[2023-03-15 15:55:16,221] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:55:16,221] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:55:16,221] [INFO] DQC Reference Directory: /var/lib/cwl/stg0af17bc8-499a-46db-aa2f-add2bd1068c3/dqc_reference
[2023-03-15 15:55:17,912] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:55:17,913] [INFO] Task started: Prodigal
[2023-03-15 15:55:17,913] [INFO] Running command: cat /var/lib/cwl/stg2a9a0016-cb90-4ba5-af31-9f68ea6226df/OceanDNA-b38972.fa | prodigal -d OceanDNA-b38972/cds.fna -a OceanDNA-b38972/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:55:40,794] [INFO] Task succeeded: Prodigal
[2023-03-15 15:55:40,794] [INFO] Task started: HMMsearch
[2023-03-15 15:55:40,794] [INFO] Running command: hmmsearch --tblout OceanDNA-b38972/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0af17bc8-499a-46db-aa2f-add2bd1068c3/dqc_reference/reference_markers.hmm OceanDNA-b38972/protein.faa > /dev/null
[2023-03-15 15:55:41,051] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:55:41,052] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2a9a0016-cb90-4ba5-af31-9f68ea6226df/OceanDNA-b38972.fa]
[2023-03-15 15:55:41,075] [INFO] Query marker FASTA was written to OceanDNA-b38972/markers.fasta
[2023-03-15 15:55:41,076] [INFO] Task started: Blastn
[2023-03-15 15:55:41,076] [INFO] Running command: blastn -query OceanDNA-b38972/markers.fasta -db /var/lib/cwl/stg0af17bc8-499a-46db-aa2f-add2bd1068c3/dqc_reference/reference_markers.fasta -out OceanDNA-b38972/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:55:41,758] [INFO] Task succeeded: Blastn
[2023-03-15 15:55:41,759] [INFO] Selected 16 target genomes.
[2023-03-15 15:55:41,759] [INFO] Target genome list was writen to OceanDNA-b38972/target_genomes.txt
[2023-03-15 15:55:41,772] [INFO] Task started: fastANI
[2023-03-15 15:55:41,772] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a9a0016-cb90-4ba5-af31-9f68ea6226df/OceanDNA-b38972.fa --refList OceanDNA-b38972/target_genomes.txt --output OceanDNA-b38972/fastani_result.tsv --threads 1
[2023-03-15 15:55:53,822] [INFO] Task succeeded: fastANI
[2023-03-15 15:55:53,822] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0af17bc8-499a-46db-aa2f-add2bd1068c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:55:53,822] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0af17bc8-499a-46db-aa2f-add2bd1068c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:55:53,832] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:55:53,832] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 15:55:53,832] [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
Marinobacter halotolerans	strain=NBRC 110910	GCA_008795985.1	1569211	1569211	type	True	94.6063	1042	1221	95	below_threshold
Marinobacter confluentis	strain=HJM-18	GCA_004785685.1	1697557	1697557	type	True	81.1148	729	1221	95	below_threshold
Marinobacter confluentis	strain=KCTC 42705	GCA_008795935.1	1697557	1697557	type	True	81.0852	733	1221	95	below_threshold
Marinobacter algicola	strain=DG893	GCA_000170835.1	236100	236100	type	True	79.5647	533	1221	95	below_threshold
Marinobacter orientalis	strain=W62	GCA_004792665.1	1928859	1928859	type	True	79.4402	524	1221	95	below_threshold
Marinobacter vulgaris	strain=F01	GCA_007559285.1	1928331	1928331	type	True	79.3939	552	1221	95	below_threshold
Marinobacter vulgaris	strain=F01	GCA_003344045.1	1928331	1928331	type	True	79.3924	552	1221	95	below_threshold
Marinobacter orientalis	strain=W62	GCA_012956055.1	1928859	1928859	type	True	79.3915	531	1221	95	below_threshold
Marinobacter denitrificans	strain=JB02H27	GCA_008795955.1	2597703	2597703	type	True	79.3796	556	1221	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	78.943	477	1221	95	below_threshold
Marinobacter sediminum	strain=R65	GCA_016820575.1	256323	256323	type	True	78.7545	422	1221	95	below_threshold
Marinobacter shengliensis subsp. alexandrii	strain=LZ-6	GCA_005871095.1	2570350	1389223	type	True	78.6439	427	1221	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	78.4993	458	1221	95	below_threshold
Marinobacter koreensis	strain=DSM 17924	GCA_023156285.1	335974	335974	type	True	78.2929	407	1221	95	below_threshold
Marinobacter bryozoorum	strain=DSM 15401	GCA_023156245.1	256324	256324	type	True	78.2749	339	1221	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	76.3905	94	1221	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 15:55:53,832] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38972/tc_result.tsv
[2023-03-15 15:55:53,832] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:55:53,832] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:55:53,833] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0af17bc8-499a-46db-aa2f-add2bd1068c3/dqc_reference/checkm_data
[2023-03-15 15:55:53,833] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:55:53,839] [INFO] Task started: CheckM
[2023-03-15 15:55:53,839] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38972/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38972/checkm_input OceanDNA-b38972/checkm_result
[2023-03-15 15:56:50,838] [INFO] Task succeeded: CheckM
[2023-03-15 15:56:50,839] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.90%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 15:56:50,842] [INFO] ===== Completeness check finished =====
[2023-03-15 15:56:50,842] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:56:50,842] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38972/markers.fasta)
[2023-03-15 15:56:50,843] [INFO] Task started: Blastn
[2023-03-15 15:56:50,843] [INFO] Running command: blastn -query OceanDNA-b38972/markers.fasta -db /var/lib/cwl/stg0af17bc8-499a-46db-aa2f-add2bd1068c3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38972/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:56:52,001] [INFO] Task succeeded: Blastn
[2023-03-15 15:56:52,002] [INFO] Selected 15 target genomes.
[2023-03-15 15:56:52,002] [INFO] Target genome list was writen to OceanDNA-b38972/target_genomes_gtdb.txt
[2023-03-15 15:56:52,015] [INFO] Task started: fastANI
[2023-03-15 15:56:52,015] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a9a0016-cb90-4ba5-af31-9f68ea6226df/OceanDNA-b38972.fa --refList OceanDNA-b38972/target_genomes_gtdb.txt --output OceanDNA-b38972/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:57:03,598] [INFO] Task succeeded: fastANI
[2023-03-15 15:57:03,607] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 15:57:03,607] [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_008795985.1	s__Marinobacter halotolerans	94.587	1043	1221	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004785685.1	s__Marinobacter confluentis	81.1297	727	1221	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005298175.1	s__Marinobacter sp005298175	79.8777	601	1221	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000686085.1	s__Marinobacter sp000686085	79.7741	606	1221	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000831005.1	s__Marinobacter salarius	79.6002	574	1221	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.84	96.73	0.88	0.79	21	-
GCF_000170835.1	s__Marinobacter algicola	79.5661	531	1221	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004792665.1	s__Marinobacter orientalis	79.4411	524	1221	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003344045.1	s__Marinobacter vulgaris	79.3835	553	1221	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008795955.1	s__Marinobacter sp008795955	79.3683	556	1221	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017643965.1	s__Marinobacter sp017643965	79.0039	378	1221	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002744715.1	s__Marinobacter profundi	78.8767	429	1221	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.28	99.28	0.94	0.94	2	-
GCA_018623515.1	s__Marinobacter sp018623515	78.8583	407	1221	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016820575.1	s__Marinobacter sediminum	78.7545	422	1221	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001447155.2	s__Marinobacter sp001447155	78.6588	445	1221	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762755.1	s__Marinobacter sp014762755	78.4879	360	1221	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 15:57:03,608] [INFO] GTDB search result was written to OceanDNA-b38972/result_gtdb.tsv
[2023-03-15 15:57:03,608] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:57:03,610] [INFO] DFAST_QC result json was written to OceanDNA-b38972/dqc_result.json
[2023-03-15 15:57:03,610] [INFO] DFAST_QC completed!
[2023-03-15 15:57:03,610] [INFO] Total running time: 0h1m47s