[2023-03-16 04:05:20,414] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:05:20,414] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:05:20,414] [INFO] DQC Reference Directory: /var/lib/cwl/stga2c6aac4-7651-4ca8-a4f0-f79357a911bb/dqc_reference
[2023-03-16 04:05:22,128] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:05:22,128] [INFO] Task started: Prodigal
[2023-03-16 04:05:22,128] [INFO] Running command: cat /var/lib/cwl/stg0e038d21-abf8-4d2d-8686-d21a3ff33908/OceanDNA-b3572.fa | prodigal -d OceanDNA-b3572/cds.fna -a OceanDNA-b3572/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:05:56,395] [INFO] Task succeeded: Prodigal
[2023-03-16 04:05:56,395] [INFO] Task started: HMMsearch
[2023-03-16 04:05:56,395] [INFO] Running command: hmmsearch --tblout OceanDNA-b3572/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga2c6aac4-7651-4ca8-a4f0-f79357a911bb/dqc_reference/reference_markers.hmm OceanDNA-b3572/protein.faa > /dev/null
[2023-03-16 04:05:56,625] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:05:56,625] [INFO] Found 6/6 markers.
[2023-03-16 04:05:56,650] [INFO] Query marker FASTA was written to OceanDNA-b3572/markers.fasta
[2023-03-16 04:05:56,651] [INFO] Task started: Blastn
[2023-03-16 04:05:56,651] [INFO] Running command: blastn -query OceanDNA-b3572/markers.fasta -db /var/lib/cwl/stga2c6aac4-7651-4ca8-a4f0-f79357a911bb/dqc_reference/reference_markers.fasta -out OceanDNA-b3572/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:05:57,191] [INFO] Task succeeded: Blastn
[2023-03-16 04:05:57,192] [INFO] Selected 17 target genomes.
[2023-03-16 04:05:57,192] [INFO] Target genome list was writen to OceanDNA-b3572/target_genomes.txt
[2023-03-16 04:05:57,201] [INFO] Task started: fastANI
[2023-03-16 04:05:57,201] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e038d21-abf8-4d2d-8686-d21a3ff33908/OceanDNA-b3572.fa --refList OceanDNA-b3572/target_genomes.txt --output OceanDNA-b3572/fastani_result.tsv --threads 1
[2023-03-16 04:06:11,180] [INFO] Task succeeded: fastANI
[2023-03-16 04:06:11,180] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga2c6aac4-7651-4ca8-a4f0-f79357a911bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:06:11,181] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga2c6aac4-7651-4ca8-a4f0-f79357a911bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:06:11,188] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:06:11,188] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:06:11,188] [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
Sunxiuqinia dokdonensis	strain=DH1	GCA_001270965.1	1409788	1409788	type	True	83.8535	1016	1390	95	below_threshold
Sunxiuqinia indica	strain=RC1_OXG_1F	GCA_009847015.1	2692584	2692584	type	True	78.1512	323	1390	95	below_threshold
Sunxiuqinia elliptica	strain=CGMCC 1.9156	GCA_900113005.1	655355	655355	type	True	77.6799	326	1390	95	below_threshold
Mangrovibacterium marinum	strain=DSM 28823	GCA_003046625.1	1639118	1639118	type	True	76.8878	151	1390	95	below_threshold
Mangrovibacterium diazotrophicum	strain=DSM 27148	GCA_003610535.1	1261403	1261403	type	True	76.6251	148	1390	95	below_threshold
Mangrovibacterium lignilyticum	strain=BM_7	GCA_010882175.1	2668052	2668052	type	True	76.6106	157	1390	95	below_threshold
Mariniphaga sediminis	strain=SY21	GCA_003573545.1	1628158	1628158	type	True	76.2557	67	1390	95	below_threshold
Maribellus sediminis	strain=Y2-1-60	GCA_011799805.1	2696285	2696285	type	True	76.189	61	1390	95	below_threshold
Maribellus maritimus	strain=5E3	GCA_022267315.1	2870838	2870838	type	True	75.9329	64	1390	95	below_threshold
Mariniphaga anaerophila	strain=DSM 26910	GCA_900129025.1	1484053	1484053	type	True	75.9266	65	1390	95	below_threshold
Maribellus comscasis	strain=WC007	GCA_009762775.1	2681766	2681766	type	True	75.7052	65	1390	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:06:11,189] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3572/tc_result.tsv
[2023-03-16 04:06:11,189] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:06:11,189] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:06:11,189] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga2c6aac4-7651-4ca8-a4f0-f79357a911bb/dqc_reference/checkm_data
[2023-03-16 04:06:11,190] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:06:11,204] [INFO] Task started: CheckM
[2023-03-16 04:06:11,204] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3572/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3572/checkm_input OceanDNA-b3572/checkm_result
[2023-03-16 04:07:36,148] [INFO] Task succeeded: CheckM
[2023-03-16 04:07:36,149] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:07:36,151] [INFO] ===== Completeness check finished =====
[2023-03-16 04:07:36,152] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:07:36,152] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3572/markers.fasta)
[2023-03-16 04:07:36,152] [INFO] Task started: Blastn
[2023-03-16 04:07:36,152] [INFO] Running command: blastn -query OceanDNA-b3572/markers.fasta -db /var/lib/cwl/stga2c6aac4-7651-4ca8-a4f0-f79357a911bb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3572/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:07:36,888] [INFO] Task succeeded: Blastn
[2023-03-16 04:07:36,889] [INFO] Selected 20 target genomes.
[2023-03-16 04:07:36,889] [INFO] Target genome list was writen to OceanDNA-b3572/target_genomes_gtdb.txt
[2023-03-16 04:07:36,955] [INFO] Task started: fastANI
[2023-03-16 04:07:36,955] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e038d21-abf8-4d2d-8686-d21a3ff33908/OceanDNA-b3572.fa --refList OceanDNA-b3572/target_genomes_gtdb.txt --output OceanDNA-b3572/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:07:51,466] [INFO] Task succeeded: fastANI
[2023-03-16 04:07:51,472] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:07:51,472] [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_001270965.1	s__Sunxiuqinia dokdonensis	83.8627	1015	1390	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Sunxiuqinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009847015.1	s__Sunxiuqinia indica	78.1512	323	1390	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Sunxiuqinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113005.1	s__Sunxiuqinia elliptica	77.6703	327	1390	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Sunxiuqinia	95.0	95.76	95.76	0.90	0.90	3	-
GCF_003046625.1	s__Mangrovibacterium marinum	76.8878	151	1390	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Mangrovibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610535.1	s__Mangrovibacterium diazotrophicum	76.6251	148	1390	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Mangrovibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010882175.1	s__Mangrovibacterium sp010882175	76.6106	157	1390	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Mangrovibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903865775.1	s__UBA6024 sp903865775	76.3573	56	1390	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__UBA6024	95.0	99.43	99.43	0.81	0.81	2	-
GCF_003573545.1	s__Mariniphaga sediminis	76.2557	67	1390	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Mariniphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011799805.1	s__Draconibacterium sp011799805	76.189	61	1390	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	96.71	96.71	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2023-03-16 04:07:51,473] [INFO] GTDB search result was written to OceanDNA-b3572/result_gtdb.tsv
[2023-03-16 04:07:51,473] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:07:51,474] [INFO] DFAST_QC result json was written to OceanDNA-b3572/dqc_result.json
[2023-03-16 04:07:51,474] [INFO] DFAST_QC completed!
[2023-03-16 04:07:51,474] [INFO] Total running time: 0h2m31s