713] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:20:08,714] [INFO] Found 6/6 markers.
[2023-03-17 11:20:08,734] [INFO] Query marker FASTA was written to OceanDNA-b23966/markers.fasta
[2023-03-17 11:20:08,734] [INFO] Task started: Blastn
[2023-03-17 11:20:08,734] [INFO] Running command: blastn -query OceanDNA-b23966/markers.fasta -db /var/lib/cwl/stga266cba5-2f63-43e7-b4ba-91b885737814/dqc_reference/reference_markers.fasta -out OceanDNA-b23966/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:20:09,557] [INFO] Task succeeded: Blastn
[2023-03-17 11:20:09,558] [INFO] Selected 14 target genomes.
[2023-03-17 11:20:09,558] [INFO] Target genome list was writen to OceanDNA-b23966/target_genomes.txt
[2023-03-17 11:20:09,568] [INFO] Task started: fastANI
[2023-03-17 11:20:09,568] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0e6d791-90b6-4e38-b253-dc7ba036d402/OceanDNA-b23966.fa --refList OceanDNA-b23966/target_genomes.txt --output OceanDNA-b23966/fastani_result.tsv --threads 1
[2023-03-17 11:20:18,591] [INFO] Task succeeded: fastANI
[2023-03-17 11:20:18,591] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga266cba5-2f63-43e7-b4ba-91b885737814/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:20:18,591] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga266cba5-2f63-43e7-b4ba-91b885737814/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:20:18,600] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:20:18,600] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 11:20:18,600] [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 alkaliphilus	strain=6B-8	GCA_004000605.1	1434191	1434191	type	True	83.6058	746	1053	95	below_threshold
Glycocaulis alkaliphilus	strain=CGMCC 1.12428	GCA_014637625.1	1434191	1434191	type	True	83.5881	741	1053	95	below_threshold
Glycocaulis albus	strain=CGMCC 1.12766	GCA_014639075.1	1382801	1382801	type	True	83.5422	752	1053	95	below_threshold
Marinicauda algicola	strain=JCM 31718	GCA_004793685.1	2029849	2029849	type	True	78.7323	355	1053	95	below_threshold
Marinicauda algicola	strain=RMAR8-3	GCA_017161425.1	2029849	2029849	type	True	78.7207	358	1053	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_004793635.1	1133559	1133559	type	True	77.9516	284	1053	95	below_threshold
Marinicauda pacifica	strain=CGMCC 1.11031	GCA_014636415.1	1133559	1133559	type	True	77.9322	282	1053	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	77.6723	311	1053	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	76.3517	112	1053	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	76.0731	93	1053	95	below_threshold
Methylorubrum rhodinum	strain=DSM 2163	GCA_014199935.1	29428	29428	type	True	76.0616	97	1053	95	below_threshold
Rhizorhabdus phycosphaerae	strain=MK52	GCA_011044255.1	2711156	2711156	type	True	75.9805	78	1053	95	below_threshold
Methylobacterium aerolatum	strain=DSM 19013	GCA_022179085.1	418708	418708	type	True	75.9653	63	1053	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 11:20:18,601] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23966/tc_result.tsv
[2023-03-17 11:20:18,601] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:20:18,601] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:20:18,601] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga266cba5-2f63-43e7-b4ba-91b885737814/dqc_reference/checkm_data
[2023-03-17 11:20:18,602] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:20:18,606] [INFO] Task started: CheckM
[2023-03-17 11:20:18,606] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23966/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23966/checkm_input OceanDNA-b23966/checkm_result
[2023-03-17 11:21:08,315] [INFO] Task succeeded: CheckM
[2023-03-17 11:21:08,316] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:21:08,318] [INFO] ===== Completeness check finished =====
[2023-03-17 11:21:08,318] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:21:08,318] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23966/markers.fasta)
[2023-03-17 11:21:08,319] [INFO] Task started: Blastn
[2023-03-17 11:21:08,319] [INFO] Running command: blastn -query OceanDNA-b23966/markers.fasta -db /var/lib/cwl/stga266cba5-2f63-43e7-b4ba-91b885737814/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23966/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:21:09,955] [INFO] Task succeeded: Blastn
[2023-03-17 11:21:09,956] [INFO] Selected 16 target genomes.
[2023-03-17 11:21:09,956] [INFO] Target genome list was writen to OceanDNA-b23966/target_genomes_gtdb.txt
[2023-03-17 11:21:10,382] [INFO] Task started: fastANI
[2023-03-17 11:21:10,382] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0e6d791-90b6-4e38-b253-dc7ba036d402/OceanDNA-b23966.fa --refList OceanDNA-b23966/target_genomes_gtdb.txt --output OceanDNA-b23966/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:21:20,365] [INFO] Task succeeded: fastANI
[2023-03-17 11:21:20,373] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:21:20,373] [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_004000605.1	s__Glycocaulis alkaliphilus	83.5925	747	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Glycocaulis	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014639075.1	s__Glycocaulis albus	83.5414	752	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Glycocaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744995.1	s__Glycocaulis sp000744995	82.6187	701	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Glycocaulis	95.0	98.48	98.48	0.95	0.95	2	-
GCF_017161425.1	s__Marinicauda algicola	78.7207	358	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Marinicauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008630495.1	s__Oceanicaulis satelles	78.7191	364	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007050995.1	s__Glycocaulis profundi	78.5673	396	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Glycocaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124675.1	s__Oceanicaulis sp016124675	78.3795	361	1053	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	78.3578	282	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	98.46	98.38	0.90	0.88	7	-
GCF_004793635.1	s__Marinicauda pacifica	77.9516	284	1053	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	77.6766	227	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	96.56	96.56	0.93	0.93	2	-
GCF_003122085.1	s__WD6-1 sp003122085	77.6627	312	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__WD6-1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199935.1	s__Methylobacterium rhodinum	76.0616	97	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:21:20,373] [INFO] GTDB search result was written to OceanDNA-b23966/result_gtdb.tsv
[2023-03-17 11:21:20,373] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:21:20,375] [INFO] DFAST_QC result json was written to OceanDNA-b23966/dqc_result.json
[2023-03-17 11:21:20,375] [INFO] DFAST_QC completed!
[2023-03-17 11:21:20,375] [INFO] Total running time: 0h1m33s