[2024-01-25 18:40:05,477] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:40:05,479] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:40:05,479] [INFO] DQC Reference Directory: /var/lib/cwl/stg5653a597-b681-4543-b72a-0a5066957a76/dqc_reference
[2024-01-25 18:40:06,617] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:40:06,618] [INFO] Task started: Prodigal
[2024-01-25 18:40:06,618] [INFO] Running command: gunzip -c /var/lib/cwl/stg0743ab73-d669-4c2a-aec7-77326f8a13b8/GCF_003589925.1_ASM358992v1_genomic.fna.gz | prodigal -d GCF_003589925.1_ASM358992v1_genomic.fna/cds.fna -a GCF_003589925.1_ASM358992v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:40:52,195] [INFO] Task succeeded: Prodigal
[2024-01-25 18:40:52,195] [INFO] Task started: HMMsearch
[2024-01-25 18:40:52,195] [INFO] Running command: hmmsearch --tblout GCF_003589925.1_ASM358992v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5653a597-b681-4543-b72a-0a5066957a76/dqc_reference/reference_markers.hmm GCF_003589925.1_ASM358992v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:40:52,487] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:40:52,488] [INFO] Found 6/6 markers.
[2024-01-25 18:40:52,547] [INFO] Query marker FASTA was written to GCF_003589925.1_ASM358992v1_genomic.fna/markers.fasta
[2024-01-25 18:40:52,547] [INFO] Task started: Blastn
[2024-01-25 18:40:52,547] [INFO] Running command: blastn -query GCF_003589925.1_ASM358992v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5653a597-b681-4543-b72a-0a5066957a76/dqc_reference/reference_markers.fasta -out GCF_003589925.1_ASM358992v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:53,116] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:53,119] [INFO] Selected 19 target genomes.
[2024-01-25 18:40:53,119] [INFO] Target genome list was writen to GCF_003589925.1_ASM358992v1_genomic.fna/target_genomes.txt
[2024-01-25 18:40:53,125] [INFO] Task started: fastANI
[2024-01-25 18:40:53,125] [INFO] Running command: fastANI --query /var/lib/cwl/stg0743ab73-d669-4c2a-aec7-77326f8a13b8/GCF_003589925.1_ASM358992v1_genomic.fna.gz --refList GCF_003589925.1_ASM358992v1_genomic.fna/target_genomes.txt --output GCF_003589925.1_ASM358992v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:41:13,016] [INFO] Task succeeded: fastANI
[2024-01-25 18:41:13,017] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5653a597-b681-4543-b72a-0a5066957a76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:41:13,017] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5653a597-b681-4543-b72a-0a5066957a76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:41:13,024] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:41:13,025] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:41:13,025] [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
Chryseolinea soli	strain=KIS68-18	GCA_003589925.1	2321403	2321403	type	True	100.0	2747	2747	95	conclusive
Chryseolinea serpens	strain=DSM 24574	GCA_900129725.1	947013	947013	type	True	88.3791	2239	2747	95	below_threshold
Dawidia soli	strain=PWU37	GCA_018598185.1	2782352	2782352	type	True	77.2048	347	2747	95	below_threshold
Dawidia cretensis	strain=PWU5	GCA_018598175.1	2782350	2782350	type	True	76.9383	302	2747	95	below_threshold
Chryseosolibacter histidini	strain=PWU4	GCA_018598225.1	2782349	2782349	type	True	76.8437	307	2747	95	below_threshold
Chryseosolibacter indicus	strain=PWU20	GCA_018598585.1	2782351	2782351	type	True	76.2962	58	2747	95	below_threshold
Pontibacter flavimaris	strain=S10-8	GCA_001907195.1	1797110	1797110	type	True	75.6211	62	2747	95	below_threshold
Hymenobacter jeongseonensis	strain=BT683	GCA_015694725.1	2791027	2791027	type	True	75.5218	52	2747	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	75.5	60	2747	95	below_threshold
Fibrella aquatilis	strain=HMF5036	GCA_017353255.1	2817059	2817059	type	True	75.2376	53	2747	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:41:13,026] [INFO] DFAST Taxonomy check result was written to GCF_003589925.1_ASM358992v1_genomic.fna/tc_result.tsv
[2024-01-25 18:41:13,026] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:41:13,027] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:41:13,027] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5653a597-b681-4543-b72a-0a5066957a76/dqc_reference/checkm_data
[2024-01-25 18:41:13,028] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:41:13,100] [INFO] Task started: CheckM
[2024-01-25 18:41:13,101] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003589925.1_ASM358992v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003589925.1_ASM358992v1_genomic.fna/checkm_input GCF_003589925.1_ASM358992v1_genomic.fna/checkm_result
[2024-01-25 18:43:14,467] [INFO] Task succeeded: CheckM
[2024-01-25 18:43:14,472] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:43:14,498] [INFO] ===== Completeness check finished =====
[2024-01-25 18:43:14,498] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:43:14,499] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003589925.1_ASM358992v1_genomic.fna/markers.fasta)
[2024-01-25 18:43:14,499] [INFO] Task started: Blastn
[2024-01-25 18:43:14,499] [INFO] Running command: blastn -query GCF_003589925.1_ASM358992v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5653a597-b681-4543-b72a-0a5066957a76/dqc_reference/reference_markers_gtdb.fasta -out GCF_003589925.1_ASM358992v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:15,323] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:15,326] [INFO] Selected 12 target genomes.
[2024-01-25 18:43:15,326] [INFO] Target genome list was writen to GCF_003589925.1_ASM358992v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:43:15,334] [INFO] Task started: fastANI
[2024-01-25 18:43:15,334] [INFO] Running command: fastANI --query /var/lib/cwl/stg0743ab73-d669-4c2a-aec7-77326f8a13b8/GCF_003589925.1_ASM358992v1_genomic.fna.gz --refList GCF_003589925.1_ASM358992v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003589925.1_ASM358992v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:43:30,650] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:30,656] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:43:30,656] [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_003589925.1	s__Chryseolinea soli	100.0	2747	2747	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Chryseolinea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900129725.1	s__Chryseolinea serpens	88.3695	2243	2747	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Chryseolinea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016735595.1	s__Chryseolinea sp016735595	80.0156	1150	2747	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Chryseolinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018598185.1	s__Ohtaekwangia sp018598185	77.2293	343	2747	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Ohtaekwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018598175.1	s__Ohtaekwangia sp018598175	76.9383	302	2747	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Ohtaekwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018598225.1	s__PWU20 sp018598225	76.8518	306	2747	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__PWU20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787565.1	s__JAEUUG01 sp016787565	76.6933	93	2747	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__JAEUUG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902168205.1	s__Ohtaekwangia sp902168205	76.3257	188	2747	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Ohtaekwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018598585.1	s__PWU20 sp018598585	76.2962	58	2747	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__PWU20	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:43:30,658] [INFO] GTDB search result was written to GCF_003589925.1_ASM358992v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:43:30,659] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:43:30,661] [INFO] DFAST_QC result json was written to GCF_003589925.1_ASM358992v1_genomic.fna/dqc_result.json
[2024-01-25 18:43:30,661] [INFO] DFAST_QC completed!
[2024-01-25 18:43:30,661] [INFO] Total running time: 0h3m25s