[2024-01-25 19:53:20,412] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:53:20,413] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:53:20,414] [INFO] DQC Reference Directory: /var/lib/cwl/stg018cb75b-ea44-459d-ad21-df9d3e2ff35e/dqc_reference
[2024-01-25 19:53:21,492] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:53:21,493] [INFO] Task started: Prodigal
[2024-01-25 19:53:21,493] [INFO] Running command: gunzip -c /var/lib/cwl/stgc4f0c1ef-515a-4b82-acec-7fbaac88c4dd/GCF_009913235.1_ASM991323v1_genomic.fna.gz | prodigal -d GCF_009913235.1_ASM991323v1_genomic.fna/cds.fna -a GCF_009913235.1_ASM991323v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:53:42,617] [INFO] Task succeeded: Prodigal
[2024-01-25 19:53:42,618] [INFO] Task started: HMMsearch
[2024-01-25 19:53:42,618] [INFO] Running command: hmmsearch --tblout GCF_009913235.1_ASM991323v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg018cb75b-ea44-459d-ad21-df9d3e2ff35e/dqc_reference/reference_markers.hmm GCF_009913235.1_ASM991323v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:53:42,877] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:53:42,878] [INFO] Found 6/6 markers.
[2024-01-25 19:53:42,910] [INFO] Query marker FASTA was written to GCF_009913235.1_ASM991323v1_genomic.fna/markers.fasta
[2024-01-25 19:53:42,910] [INFO] Task started: Blastn
[2024-01-25 19:53:42,911] [INFO] Running command: blastn -query GCF_009913235.1_ASM991323v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg018cb75b-ea44-459d-ad21-df9d3e2ff35e/dqc_reference/reference_markers.fasta -out GCF_009913235.1_ASM991323v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:53:43,467] [INFO] Task succeeded: Blastn
[2024-01-25 19:53:43,475] [INFO] Selected 14 target genomes.
[2024-01-25 19:53:43,475] [INFO] Target genome list was writen to GCF_009913235.1_ASM991323v1_genomic.fna/target_genomes.txt
[2024-01-25 19:53:43,489] [INFO] Task started: fastANI
[2024-01-25 19:53:43,489] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4f0c1ef-515a-4b82-acec-7fbaac88c4dd/GCF_009913235.1_ASM991323v1_genomic.fna.gz --refList GCF_009913235.1_ASM991323v1_genomic.fna/target_genomes.txt --output GCF_009913235.1_ASM991323v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:53:57,175] [INFO] Task succeeded: fastANI
[2024-01-25 19:53:57,175] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg018cb75b-ea44-459d-ad21-df9d3e2ff35e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:53:57,175] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg018cb75b-ea44-459d-ad21-df9d3e2ff35e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:53:57,184] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:53:57,185] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:53:57,185] [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 radiotolerans	strain=DG31D	GCA_001078055.1	1379910	1379910	type	True	79.658	697	1450	95	below_threshold
Rufibacter immobilis	strain=MCC P1	GCA_003721565.1	1348778	1348778	type	True	79.1652	640	1450	95	below_threshold
Rufibacter sediminis	strain=CGMCC 1.16289	GCA_024436355.1	2762756	2762756	type	True	79.0625	675	1450	95	below_threshold
Rufibacter glacialis	strain=MDT1-10-3	GCA_008271745.1	1259555	1259555	type	True	79.043	646	1450	95	below_threshold
Rufibacter sediminis	strain=H-1	GCA_014269285.1	2762756	2762756	type	True	79.0392	685	1450	95	below_threshold
Rufibacter glacialis	strain=CGMCC 1.9789	GCA_014645715.1	1259555	1259555	type	True	79.037	647	1450	95	below_threshold
Rufibacter hautae	strain=NBS58-1	GCA_008271695.1	2595005	2595005	type	True	78.9001	688	1450	95	below_threshold
Rufibacter latericius	strain=R-22-1 c-1	GCA_003721515.1	2487040	2487040	type	True	78.8068	622	1450	95	below_threshold
Rufibacter tibetensis	strain=1351	GCA_001310085.1	512763	512763	type	True	78.5437	536	1450	95	below_threshold
Pontibacter arcticus	strain=2b14	GCA_003284895.1	2080288	2080288	type	True	77.1349	95	1450	95	below_threshold
Pontibacter russatus	strain=BT326	GCA_009931655.1	2694929	2694929	type	True	76.642	140	1450	95	below_threshold
Pontibacter pamirensis	strain=TRT317	GCA_010015475.1	2562824	2562824	type	True	76.3892	95	1450	95	below_threshold
Pontibacter oryzae	strain=KIRAN	GCA_003576375.1	2304593	2304593	type	True	76.2684	104	1450	95	below_threshold
Hymenobacter terricola	strain=3F2	GCA_017921975.2	2819236	2819236	type	True	75.3912	66	1450	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:53:57,186] [INFO] DFAST Taxonomy check result was written to GCF_009913235.1_ASM991323v1_genomic.fna/tc_result.tsv
[2024-01-25 19:53:57,187] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:53:57,187] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:53:57,187] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg018cb75b-ea44-459d-ad21-df9d3e2ff35e/dqc_reference/checkm_data
[2024-01-25 19:53:57,188] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:53:57,234] [INFO] Task started: CheckM
[2024-01-25 19:53:57,234] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009913235.1_ASM991323v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009913235.1_ASM991323v1_genomic.fna/checkm_input GCF_009913235.1_ASM991323v1_genomic.fna/checkm_result
[2024-01-25 19:54:53,915] [INFO] Task succeeded: CheckM
[2024-01-25 19:54:53,916] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 96.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:54:53,933] [INFO] ===== Completeness check finished =====
[2024-01-25 19:54:53,933] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:54:53,934] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009913235.1_ASM991323v1_genomic.fna/markers.fasta)
[2024-01-25 19:54:53,934] [INFO] Task started: Blastn
[2024-01-25 19:54:53,934] [INFO] Running command: blastn -query GCF_009913235.1_ASM991323v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg018cb75b-ea44-459d-ad21-df9d3e2ff35e/dqc_reference/reference_markers_gtdb.fasta -out GCF_009913235.1_ASM991323v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:54:54,786] [INFO] Task succeeded: Blastn
[2024-01-25 19:54:54,789] [INFO] Selected 13 target genomes.
[2024-01-25 19:54:54,789] [INFO] Target genome list was writen to GCF_009913235.1_ASM991323v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:54:54,800] [INFO] Task started: fastANI
[2024-01-25 19:54:54,800] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4f0c1ef-515a-4b82-acec-7fbaac88c4dd/GCF_009913235.1_ASM991323v1_genomic.fna.gz --refList GCF_009913235.1_ASM991323v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009913235.1_ASM991323v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:55:09,555] [INFO] Task succeeded: fastANI
[2024-01-25 19:55:09,564] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:55:09,564] [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_009913235.1	s__Nibribacter ruber	100.0	1448	1450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Nibribacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001577755.1	s__Nibribacter sp001577755	84.2168	1055	1450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Nibribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001078055.1	s__Rufibacter radiotolerans	79.6389	697	1450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014876185.1	s__Rufibacter sp014876185	79.3495	710	1450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	100.00	99.99	1.00	1.00	10	-
GCF_001647275.1	s__Rufibacter ruber	79.2551	633	1450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	98.26	98.26	0.93	0.93	2	-
GCF_003721565.1	s__Rufibacter immobilis	79.1433	643	1450	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	79.0299	686	1450	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	79.0222	649	1450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016924645.1	s__Rufibacter sp016924645	78.941	653	1450	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	78.8811	656	1450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	95.42	95.42	0.94	0.94	2	-
GCF_017355955.1	s__Rufibacter sp017355955	78.6371	617	1450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001310085.1	s__Rufibacter tibetensis	78.5183	534	1450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001647285.1	s__Rufibacter roseus	78.0711	430	1450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:55:09,565] [INFO] GTDB search result was written to GCF_009913235.1_ASM991323v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:55:09,565] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:55:09,571] [INFO] DFAST_QC result json was written to GCF_009913235.1_ASM991323v1_genomic.fna/dqc_result.json
[2024-01-25 19:55:09,571] [INFO] DFAST_QC completed!
[2024-01-25 19:55:09,571] [INFO] Total running time: 0h1m49s