[2024-01-24 11:05:49,402] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:49,405] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:49,405] [INFO] DQC Reference Directory: /var/lib/cwl/stg5baeffbf-ae70-40b9-8162-f321ed495e2e/dqc_reference
[2024-01-24 11:05:51,282] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:51,283] [INFO] Task started: Prodigal
[2024-01-24 11:05:51,283] [INFO] Running command: gunzip -c /var/lib/cwl/stgbeaba6fb-2fce-49ce-9938-4221ecb2c97c/GCF_003149515.1_ASM314951v1_genomic.fna.gz | prodigal -d GCF_003149515.1_ASM314951v1_genomic.fna/cds.fna -a GCF_003149515.1_ASM314951v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:06:21,084] [INFO] Task succeeded: Prodigal
[2024-01-24 11:06:21,085] [INFO] Task started: HMMsearch
[2024-01-24 11:06:21,085] [INFO] Running command: hmmsearch --tblout GCF_003149515.1_ASM314951v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5baeffbf-ae70-40b9-8162-f321ed495e2e/dqc_reference/reference_markers.hmm GCF_003149515.1_ASM314951v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:06:21,296] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:06:21,297] [INFO] Found 6/6 markers.
[2024-01-24 11:06:21,334] [INFO] Query marker FASTA was written to GCF_003149515.1_ASM314951v1_genomic.fna/markers.fasta
[2024-01-24 11:06:21,334] [INFO] Task started: Blastn
[2024-01-24 11:06:21,334] [INFO] Running command: blastn -query GCF_003149515.1_ASM314951v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5baeffbf-ae70-40b9-8162-f321ed495e2e/dqc_reference/reference_markers.fasta -out GCF_003149515.1_ASM314951v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:21,943] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:21,946] [INFO] Selected 16 target genomes.
[2024-01-24 11:06:21,947] [INFO] Target genome list was writen to GCF_003149515.1_ASM314951v1_genomic.fna/target_genomes.txt
[2024-01-24 11:06:21,953] [INFO] Task started: fastANI
[2024-01-24 11:06:21,953] [INFO] Running command: fastANI --query /var/lib/cwl/stgbeaba6fb-2fce-49ce-9938-4221ecb2c97c/GCF_003149515.1_ASM314951v1_genomic.fna.gz --refList GCF_003149515.1_ASM314951v1_genomic.fna/target_genomes.txt --output GCF_003149515.1_ASM314951v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:40,738] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:40,738] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5baeffbf-ae70-40b9-8162-f321ed495e2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:40,738] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5baeffbf-ae70-40b9-8162-f321ed495e2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:40,750] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:06:40,750] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:40,750] [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 nivis	strain=NBRC 111535	GCA_003149515.1	1850093	1850093	type	True	100.0	1675	1675	95	conclusive
Hymenobacter coccineus	strain=CCM 8649	GCA_001816125.1	1908235	1908235	type	True	88.9905	1184	1675	95	below_threshold
Hymenobacter caeli	strain=9A	GCA_013294115.1	2735894	2735894	type	True	87.2161	1210	1675	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	81.1229	958	1675	95	below_threshold
Hymenobacter terricola	strain=3F2	GCA_017921975.2	2819236	2819236	type	True	81.05	959	1675	95	below_threshold
Hymenobacter properus	strain=BT439	GCA_015694735.1	2791026	2791026	type	True	80.7864	919	1675	95	below_threshold
Hymenobacter lapidarius	strain=CCM 8643	GCA_001816145.1	1908237	1908237	type	True	80.6132	823	1675	95	below_threshold
Hymenobacter sedentarius	strain=DG5B	GCA_001507645.1	1411621	1411621	type	True	80.5591	875	1675	95	below_threshold
Hymenobacter rubidus	strain=DG7B	GCA_016734815.1	1441626	1441626	type	True	80.4142	876	1675	95	below_threshold
Hymenobacter frigidus	strain=CGMCC 1.14966	GCA_014640435.1	1524095	1524095	type	True	80.2757	874	1675	95	below_threshold
Hymenobacter montanus	strain=BT664	GCA_014699115.1	2771359	2771359	type	True	79.4299	714	1675	95	below_threshold
Hymenobacter terrenus	strain=MIMtkLc17	GCA_000972495.1	1629124	1629124	type	True	79.1763	725	1675	95	below_threshold
Hymenobacter setariae	strain=Fur1	GCA_007713685.1	2594794	2594794	type	True	78.8155	724	1675	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	78.4599	629	1675	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	78.2738	586	1675	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:40,752] [INFO] DFAST Taxonomy check result was written to GCF_003149515.1_ASM314951v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:40,753] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:40,753] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:40,753] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5baeffbf-ae70-40b9-8162-f321ed495e2e/dqc_reference/checkm_data
[2024-01-24 11:06:40,754] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:40,801] [INFO] Task started: CheckM
[2024-01-24 11:06:40,801] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003149515.1_ASM314951v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003149515.1_ASM314951v1_genomic.fna/checkm_input GCF_003149515.1_ASM314951v1_genomic.fna/checkm_result
[2024-01-24 11:07:54,695] [INFO] Task succeeded: CheckM
[2024-01-24 11:07:54,696] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.02%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:07:54,713] [INFO] ===== Completeness check finished =====
[2024-01-24 11:07:54,714] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:07:54,714] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003149515.1_ASM314951v1_genomic.fna/markers.fasta)
[2024-01-24 11:07:54,714] [INFO] Task started: Blastn
[2024-01-24 11:07:54,714] [INFO] Running command: blastn -query GCF_003149515.1_ASM314951v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5baeffbf-ae70-40b9-8162-f321ed495e2e/dqc_reference/reference_markers_gtdb.fasta -out GCF_003149515.1_ASM314951v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:07:55,626] [INFO] Task succeeded: Blastn
[2024-01-24 11:07:55,629] [INFO] Selected 11 target genomes.
[2024-01-24 11:07:55,629] [INFO] Target genome list was writen to GCF_003149515.1_ASM314951v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:07:55,640] [INFO] Task started: fastANI
[2024-01-24 11:07:55,640] [INFO] Running command: fastANI --query /var/lib/cwl/stgbeaba6fb-2fce-49ce-9938-4221ecb2c97c/GCF_003149515.1_ASM314951v1_genomic.fna.gz --refList GCF_003149515.1_ASM314951v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003149515.1_ASM314951v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:08:08,802] [INFO] Task succeeded: fastANI
[2024-01-24 11:08:08,810] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:08:08,810] [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_003149515.1	s__Hymenobacter nivis	100.0	1675	1675	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_001562275.1	s__Hymenobacter sp001562275	89.5516	1343	1675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001816125.1	s__Hymenobacter coccineus	88.9836	1184	1675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006439025.1	s__Hymenobacter nivis_A	88.9392	1266	1675	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	87.1924	1212	1675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016427455.1	s__Hymenobacter sp016427455	80.9597	943	1675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	95.46	95.46	0.89	0.89	2	-
GCF_001507645.1	s__Hymenobacter sedentarius	80.5477	878	1675	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	80.4421	855	1675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000972495.1	s__Hymenobacter terrenus	79.1894	723	1675	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 11:08:08,812] [INFO] GTDB search result was written to GCF_003149515.1_ASM314951v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:08:08,812] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:08:08,816] [INFO] DFAST_QC result json was written to GCF_003149515.1_ASM314951v1_genomic.fna/dqc_result.json
[2024-01-24 11:08:08,816] [INFO] DFAST_QC completed!
[2024-01-24 11:08:08,816] [INFO] Total running time: 0h2m19s