[2024-01-24 14:19:46,643] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:46,644] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:46,644] [INFO] DQC Reference Directory: /var/lib/cwl/stge8cfca0f-ec5e-4d0b-91c5-cd28034c3138/dqc_reference
[2024-01-24 14:19:47,940] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:47,941] [INFO] Task started: Prodigal
[2024-01-24 14:19:47,941] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f26e329-a0ef-46b0-9da4-7a75507999c6/GCF_005771675.1_ASM577167v1_genomic.fna.gz | prodigal -d GCF_005771675.1_ASM577167v1_genomic.fna/cds.fna -a GCF_005771675.1_ASM577167v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:25,864] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:25,865] [INFO] Task started: HMMsearch
[2024-01-24 14:20:25,865] [INFO] Running command: hmmsearch --tblout GCF_005771675.1_ASM577167v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8cfca0f-ec5e-4d0b-91c5-cd28034c3138/dqc_reference/reference_markers.hmm GCF_005771675.1_ASM577167v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:26,163] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:26,165] [INFO] Found 6/6 markers.
[2024-01-24 14:20:26,216] [INFO] Query marker FASTA was written to GCF_005771675.1_ASM577167v1_genomic.fna/markers.fasta
[2024-01-24 14:20:26,217] [INFO] Task started: Blastn
[2024-01-24 14:20:26,217] [INFO] Running command: blastn -query GCF_005771675.1_ASM577167v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8cfca0f-ec5e-4d0b-91c5-cd28034c3138/dqc_reference/reference_markers.fasta -out GCF_005771675.1_ASM577167v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:26,932] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:26,935] [INFO] Selected 15 target genomes.
[2024-01-24 14:20:26,936] [INFO] Target genome list was writen to GCF_005771675.1_ASM577167v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:26,949] [INFO] Task started: fastANI
[2024-01-24 14:20:26,950] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f26e329-a0ef-46b0-9da4-7a75507999c6/GCF_005771675.1_ASM577167v1_genomic.fna.gz --refList GCF_005771675.1_ASM577167v1_genomic.fna/target_genomes.txt --output GCF_005771675.1_ASM577167v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:46,724] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:46,725] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8cfca0f-ec5e-4d0b-91c5-cd28034c3138/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:46,725] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8cfca0f-ec5e-4d0b-91c5-cd28034c3138/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:46,737] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:46,737] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:46,737] [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 jeollabukensis	strain=1-3-3-8	GCA_005771675.1	2025313	2025313	type	True	100.0	2044	2046	95	conclusive
Hymenobacter edaphi	strain=NL	GCA_003258365.1	2211146	2211146	type	True	92.1358	1685	2046	95	below_threshold
Hymenobacter gummosus	strain=KCTC 52166	GCA_003970915.1	1776032	1776032	type	True	87.3423	1566	2046	95	below_threshold
Hymenobacter busanensis	strain=MA3	GCA_008727865.1	2607656	2607656	type	True	83.1354	1215	2046	95	below_threshold
Hymenobacter oligotrophus	strain=sh-6	GCA_003574965.1	2319843	2319843	type	True	81.4001	931	2046	95	below_threshold
Hymenobacter persicinus	strain=1-3-3-3	GCA_004167665.1	2025506	2025506	type	True	80.8873	976	2046	95	below_threshold
Hymenobacter piscis	strain=NST-14	GCA_018760735.1	2839984	2839984	type	True	80.539	968	2046	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	80.1982	920	2046	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	79.8949	963	2046	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	79.8021	920	2046	95	below_threshold
Hymenobacter glacialis	strain=CCM 8648	GCA_001816165.1	1908236	1908236	type	True	79.1334	670	2046	95	below_threshold
Hymenobacter terricola	strain=3F2	GCA_017921975.2	2819236	2819236	type	True	78.9817	902	2046	95	below_threshold
Hymenobacter montanus	strain=BT664	GCA_014699115.1	2771359	2771359	type	True	78.6122	642	2046	95	below_threshold
Actinokineospora bangkokensis	strain=44EHW	GCA_001940455.1	1193682	1193682	type	True	74.7349	225	2046	95	below_threshold
Amycolatopsis anabasis	strain=EGI 650086	GCA_009765355.1	1840409	1840409	type	True	74.6567	171	2046	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:46,739] [INFO] DFAST Taxonomy check result was written to GCF_005771675.1_ASM577167v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:46,739] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:46,739] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:46,739] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8cfca0f-ec5e-4d0b-91c5-cd28034c3138/dqc_reference/checkm_data
[2024-01-24 14:20:46,740] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:46,798] [INFO] Task started: CheckM
[2024-01-24 14:20:46,798] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005771675.1_ASM577167v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005771675.1_ASM577167v1_genomic.fna/checkm_input GCF_005771675.1_ASM577167v1_genomic.fna/checkm_result
[2024-01-24 14:22:13,626] [INFO] Task succeeded: CheckM
[2024-01-24 14:22:13,627] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:22:13,643] [INFO] ===== Completeness check finished =====
[2024-01-24 14:22:13,643] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:22:13,643] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005771675.1_ASM577167v1_genomic.fna/markers.fasta)
[2024-01-24 14:22:13,644] [INFO] Task started: Blastn
[2024-01-24 14:22:13,644] [INFO] Running command: blastn -query GCF_005771675.1_ASM577167v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8cfca0f-ec5e-4d0b-91c5-cd28034c3138/dqc_reference/reference_markers_gtdb.fasta -out GCF_005771675.1_ASM577167v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:14,667] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:14,671] [INFO] Selected 11 target genomes.
[2024-01-24 14:22:14,671] [INFO] Target genome list was writen to GCF_005771675.1_ASM577167v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:22:14,684] [INFO] Task started: fastANI
[2024-01-24 14:22:14,685] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f26e329-a0ef-46b0-9da4-7a75507999c6/GCF_005771675.1_ASM577167v1_genomic.fna.gz --refList GCF_005771675.1_ASM577167v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005771675.1_ASM577167v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:22:30,865] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:30,876] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:22:30,876] [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_005771675.1	s__Solirubrum jeollabukense	100.0	2044	2046	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Solirubrum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003258365.1	s__Solirubrum edaphi	92.153	1683	2046	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Solirubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970915.1	s__Solirubrum gummosum	87.3705	1562	2046	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Solirubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002007105.1	s__Solirubrum sp002007105	85.6721	1425	2046	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Solirubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008727865.1	s__Solirubrum busanensis	83.164	1211	2046	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Solirubrum	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003574965.1	s__Solirubrum oligotrophum	81.4027	931	2046	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Solirubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001483135.1	s__Solirubrum puertoriconensis	80.7461	947	2046	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Solirubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583925.1	s__Hymenobacter rubripertinctus	79.8336	890	2046	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	79.8156	864	2046	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	79.4334	880	2046	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745955.1	s__Hymenobacter elongatus	79.2003	754	2046	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 14:22:30,878] [INFO] GTDB search result was written to GCF_005771675.1_ASM577167v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:22:30,878] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:22:30,882] [INFO] DFAST_QC result json was written to GCF_005771675.1_ASM577167v1_genomic.fna/dqc_result.json
[2024-01-24 14:22:30,882] [INFO] DFAST_QC completed!
[2024-01-24 14:22:30,883] [INFO] Total running time: 0h2m44s