[2024-01-24 13:55:40,609] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:40,610] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:40,611] [INFO] DQC Reference Directory: /var/lib/cwl/stgd926f800-6443-4b0a-b3aa-7e3edb2737f3/dqc_reference
[2024-01-24 13:55:41,812] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:41,813] [INFO] Task started: Prodigal
[2024-01-24 13:55:41,813] [INFO] Running command: gunzip -c /var/lib/cwl/stga406d15b-b2e8-4ab7-80c9-54c768e36b59/GCF_013294115.1_ASM1329411v1_genomic.fna.gz | prodigal -d GCF_013294115.1_ASM1329411v1_genomic.fna/cds.fna -a GCF_013294115.1_ASM1329411v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:12,711] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:12,712] [INFO] Task started: HMMsearch
[2024-01-24 13:56:12,712] [INFO] Running command: hmmsearch --tblout GCF_013294115.1_ASM1329411v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd926f800-6443-4b0a-b3aa-7e3edb2737f3/dqc_reference/reference_markers.hmm GCF_013294115.1_ASM1329411v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:13,048] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:13,050] [INFO] Found 6/6 markers.
[2024-01-24 13:56:13,091] [INFO] Query marker FASTA was written to GCF_013294115.1_ASM1329411v1_genomic.fna/markers.fasta
[2024-01-24 13:56:13,091] [INFO] Task started: Blastn
[2024-01-24 13:56:13,092] [INFO] Running command: blastn -query GCF_013294115.1_ASM1329411v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd926f800-6443-4b0a-b3aa-7e3edb2737f3/dqc_reference/reference_markers.fasta -out GCF_013294115.1_ASM1329411v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:13,731] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:13,735] [INFO] Selected 16 target genomes.
[2024-01-24 13:56:13,736] [INFO] Target genome list was writen to GCF_013294115.1_ASM1329411v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:13,762] [INFO] Task started: fastANI
[2024-01-24 13:56:13,763] [INFO] Running command: fastANI --query /var/lib/cwl/stga406d15b-b2e8-4ab7-80c9-54c768e36b59/GCF_013294115.1_ASM1329411v1_genomic.fna.gz --refList GCF_013294115.1_ASM1329411v1_genomic.fna/target_genomes.txt --output GCF_013294115.1_ASM1329411v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:33,332] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:33,333] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd926f800-6443-4b0a-b3aa-7e3edb2737f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:33,333] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd926f800-6443-4b0a-b3aa-7e3edb2737f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:33,350] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:33,350] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:33,350] [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 caeli	strain=9A	GCA_013294115.1	2735894	2735894	type	True	100.0	1635	1638	95	conclusive
Hymenobacter coccineus	strain=CCM 8649	GCA_001816125.1	1908235	1908235	type	True	87.608	1155	1638	95	below_threshold
Hymenobacter nivis	strain=NBRC 111535	GCA_003149515.1	1850093	1850093	type	True	87.1967	1217	1638	95	below_threshold
Hymenobacter ruricola	strain=BT662	GCA_015694525.1	2791023	2791023	type	True	82.0918	1014	1638	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	81.986	1037	1638	95	below_threshold
Hymenobacter terricola	strain=3F2	GCA_017921975.2	2819236	2819236	type	True	81.7807	1070	1638	95	below_threshold
Hymenobacter sedentarius	strain=DG5B	GCA_001507645.1	1411621	1411621	type	True	81.379	938	1638	95	below_threshold
Hymenobacter rubidus	strain=DG7B	GCA_016734815.1	1441626	1441626	type	True	81.1178	956	1638	95	below_threshold
Hymenobacter lapidarius	strain=CCM 8643	GCA_001816145.1	1908237	1908237	type	True	81.0441	887	1638	95	below_threshold
Hymenobacter glacialis	strain=CCM 8648	GCA_001816165.1	1908236	1908236	type	True	80.8861	859	1638	95	below_threshold
Hymenobacter polaris	strain=RP-2-7	GCA_012927305.1	2682546	2682546	type	True	80.8771	995	1638	95	below_threshold
Hymenobacter jeongseonensis	strain=BT683	GCA_015694725.1	2791027	2791027	type	True	80.354	864	1638	95	below_threshold
Hymenobacter montanus	strain=BT664	GCA_014699115.1	2771359	2771359	type	True	80.1127	817	1638	95	below_threshold
Hymenobacter piscis	strain=NST-14	GCA_018760735.1	2839984	2839984	type	True	80.0428	805	1638	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	78.8611	686	1638	95	below_threshold
Glycomyces tenuis	strain=DSM 44171	GCA_000427885.1	58116	58116	type	True	74.6515	88	1638	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:33,352] [INFO] DFAST Taxonomy check result was written to GCF_013294115.1_ASM1329411v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:33,352] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:33,353] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:33,353] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd926f800-6443-4b0a-b3aa-7e3edb2737f3/dqc_reference/checkm_data
[2024-01-24 13:56:33,355] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:33,413] [INFO] Task started: CheckM
[2024-01-24 13:56:33,413] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013294115.1_ASM1329411v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013294115.1_ASM1329411v1_genomic.fna/checkm_input GCF_013294115.1_ASM1329411v1_genomic.fna/checkm_result
[2024-01-24 13:57:50,964] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:50,965] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:50,988] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:50,988] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:50,989] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013294115.1_ASM1329411v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:50,989] [INFO] Task started: Blastn
[2024-01-24 13:57:50,989] [INFO] Running command: blastn -query GCF_013294115.1_ASM1329411v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd926f800-6443-4b0a-b3aa-7e3edb2737f3/dqc_reference/reference_markers_gtdb.fasta -out GCF_013294115.1_ASM1329411v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:52,013] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:52,018] [INFO] Selected 11 target genomes.
[2024-01-24 13:57:52,018] [INFO] Target genome list was writen to GCF_013294115.1_ASM1329411v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:52,026] [INFO] Task started: fastANI
[2024-01-24 13:57:52,026] [INFO] Running command: fastANI --query /var/lib/cwl/stga406d15b-b2e8-4ab7-80c9-54c768e36b59/GCF_013294115.1_ASM1329411v1_genomic.fna.gz --refList GCF_013294115.1_ASM1329411v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013294115.1_ASM1329411v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:07,317] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:07,327] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:07,327] [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_013294115.1	s__Hymenobacter caeli	100.0	1635	1638	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	87.7031	1284	1638	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	87.6212	1235	1638	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	87.6141	1155	1638	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003149515.1	s__Hymenobacter nivis	87.1779	1219	1638	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015694525.1	s__Hymenobacter ruricola	82.0611	1018	1638	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012275535.1	s__Hymenobacter artigasi	81.5184	1047	1638	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	81.0115	901	1638	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001816165.1	s__Hymenobacter glacialis	80.894	857	1638	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141805.1	s__Hymenobacter daecheongensis	79.67	760	1638	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	79.2863	667	1638	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 13:58:07,329] [INFO] GTDB search result was written to GCF_013294115.1_ASM1329411v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:07,329] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:07,334] [INFO] DFAST_QC result json was written to GCF_013294115.1_ASM1329411v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:07,334] [INFO] DFAST_QC completed!
[2024-01-24 13:58:07,334] [INFO] Total running time: 0h2m27s