[2024-01-24 15:26:39,072] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:39,081] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:39,082] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f5d0412-a402-4543-aae6-169b65c7b625/dqc_reference
[2024-01-24 15:26:40,479] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:40,480] [INFO] Task started: Prodigal
[2024-01-24 15:26:40,481] [INFO] Running command: gunzip -c /var/lib/cwl/stg71f49337-a382-42d8-9feb-4dff051c3e4b/GCF_008728635.1_ASM872863v1_genomic.fna.gz | prodigal -d GCF_008728635.1_ASM872863v1_genomic.fna/cds.fna -a GCF_008728635.1_ASM872863v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:04,768] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:04,769] [INFO] Task started: HMMsearch
[2024-01-24 15:27:04,769] [INFO] Running command: hmmsearch --tblout GCF_008728635.1_ASM872863v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f5d0412-a402-4543-aae6-169b65c7b625/dqc_reference/reference_markers.hmm GCF_008728635.1_ASM872863v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:05,089] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:05,091] [INFO] Found 6/6 markers.
[2024-01-24 15:27:05,130] [INFO] Query marker FASTA was written to GCF_008728635.1_ASM872863v1_genomic.fna/markers.fasta
[2024-01-24 15:27:05,130] [INFO] Task started: Blastn
[2024-01-24 15:27:05,130] [INFO] Running command: blastn -query GCF_008728635.1_ASM872863v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f5d0412-a402-4543-aae6-169b65c7b625/dqc_reference/reference_markers.fasta -out GCF_008728635.1_ASM872863v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:05,801] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:05,804] [INFO] Selected 17 target genomes.
[2024-01-24 15:27:05,805] [INFO] Target genome list was writen to GCF_008728635.1_ASM872863v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:05,812] [INFO] Task started: fastANI
[2024-01-24 15:27:05,812] [INFO] Running command: fastANI --query /var/lib/cwl/stg71f49337-a382-42d8-9feb-4dff051c3e4b/GCF_008728635.1_ASM872863v1_genomic.fna.gz --refList GCF_008728635.1_ASM872863v1_genomic.fna/target_genomes.txt --output GCF_008728635.1_ASM872863v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:22,983] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:22,983] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f5d0412-a402-4543-aae6-169b65c7b625/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:22,984] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f5d0412-a402-4543-aae6-169b65c7b625/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:22,996] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:22,996] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:22,996] [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
Hymenobacter baengnokdamensis	strain=BRD72	GCA_008728635.1	2615203	2615203	type	True	100.0	1476	1476	95	conclusive
Hymenobacter ginkgonis	strain=HMF4947	GCA_009755225.1	2682976	2682976	type	True	81.553	954	1476	95	below_threshold
Hymenobacter polaris	strain=RP-2-7	GCA_012927305.1	2682546	2682546	type	True	81.1842	938	1476	95	below_threshold
Hymenobacter setariae	strain=Fur1	GCA_007713685.1	2594794	2594794	type	True	80.2599	850	1476	95	below_threshold
Hymenobacter caeli	strain=9A	GCA_013294115.1	2735894	2735894	type	True	80.1557	817	1476	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	79.721	767	1476	95	below_threshold
Hymenobacter properus	strain=BT439	GCA_015694735.1	2791026	2791026	type	True	79.3546	773	1476	95	below_threshold
Hymenobacter terricola	strain=3F2	GCA_017921975.2	2819236	2819236	type	True	79.3375	812	1476	95	below_threshold
Hymenobacter glacialis	strain=CCM 8648	GCA_001816165.1	1908236	1908236	type	True	79.2692	611	1476	95	below_threshold
Hymenobacter frigidus	strain=CGMCC 1.14966	GCA_014640435.1	1524095	1524095	type	True	79.2676	643	1476	95	below_threshold
Hymenobacter montanus	strain=BT664	GCA_014699115.1	2771359	2771359	type	True	78.8588	544	1476	95	below_threshold
Hymenobacter aerophilus	strain=DSM 13606	GCA_000382225.1	119644	119644	type	True	78.6966	572	1476	95	below_threshold
Hymenobacter actinosclerus	strain=DSM 15310	GCA_900111515.1	82805	82805	type	True	78.6123	570	1476	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	78.3028	500	1476	95	below_threshold
Hymenobacter roseosalivarius	strain=DSM 11622	GCA_900176135.1	89967	89967	type	True	77.5763	384	1476	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:22,998] [INFO] DFAST Taxonomy check result was written to GCF_008728635.1_ASM872863v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:22,999] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:22,999] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:22,999] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f5d0412-a402-4543-aae6-169b65c7b625/dqc_reference/checkm_data
[2024-01-24 15:27:23,000] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:23,043] [INFO] Task started: CheckM
[2024-01-24 15:27:23,044] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008728635.1_ASM872863v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008728635.1_ASM872863v1_genomic.fna/checkm_input GCF_008728635.1_ASM872863v1_genomic.fna/checkm_result
[2024-01-24 15:28:25,655] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:25,656] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:25,675] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:25,676] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:25,676] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008728635.1_ASM872863v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:25,677] [INFO] Task started: Blastn
[2024-01-24 15:28:25,677] [INFO] Running command: blastn -query GCF_008728635.1_ASM872863v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f5d0412-a402-4543-aae6-169b65c7b625/dqc_reference/reference_markers_gtdb.fasta -out GCF_008728635.1_ASM872863v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:26,588] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:26,592] [INFO] Selected 17 target genomes.
[2024-01-24 15:28:26,593] [INFO] Target genome list was writen to GCF_008728635.1_ASM872863v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:26,605] [INFO] Task started: fastANI
[2024-01-24 15:28:26,605] [INFO] Running command: fastANI --query /var/lib/cwl/stg71f49337-a382-42d8-9feb-4dff051c3e4b/GCF_008728635.1_ASM872863v1_genomic.fna.gz --refList GCF_008728635.1_ASM872863v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008728635.1_ASM872863v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:44,632] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:44,654] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:44,654] [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_008728635.1	s__Hymenobacter baengnokdamensis	100.0	1476	1476	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013256425.1	s__Hymenobacter sp013256425	93.8079	1303	1476	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013256625.1	s__Hymenobacter sp013256625	83.7756	1073	1476	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004684095.1	s__Hymenobacter sp004684095	83.2535	1070	1476	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001596155.1	s__Hymenobacter sp001596155	83.0588	1051	1476	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017571525.1	s__Hymenobacter sp017571525	83.0436	1072	1476	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009755225.1	s__Hymenobacter sp009755225	81.5632	952	1476	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007713685.1	s__Hymenobacter sp007713685	80.2487	852	1476	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013294115.1	s__Hymenobacter caeli	80.1714	815	1476	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000715495.1	s__Hymenobacter sp000715495	79.3328	644	1476	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382225.1	s__Hymenobacter aerophilus	78.6893	573	1476	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111515.1	s__Hymenobacter actinosclerus	78.6151	569	1476	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613725.1	s__Hymenobacter sp018613725	78.3867	490	1476	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014333525.1	s__Hymenobacter sp014333525	78.15	505	1476	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176135.1	s__Hymenobacter roseosalivarius	77.5708	384	1476	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:44,656] [INFO] GTDB search result was written to GCF_008728635.1_ASM872863v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:44,656] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:44,660] [INFO] DFAST_QC result json was written to GCF_008728635.1_ASM872863v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:44,660] [INFO] DFAST_QC completed!
[2024-01-24 15:28:44,660] [INFO] Total running time: 0h2m6s