[2024-01-24 13:57:43,721] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:43,723] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:43,723] [INFO] DQC Reference Directory: /var/lib/cwl/stg71cd8f79-af0c-4738-bea1-1dc325ab2722/dqc_reference
[2024-01-24 13:57:44,977] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:44,978] [INFO] Task started: Prodigal
[2024-01-24 13:57:44,978] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d9a7093-e932-407c-9285-ca6db6a15707/GCF_018760735.1_ASM1876073v1_genomic.fna.gz | prodigal -d GCF_018760735.1_ASM1876073v1_genomic.fna/cds.fna -a GCF_018760735.1_ASM1876073v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:14,422] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:14,422] [INFO] Task started: HMMsearch
[2024-01-24 13:58:14,423] [INFO] Running command: hmmsearch --tblout GCF_018760735.1_ASM1876073v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg71cd8f79-af0c-4738-bea1-1dc325ab2722/dqc_reference/reference_markers.hmm GCF_018760735.1_ASM1876073v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:14,731] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:14,732] [INFO] Found 6/6 markers.
[2024-01-24 13:58:14,780] [INFO] Query marker FASTA was written to GCF_018760735.1_ASM1876073v1_genomic.fna/markers.fasta
[2024-01-24 13:58:14,780] [INFO] Task started: Blastn
[2024-01-24 13:58:14,780] [INFO] Running command: blastn -query GCF_018760735.1_ASM1876073v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71cd8f79-af0c-4738-bea1-1dc325ab2722/dqc_reference/reference_markers.fasta -out GCF_018760735.1_ASM1876073v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:15,440] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:15,444] [INFO] Selected 20 target genomes.
[2024-01-24 13:58:15,445] [INFO] Target genome list was writen to GCF_018760735.1_ASM1876073v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:15,452] [INFO] Task started: fastANI
[2024-01-24 13:58:15,452] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d9a7093-e932-407c-9285-ca6db6a15707/GCF_018760735.1_ASM1876073v1_genomic.fna.gz --refList GCF_018760735.1_ASM1876073v1_genomic.fna/target_genomes.txt --output GCF_018760735.1_ASM1876073v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:39,278] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:39,278] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg71cd8f79-af0c-4738-bea1-1dc325ab2722/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:39,278] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg71cd8f79-af0c-4738-bea1-1dc325ab2722/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:39,291] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:39,292] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:39,292] [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 piscis	strain=NST-14	GCA_018760735.1	2839984	2839984	type	True	100.0	1605	1605	95	conclusive
Hymenobacter actinosclerus	strain=DSM 15310	GCA_900111515.1	82805	82805	type	True	84.4652	1070	1605	95	below_threshold
Hymenobacter aerophilus	strain=DSM 13606	GCA_000382225.1	119644	119644	type	True	84.4106	1055	1605	95	below_threshold
Hymenobacter amundsenii	strain=CCM 8682	GCA_002204745.1	2006685	2006685	type	True	84.3871	1069	1605	95	below_threshold
Hymenobacter perfusus	strain=LMG 26000	GCA_003944765.1	1236770	1236770	type	True	84.084	1136	1605	95	below_threshold
Hymenobacter psychrophilus	strain=CGMCC 1.8975	GCA_900107135.1	651662	651662	type	True	83.6874	1062	1605	95	below_threshold
Hymenobacter swuensis	strain=DY53	GCA_000576555.1	1446467	1446467	type	True	83.6223	1100	1605	95	below_threshold
Hymenobacter rigui	strain=KCTC 12533	GCA_003944715.1	334424	334424	type	True	83.508	1096	1605	95	below_threshold
Hymenobacter lapidiphilus	strain=P5342	GCA_013377885.1	2608003	2608003	type	True	83.1083	1028	1605	95	below_threshold
Hymenobacter metallilatus	strain=9PBR-2	GCA_003944705.1	2493666	2493666	type	True	82.9331	1106	1605	95	below_threshold
Hymenobacter terrestris	strain=P5252	GCA_013377905.1	2748310	2748310	type	True	82.8598	957	1605	95	below_threshold
Hymenobacter glacieicola	strain=CGMCC 1.12990	GCA_014640315.1	1562124	1562124	type	True	82.0459	995	1605	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	81.4046	910	1605	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	80.5451	894	1605	95	below_threshold
Hymenobacter telluris	strain=BT186	GCA_017313265.1	2816474	2816474	type	True	80.3097	873	1605	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	80.0072	780	1605	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:39,294] [INFO] DFAST Taxonomy check result was written to GCF_018760735.1_ASM1876073v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:39,294] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:39,294] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:39,295] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg71cd8f79-af0c-4738-bea1-1dc325ab2722/dqc_reference/checkm_data
[2024-01-24 13:58:39,295] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:39,356] [INFO] Task started: CheckM
[2024-01-24 13:58:39,356] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018760735.1_ASM1876073v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018760735.1_ASM1876073v1_genomic.fna/checkm_input GCF_018760735.1_ASM1876073v1_genomic.fna/checkm_result
[2024-01-24 13:59:50,231] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:50,232] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:50,253] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:50,253] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:50,254] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018760735.1_ASM1876073v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:50,254] [INFO] Task started: Blastn
[2024-01-24 13:59:50,254] [INFO] Running command: blastn -query GCF_018760735.1_ASM1876073v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71cd8f79-af0c-4738-bea1-1dc325ab2722/dqc_reference/reference_markers_gtdb.fasta -out GCF_018760735.1_ASM1876073v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:51,286] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:51,291] [INFO] Selected 17 target genomes.
[2024-01-24 13:59:51,292] [INFO] Target genome list was writen to GCF_018760735.1_ASM1876073v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:51,335] [INFO] Task started: fastANI
[2024-01-24 13:59:51,335] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d9a7093-e932-407c-9285-ca6db6a15707/GCF_018760735.1_ASM1876073v1_genomic.fna.gz --refList GCF_018760735.1_ASM1876073v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018760735.1_ASM1876073v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:11,529] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:11,548] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:11,548] [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_018760735.1	s__Hymenobacter sp018760735	100.0	1605	1605	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_003583925.1	s__Hymenobacter rubripertinctus	87.0566	1173	1605	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	84.4844	1068	1605	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	84.4042	1056	1605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002204745.1	s__Hymenobacter amundsenii	84.3824	1070	1605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003944765.1	s__Hymenobacter perfusus	84.0823	1137	1605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107135.1	s__Hymenobacter psychrophilus	83.6936	1063	1605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000576555.1	s__Hymenobacter swuensis	83.6002	1103	1605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003944715.1	s__Hymenobacter rigui	83.5139	1095	1605	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	83.4134	967	1605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003944705.1	s__Hymenobacter metallilatus	82.9488	1104	1605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015773195.1	s__Hymenobacter sp015773195	81.394	912	1605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012273015.1	s__Hymenobacter sp012273015	81.2755	860	1605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	97.59	97.59	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:11,549] [INFO] GTDB search result was written to GCF_018760735.1_ASM1876073v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:11,550] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:11,553] [INFO] DFAST_QC result json was written to GCF_018760735.1_ASM1876073v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:11,553] [INFO] DFAST_QC completed!
[2024-01-24 14:00:11,553] [INFO] Total running time: 0h2m28s