[2023-03-16 16:26:08,050] [INFO] DFAST_QC pipeline started.
[2023-03-16 16:26:08,050] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 16:26:08,050] [INFO] DQC Reference Directory: /var/lib/cwl/stg57252072-da36-4a03-b020-648a46794e17/dqc_reference
[2023-03-16 16:26:09,223] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 16:26:09,224] [INFO] Task started: Prodigal
[2023-03-16 16:26:09,224] [INFO] Running command: cat /var/lib/cwl/stga8f81936-7d8d-40fc-9818-479c6b084bf5/OceanDNA-b27593.fa | prodigal -d OceanDNA-b27593/cds.fna -a OceanDNA-b27593/protein.faa -g 11 -q > /dev/null
[2023-03-16 16:26:30,967] [INFO] Task succeeded: Prodigal
[2023-03-16 16:26:30,968] [INFO] Task started: HMMsearch
[2023-03-16 16:26:30,968] [INFO] Running command: hmmsearch --tblout OceanDNA-b27593/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57252072-da36-4a03-b020-648a46794e17/dqc_reference/reference_markers.hmm OceanDNA-b27593/protein.faa > /dev/null
[2023-03-16 16:26:31,165] [INFO] Task succeeded: HMMsearch
[2023-03-16 16:26:31,166] [WARNING] Found 4/6 markers. [/var/lib/cwl/stga8f81936-7d8d-40fc-9818-479c6b084bf5/OceanDNA-b27593.fa]
[2023-03-16 16:26:31,193] [INFO] Query marker FASTA was written to OceanDNA-b27593/markers.fasta
[2023-03-16 16:26:31,193] [INFO] Task started: Blastn
[2023-03-16 16:26:31,193] [INFO] Running command: blastn -query OceanDNA-b27593/markers.fasta -db /var/lib/cwl/stg57252072-da36-4a03-b020-648a46794e17/dqc_reference/reference_markers.fasta -out OceanDNA-b27593/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:26:31,670] [INFO] Task succeeded: Blastn
[2023-03-16 16:26:31,671] [INFO] Selected 20 target genomes.
[2023-03-16 16:26:31,671] [INFO] Target genome list was writen to OceanDNA-b27593/target_genomes.txt
[2023-03-16 16:26:31,707] [INFO] Task started: fastANI
[2023-03-16 16:26:31,707] [INFO] Running command: fastANI --query /var/lib/cwl/stga8f81936-7d8d-40fc-9818-479c6b084bf5/OceanDNA-b27593.fa --refList OceanDNA-b27593/target_genomes.txt --output OceanDNA-b27593/fastani_result.tsv --threads 1
[2023-03-16 16:26:44,661] [INFO] Task succeeded: fastANI
[2023-03-16 16:26:44,661] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57252072-da36-4a03-b020-648a46794e17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 16:26:44,661] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57252072-da36-4a03-b020-648a46794e17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 16:26:44,673] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 16:26:44,673] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 16:26:44,673] [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
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	76.6097	93	885	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	76.6047	131	885	95	below_threshold
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	76.5982	105	885	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	76.5767	109	885	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	76.5509	128	885	95	below_threshold
Pontivivens ytuae	strain=MT2928	GCA_015679265.1	2789856	2789856	type	True	76.3802	122	885	95	below_threshold
Jannaschia seohaensis	strain=DSM 25227	GCA_900116765.1	475081	475081	type	True	76.1814	131	885	95	below_threshold
Jannaschia seohaensis	strain=DSM 25227	GCA_003149265.1	475081	475081	type	True	76.1814	131	885	95	below_threshold
Cereibacter changlensis	strain=JA139	GCA_003034985.1	402884	402884	type	True	76.1708	143	885	95	below_threshold
Thioclava electrotropha	strain=Elox9	GCA_002085925.2	1549850	1549850	type	True	76.1343	87	885	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	76.1184	149	885	95	below_threshold
Paroceanicella profunda	strain=D4M1	GCA_005887635.2	2579971	2579971	type	True	76.1043	143	885	95	below_threshold
Mangrovicoccus ximenensis	strain=T1lg56	GCA_003056725.1	1911570	1911570	type	True	76.027	129	885	95	below_threshold
Cereibacter johrii	strain=JA192	GCA_001720585.1	445629	445629	type	True	76.012	117	885	95	below_threshold
Cereibacter johrii	strain=JA192	GCA_003046325.1	445629	445629	type	True	76.0106	119	885	95	below_threshold
Paracoccus acridae	strain=CGMCC 1.15419	GCA_014642735.1	1795310	1795310	type	True	75.9766	107	885	95	below_threshold
Rubrimonas cliftonensis	strain=DSM 15345	GCA_900107585.1	89524	89524	type	True	75.8924	168	885	95	below_threshold
Rubellimicrobium aerolatum	strain=DSM 19297	GCA_017872975.1	490979	490979	type	True	75.8269	102	885	95	below_threshold
Rhodobacter tardus	strain=CYK-10	GCA_009925085.1	2699202	2699202	type	True	75.6813	84	885	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	75.5053	78	885	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 16:26:44,673] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27593/tc_result.tsv
[2023-03-16 16:26:44,673] [INFO] ===== Taxonomy check completed =====
[2023-03-16 16:26:44,673] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 16:26:44,673] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57252072-da36-4a03-b020-648a46794e17/dqc_reference/checkm_data
[2023-03-16 16:26:44,674] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 16:26:44,680] [INFO] Task started: CheckM
[2023-03-16 16:26:44,680] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27593/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27593/checkm_input OceanDNA-b27593/checkm_result
[2023-03-16 16:27:44,558] [INFO] Task succeeded: CheckM
[2023-03-16 16:27:44,558] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.43%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 16:27:44,563] [INFO] ===== Completeness check finished =====
[2023-03-16 16:27:44,563] [INFO] ===== Start GTDB Search =====
[2023-03-16 16:27:44,563] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27593/markers.fasta)
[2023-03-16 16:27:44,565] [INFO] Task started: Blastn
[2023-03-16 16:27:44,565] [INFO] Running command: blastn -query OceanDNA-b27593/markers.fasta -db /var/lib/cwl/stg57252072-da36-4a03-b020-648a46794e17/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27593/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:27:46,221] [INFO] Task succeeded: Blastn
[2023-03-16 16:27:46,222] [INFO] Selected 20 target genomes.
[2023-03-16 16:27:46,222] [INFO] Target genome list was writen to OceanDNA-b27593/target_genomes_gtdb.txt
[2023-03-16 16:27:46,539] [INFO] Task started: fastANI
[2023-03-16 16:27:46,539] [INFO] Running command: fastANI --query /var/lib/cwl/stga8f81936-7d8d-40fc-9818-479c6b084bf5/OceanDNA-b27593.fa --refList OceanDNA-b27593/target_genomes_gtdb.txt --output OceanDNA-b27593/fastani_result_gtdb.tsv --threads 1
[2023-03-16 16:28:08,497] [INFO] Task succeeded: fastANI
[2023-03-16 16:28:08,509] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 16:28:08,509] [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_900129345.1	s__Ruegeria intermedia	76.5889	132	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009830125.1	s__GH1-50 sp009830125	76.5786	106	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__GH1-50	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797755.1	s__Brevirhabdus pacifica	76.5767	109	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Brevirhabdus	95.0	99.99	99.97	0.99	0.98	4	-
GCF_001507595.1	s__Ruegeria marisrubri	76.5509	128	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019104745.1	s__CAU-1522 sp019104745	76.5397	140	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1522	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011620265.1	s__Albidovulum sp011620265	76.4291	138	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015679265.1	s__MT2928 sp015679265	76.3802	122	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MT2928	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000018145.1	s__Dinoroseobacter shibae	76.3208	103	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Dinoroseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003008555.2	s__Pukyongiella litopenaei	76.232	148	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pukyongiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002814095.1	s__Sagittula sp002814095	76.1912	129	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034985.1	s__Cereibacter changlensis	76.1832	142	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter	95.0	98.07	96.18	0.89	0.78	3	-
GCF_005887635.2	s__Paroceanicella profunda	76.1259	141	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paroceanicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002085925.2	s__Thioclava electrotropha	76.0904	88	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	96.2561	N/A	N/A	N/A	N/A	1	-
GCF_009296265.1	s__Thioclava sp009296265	76.0509	101	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	96.2474	N/A	N/A	N/A	N/A	1	-
GCF_001720585.1	s__Cereibacter_A johrii	76.012	117	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.1736	98.42	97.86	0.94	0.91	6	-
GCF_003056725.1	s__Mangrovicoccus ximenensis	75.993	132	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014642735.1	s__Paracoccus acridae	75.9766	107	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.80	97.80	0.86	0.86	2	-
GCF_003390865.1	s__HLUCCA09 sp003390865	75.9143	85	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HLUCCA09	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009925085.1	s__CYK-10 sp009925085	75.6813	84	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CYK-10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002298965.1	s__Pinisolibacter sp002298965	75.4788	75	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Pinisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 16:28:08,509] [INFO] GTDB search result was written to OceanDNA-b27593/result_gtdb.tsv
[2023-03-16 16:28:08,510] [INFO] ===== GTDB Search completed =====
[2023-03-16 16:28:08,512] [INFO] DFAST_QC result json was written to OceanDNA-b27593/dqc_result.json
[2023-03-16 16:28:08,512] [INFO] DFAST_QC completed!
[2023-03-16 16:28:08,512] [INFO] Total running time: 0h2m0s