[2024-01-24 13:23:10,863] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:23:10,864] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:23:10,865] [INFO] DQC Reference Directory: /var/lib/cwl/stgadf8e171-8247-41be-b2be-c045a97bfc48/dqc_reference
[2024-01-24 13:23:12,181] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:23:12,182] [INFO] Task started: Prodigal
[2024-01-24 13:23:12,182] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f24e8cd-bcb3-45a0-8bab-a59af7684bca/GCF_014138425.1_ASM1413842v1_genomic.fna.gz | prodigal -d GCF_014138425.1_ASM1413842v1_genomic.fna/cds.fna -a GCF_014138425.1_ASM1413842v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:23:42,854] [INFO] Task succeeded: Prodigal
[2024-01-24 13:23:42,854] [INFO] Task started: HMMsearch
[2024-01-24 13:23:42,854] [INFO] Running command: hmmsearch --tblout GCF_014138425.1_ASM1413842v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgadf8e171-8247-41be-b2be-c045a97bfc48/dqc_reference/reference_markers.hmm GCF_014138425.1_ASM1413842v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:23:43,108] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:23:43,109] [INFO] Found 6/6 markers.
[2024-01-24 13:23:43,151] [INFO] Query marker FASTA was written to GCF_014138425.1_ASM1413842v1_genomic.fna/markers.fasta
[2024-01-24 13:23:43,152] [INFO] Task started: Blastn
[2024-01-24 13:23:43,152] [INFO] Running command: blastn -query GCF_014138425.1_ASM1413842v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgadf8e171-8247-41be-b2be-c045a97bfc48/dqc_reference/reference_markers.fasta -out GCF_014138425.1_ASM1413842v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:43,729] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:43,732] [INFO] Selected 11 target genomes.
[2024-01-24 13:23:43,733] [INFO] Target genome list was writen to GCF_014138425.1_ASM1413842v1_genomic.fna/target_genomes.txt
[2024-01-24 13:23:43,746] [INFO] Task started: fastANI
[2024-01-24 13:23:43,746] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f24e8cd-bcb3-45a0-8bab-a59af7684bca/GCF_014138425.1_ASM1413842v1_genomic.fna.gz --refList GCF_014138425.1_ASM1413842v1_genomic.fna/target_genomes.txt --output GCF_014138425.1_ASM1413842v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:54,631] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:54,632] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgadf8e171-8247-41be-b2be-c045a97bfc48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:54,632] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgadf8e171-8247-41be-b2be-c045a97bfc48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:54,642] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:23:54,643] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:23:54,643] [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
Rufibacter immobilis	strain=MCC P1	GCA_003721565.1	1348778	1348778	type	True	81.8695	869	1837	95	below_threshold
Rufibacter sediminis	strain=CGMCC 1.16289	GCA_024436355.1	2762756	2762756	type	True	80.8298	864	1837	95	below_threshold
Rufibacter sediminis	strain=H-1	GCA_014269285.1	2762756	2762756	type	True	80.7729	866	1837	95	below_threshold
Rufibacter hautae	strain=NBS58-1	GCA_008271695.1	2595005	2595005	type	True	79.9589	798	1837	95	below_threshold
Rufibacter glacialis	strain=MDT1-10-3	GCA_008271745.1	1259555	1259555	type	True	79.9366	778	1837	95	below_threshold
Rufibacter glacialis	strain=CGMCC 1.9789	GCA_014645715.1	1259555	1259555	type	True	79.9056	783	1837	95	below_threshold
Rufibacter radiotolerans	strain=DG31D	GCA_001078055.1	1379910	1379910	type	True	79.6104	784	1837	95	below_threshold
Rufibacter latericius	strain=R-22-1 c-1	GCA_003721515.1	2487040	2487040	type	True	79.4023	736	1837	95	below_threshold
Pontibacter deserti	strain=JC215	GCA_023630255.1	1343896	1343896	type	True	76.4378	90	1837	95	below_threshold
Pontibacter pamirensis	strain=TRT317	GCA_010015475.1	2562824	2562824	type	True	76.3136	142	1837	95	below_threshold
Pontibacter silvestris	strain=XAAS-R86T	GCA_020907275.1	2305183	2305183	type	True	76.2472	81	1837	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:54,644] [INFO] DFAST Taxonomy check result was written to GCF_014138425.1_ASM1413842v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:54,645] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:54,645] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:54,645] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgadf8e171-8247-41be-b2be-c045a97bfc48/dqc_reference/checkm_data
[2024-01-24 13:23:54,647] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:54,698] [INFO] Task started: CheckM
[2024-01-24 13:23:54,699] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014138425.1_ASM1413842v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014138425.1_ASM1413842v1_genomic.fna/checkm_input GCF_014138425.1_ASM1413842v1_genomic.fna/checkm_result
[2024-01-24 13:25:12,703] [INFO] Task succeeded: CheckM
[2024-01-24 13:25:12,704] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 96.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:25:12,721] [INFO] ===== Completeness check finished =====
[2024-01-24 13:25:12,722] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:25:12,722] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014138425.1_ASM1413842v1_genomic.fna/markers.fasta)
[2024-01-24 13:25:12,722] [INFO] Task started: Blastn
[2024-01-24 13:25:12,722] [INFO] Running command: blastn -query GCF_014138425.1_ASM1413842v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgadf8e171-8247-41be-b2be-c045a97bfc48/dqc_reference/reference_markers_gtdb.fasta -out GCF_014138425.1_ASM1413842v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:13,508] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:13,511] [INFO] Selected 13 target genomes.
[2024-01-24 13:25:13,511] [INFO] Target genome list was writen to GCF_014138425.1_ASM1413842v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:25:13,535] [INFO] Task started: fastANI
[2024-01-24 13:25:13,536] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f24e8cd-bcb3-45a0-8bab-a59af7684bca/GCF_014138425.1_ASM1413842v1_genomic.fna.gz --refList GCF_014138425.1_ASM1413842v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014138425.1_ASM1413842v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:25:30,121] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:30,132] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:25:30,132] [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_001647275.1	s__Rufibacter ruber	98.1439	1648	1837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	98.26	98.26	0.93	0.93	2	conclusive
GCF_003721565.1	s__Rufibacter immobilis	81.8556	870	1837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014269285.1	s__Rufibacter sediminis	80.7762	864	1837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016924645.1	s__Rufibacter sp016924645	80.3729	854	1837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013623775.1	s__Rufibacter sp013623775	80.1219	806	1837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008271695.1	s__Rufibacter sp008271695	79.9666	796	1837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008271745.1	s__Rufibacter glacialis	79.919	780	1837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017355955.1	s__Rufibacter sp017355955	79.7945	780	1837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017916365.1	s__Rufibacter sp017916365	79.6901	760	1837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	95.42	95.42	0.94	0.94	2	-
GCF_001078055.1	s__Rufibacter radiotolerans	79.6614	774	1837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003721515.1	s__Rufibacter latericius	79.4099	733	1837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009913235.1	s__Nibribacter ruber	79.2334	663	1837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Nibribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001647285.1	s__Rufibacter roseus	78.9465	628	1837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:25:30,133] [INFO] GTDB search result was written to GCF_014138425.1_ASM1413842v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:25:30,134] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:25:30,137] [INFO] DFAST_QC result json was written to GCF_014138425.1_ASM1413842v1_genomic.fna/dqc_result.json
[2024-01-24 13:25:30,137] [INFO] DFAST_QC completed!
[2024-01-24 13:25:30,137] [INFO] Total running time: 0h2m19s