[2023-03-14 12:56:11,111] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:56:11,111] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:56:11,111] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf119be1-5345-43c5-a528-5783aa5236a6/dqc_reference
[2023-03-14 12:56:12,268] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:56:12,269] [INFO] Task started: Prodigal
[2023-03-14 12:56:12,269] [INFO] Running command: cat /var/lib/cwl/stgf4366513-450f-404e-b379-94b7fb621fa9/OceanDNA-b30045.fa | prodigal -d OceanDNA-b30045/cds.fna -a OceanDNA-b30045/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:56:31,980] [INFO] Task succeeded: Prodigal
[2023-03-14 12:56:31,980] [INFO] Task started: HMMsearch
[2023-03-14 12:56:31,980] [INFO] Running command: hmmsearch --tblout OceanDNA-b30045/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf119be1-5345-43c5-a528-5783aa5236a6/dqc_reference/reference_markers.hmm OceanDNA-b30045/protein.faa > /dev/null
[2023-03-14 12:56:32,176] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:56:32,177] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgf4366513-450f-404e-b379-94b7fb621fa9/OceanDNA-b30045.fa]
[2023-03-14 12:56:32,203] [INFO] Query marker FASTA was written to OceanDNA-b30045/markers.fasta
[2023-03-14 12:56:32,203] [INFO] Task started: Blastn
[2023-03-14 12:56:32,204] [INFO] Running command: blastn -query OceanDNA-b30045/markers.fasta -db /var/lib/cwl/stgbf119be1-5345-43c5-a528-5783aa5236a6/dqc_reference/reference_markers.fasta -out OceanDNA-b30045/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:56:32,801] [INFO] Task succeeded: Blastn
[2023-03-14 12:56:32,802] [INFO] Selected 18 target genomes.
[2023-03-14 12:56:32,802] [INFO] Target genome list was writen to OceanDNA-b30045/target_genomes.txt
[2023-03-14 12:56:32,816] [INFO] Task started: fastANI
[2023-03-14 12:56:32,816] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4366513-450f-404e-b379-94b7fb621fa9/OceanDNA-b30045.fa --refList OceanDNA-b30045/target_genomes.txt --output OceanDNA-b30045/fastani_result.tsv --threads 1
[2023-03-14 12:56:44,677] [INFO] Task succeeded: fastANI
[2023-03-14 12:56:44,678] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf119be1-5345-43c5-a528-5783aa5236a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:56:44,678] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf119be1-5345-43c5-a528-5783aa5236a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:56:44,689] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:56:44,689] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 12:56:44,689] [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
Oceaniglobus trochenteri	strain=G4	GCA_020529025.1	2763260	2763260	type	True	76.6789	196	1026	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	76.6527	219	1026	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	76.6187	213	1026	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	76.6109	215	1026	95	below_threshold
Roseovarius litorisediminis	strain=CECT 8287	GCA_900172295.1	1312363	1312363	type	True	76.6011	134	1026	95	below_threshold
Antarcticimicrobium sediminis	strain=S4J41	GCA_004348975.1	2546227	2546227	type	True	76.587	210	1026	95	below_threshold
Roseovarius faecimaris	strain=MME-070	GCA_009762325.1	2494550	2494550	type	True	76.5844	167	1026	95	below_threshold
Pseudoprimorskyibacter insulae	strain=CECT 8871	GCA_900302505.1	1695997	1695997	type	True	76.4972	168	1026	95	below_threshold
Thalassobius autumnalis	strain=CECT 5118	GCA_001458255.1	2072972	2072972	type	True	76.3842	132	1026	95	below_threshold
Salibaculum halophilum	strain=WDS1C4	GCA_002094885.1	1914408	1914408	type	True	76.3759	125	1026	95	below_threshold
Sulfitobacter aestuariivivens	strain=TSTF-M16	GCA_014763045.1	2766981	2766981	type	True	76.3558	124	1026	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	76.3365	195	1026	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	76.2899	173	1026	95	below_threshold
Thalassococcus halodurans	strain=DSM 26915	GCA_900108225.1	373675	373675	type	True	76.2839	122	1026	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	76.2806	137	1026	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	76.2716	140	1026	95	below_threshold
Shimia haliotis	strain=DSM 28453	GCA_900114415.1	1280847	1280847	type	True	76.2292	120	1026	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	76.1353	131	1026	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:56:44,690] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30045/tc_result.tsv
[2023-03-14 12:56:44,690] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:56:44,690] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:56:44,690] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf119be1-5345-43c5-a528-5783aa5236a6/dqc_reference/checkm_data
[2023-03-14 12:56:44,691] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:56:44,736] [INFO] Task started: CheckM
[2023-03-14 12:56:44,736] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30045/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30045/checkm_input OceanDNA-b30045/checkm_result
[2023-03-14 12:57:47,061] [INFO] Task succeeded: CheckM
[2023-03-14 12:57:47,062] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.59%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:57:47,065] [INFO] ===== Completeness check finished =====
[2023-03-14 12:57:47,066] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:57:47,066] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30045/markers.fasta)
[2023-03-14 12:57:47,068] [INFO] Task started: Blastn
[2023-03-14 12:57:47,068] [INFO] Running command: blastn -query OceanDNA-b30045/markers.fasta -db /var/lib/cwl/stgbf119be1-5345-43c5-a528-5783aa5236a6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30045/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:57:48,052] [INFO] Task succeeded: Blastn
[2023-03-14 12:57:48,053] [INFO] Selected 18 target genomes.
[2023-03-14 12:57:48,053] [INFO] Target genome list was writen to OceanDNA-b30045/target_genomes_gtdb.txt
[2023-03-14 12:57:48,092] [INFO] Task started: fastANI
[2023-03-14 12:57:48,092] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4366513-450f-404e-b379-94b7fb621fa9/OceanDNA-b30045.fa --refList OceanDNA-b30045/target_genomes_gtdb.txt --output OceanDNA-b30045/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:58:01,425] [INFO] Task succeeded: fastANI
[2023-03-14 12:58:01,436] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:58:01,436] [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_002285435.1	s__Actibacterium ureilyticum	76.9258	216	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744955.1	s__Actibacterium sp000744955	76.8802	211	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001078595.1	s__Rhodobacter_B lobularis	76.828	253	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016888515.1	s__Shimia_A biformata	76.81	174	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013003075.1	s__IMCC34051 sp013003075	76.7857	100	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__IMCC34051	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016806125.1	s__AWRV01 sp000504185	76.7706	180	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__AWRV01	95.0	99.97	99.97	1.00	1.00	2	-
GCF_900101505.1	s__Mameliella alba	76.6187	213	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mameliella	95.0	98.60	98.14	0.96	0.94	14	-
GCF_900172295.1	s__Roseovarius litorisediminis	76.6011	134	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348975.1	s__Antarcticimicrobium sediminis	76.598	211	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009762325.1	s__Roseovarius faecimaris	76.5977	167	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005434965.1	s__Marimonas lutisalis	76.4987	149	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013184805.1	s__Rhodobacter_B sp013184805	76.4703	184	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069895.1	s__Roseovarius sp018069895	76.4586	170	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.42	99.42	0.86	0.86	2	-
GCF_001458255.1	s__Thalassobius autumnalis	76.3842	132	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	99.93	99.93	0.99	0.99	2	-
GCF_009857745.1	s__Thalassobius mangrovi	76.3275	196	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000172095.1	s__Sulfitobacter indolifex	76.2838	138	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129565.1	s__Salibaculum griseiflavum	76.2755	150	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017592335.1	s__Sulfitobacter_F sp017592335	76.2661	120	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:58:01,437] [INFO] GTDB search result was written to OceanDNA-b30045/result_gtdb.tsv
[2023-03-14 12:58:01,437] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:58:01,439] [INFO] DFAST_QC result json was written to OceanDNA-b30045/dqc_result.json
[2023-03-14 12:58:01,439] [INFO] DFAST_QC completed!
[2023-03-14 12:58:01,439] [INFO] Total running time: 0h1m50s