[2023-03-14 14:09:10,658] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:09:10,659] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:09:10,659] [INFO] DQC Reference Directory: /var/lib/cwl/stg1887d420-13fb-4dfb-8d0f-74d267050d3e/dqc_reference
[2023-03-14 14:09:12,178] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:09:12,178] [INFO] Task started: Prodigal
[2023-03-14 14:09:12,178] [INFO] Running command: cat /var/lib/cwl/stge7650cef-a9b8-4444-ac1b-a3d645722a55/OceanDNA-b4022.fa | prodigal -d OceanDNA-b4022/cds.fna -a OceanDNA-b4022/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:10:13,269] [INFO] Task succeeded: Prodigal
[2023-03-14 14:10:13,270] [INFO] Task started: HMMsearch
[2023-03-14 14:10:13,270] [INFO] Running command: hmmsearch --tblout OceanDNA-b4022/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1887d420-13fb-4dfb-8d0f-74d267050d3e/dqc_reference/reference_markers.hmm OceanDNA-b4022/protein.faa > /dev/null
[2023-03-14 14:10:13,556] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:10:13,557] [INFO] Found 6/6 markers.
[2023-03-14 14:10:13,593] [INFO] Query marker FASTA was written to OceanDNA-b4022/markers.fasta
[2023-03-14 14:10:13,594] [INFO] Task started: Blastn
[2023-03-14 14:10:13,594] [INFO] Running command: blastn -query OceanDNA-b4022/markers.fasta -db /var/lib/cwl/stg1887d420-13fb-4dfb-8d0f-74d267050d3e/dqc_reference/reference_markers.fasta -out OceanDNA-b4022/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:10:14,164] [INFO] Task succeeded: Blastn
[2023-03-14 14:10:14,165] [INFO] Selected 15 target genomes.
[2023-03-14 14:10:14,165] [INFO] Target genome list was writen to OceanDNA-b4022/target_genomes.txt
[2023-03-14 14:10:14,171] [INFO] Task started: fastANI
[2023-03-14 14:10:14,171] [INFO] Running command: fastANI --query /var/lib/cwl/stge7650cef-a9b8-4444-ac1b-a3d645722a55/OceanDNA-b4022.fa --refList OceanDNA-b4022/target_genomes.txt --output OceanDNA-b4022/fastani_result.tsv --threads 1
[2023-03-14 14:10:29,237] [INFO] Task succeeded: fastANI
[2023-03-14 14:10:29,237] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1887d420-13fb-4dfb-8d0f-74d267050d3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:10:29,237] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1887d420-13fb-4dfb-8d0f-74d267050d3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:10:29,245] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2023-03-14 14:10:29,245] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-14 14:10:29,245] [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
Cyclobacterium marinum	strain=DSM 745	GCA_000222485.1	104	104	type	True	98.864	1882	2050	95	conclusive
Cyclobacterium amurskyense	strain=KCTC 12363	GCA_001050135.1	320787	320787	type	True	82.8057	1149	2050	95	below_threshold
Cyclobacterium qasimii	strain=M12-11B	GCA_000427295.1	1350429	1350429	type	True	80.14	1002	2050	95	below_threshold
Cyclobacterium qasimii	strain=NBRC 106168	GCA_007991695.1	1350429	1350429	type	True	80.0479	1045	2050	95	below_threshold
Cyclobacterium plantarum	strain=GBPx2	GCA_011290685.1	2716263	2716263	type	True	77.8705	307	2050	95	below_threshold
Cyclobacterium xiamenense	strain=CGMCC 1.12432	GCA_009467825.1	1297121	1297121	type	True	77.0494	191	2050	95	below_threshold
Cyclobacterium salsum	strain=SYSU L10167	GCA_010119245.1	2666329	2666329	type	True	77.0421	239	2050	95	below_threshold
Pleomorphovibrio marinus	strain=SW125	GCA_003347495.1	2164132	2164132	type	True	76.4159	102	2050	95	below_threshold
Mongoliitalea daihaiensis	strain=X100-76	GCA_021596945.1	2782006	2782006	type	True	75.959	54	2050	95	below_threshold
Cecembia lonarensis	strain=LW9	GCA_000298295.1	645110	645110	type	True	75.7659	62	2050	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 14:10:29,245] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4022/tc_result.tsv
[2023-03-14 14:10:29,245] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:10:29,245] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:10:29,245] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1887d420-13fb-4dfb-8d0f-74d267050d3e/dqc_reference/checkm_data
[2023-03-14 14:10:29,246] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:10:29,430] [INFO] Task started: CheckM
[2023-03-14 14:10:29,430] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4022/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4022/checkm_input OceanDNA-b4022/checkm_result
[2023-03-14 14:12:31,708] [INFO] Task succeeded: CheckM
[2023-03-14 14:12:31,708] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 14:12:31,714] [INFO] ===== Completeness check finished =====
[2023-03-14 14:12:31,715] [INFO] ===== Start GTDB Search =====
[2023-03-14 14:12:31,715] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4022/markers.fasta)
[2023-03-14 14:12:31,716] [INFO] Task started: Blastn
[2023-03-14 14:12:31,716] [INFO] Running command: blastn -query OceanDNA-b4022/markers.fasta -db /var/lib/cwl/stg1887d420-13fb-4dfb-8d0f-74d267050d3e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4022/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:12:33,964] [INFO] Task succeeded: Blastn
[2023-03-14 14:12:33,965] [INFO] Selected 16 target genomes.
[2023-03-14 14:12:33,965] [INFO] Target genome list was writen to OceanDNA-b4022/target_genomes_gtdb.txt
[2023-03-14 14:12:34,133] [INFO] Task started: fastANI
[2023-03-14 14:12:34,133] [INFO] Running command: fastANI --query /var/lib/cwl/stge7650cef-a9b8-4444-ac1b-a3d645722a55/OceanDNA-b4022.fa --refList OceanDNA-b4022/target_genomes_gtdb.txt --output OceanDNA-b4022/fastani_result_gtdb.tsv --threads 1
[2023-03-14 14:12:50,595] [INFO] Task succeeded: fastANI
[2023-03-14 14:12:50,604] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 14:12:50,604] [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_000222485.1	s__Cyclobacterium marinum	98.864	1882	2050	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	98.85	98.76	0.93	0.93	3	conclusive
GCF_001050135.1	s__Cyclobacterium amurskyense	82.8179	1147	2050	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000427295.1	s__Cyclobacterium qasimii	80.1273	1005	2050	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	99.96	99.96	0.99	0.99	2	-
GCA_014762705.1	s__Cyclobacterium sp014762705	79.1201	350	2050	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011290685.1	s__Cyclobacterium plantarum	77.8815	306	2050	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216715.1	s__Cecembia calidifontis	77.5684	85	2050	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993705.1	s__Cyclobacterium sp010993705	77.5007	282	2050	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010119225.1	s__Cyclobacterium sp010119225	77.0509	243	2050	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009467825.1	s__Cyclobacterium xiamenense	77.0494	191	2050	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	97.69	97.69	0.89	0.89	2	-
GCF_010119245.1	s__Cyclobacterium sp010119245	77.0421	239	2050	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652135.1	s__Mongoliitalea lutea	75.8222	57	2050	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000298295.1	s__Cecembia lonarensis	75.7659	62	2050	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007126775.1	s__Cecembia sp007126775	75.7299	65	2050	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	99.59	99.59	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-03-14 14:12:50,604] [INFO] GTDB search result was written to OceanDNA-b4022/result_gtdb.tsv
[2023-03-14 14:12:50,604] [INFO] ===== GTDB Search completed =====
[2023-03-14 14:12:50,606] [INFO] DFAST_QC result json was written to OceanDNA-b4022/dqc_result.json
[2023-03-14 14:12:50,606] [INFO] DFAST_QC completed!
[2023-03-14 14:12:50,606] [INFO] Total running time: 0h3m40s