[2024-01-24 12:57:50,061] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:57:50,064] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:57:50,064] [INFO] DQC Reference Directory: /var/lib/cwl/stg0edf26e2-81b0-406c-82f3-53bf4e7191eb/dqc_reference
[2024-01-24 12:57:51,261] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:57:51,262] [INFO] Task started: Prodigal
[2024-01-24 12:57:51,263] [INFO] Running command: gunzip -c /var/lib/cwl/stg756bd795-44bc-4b6f-b4fd-8e24498ec373/GCF_007785775.2_ASM778577v2_genomic.fna.gz | prodigal -d GCF_007785775.2_ASM778577v2_genomic.fna/cds.fna -a GCF_007785775.2_ASM778577v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:58:17,836] [INFO] Task succeeded: Prodigal
[2024-01-24 12:58:17,837] [INFO] Task started: HMMsearch
[2024-01-24 12:58:17,837] [INFO] Running command: hmmsearch --tblout GCF_007785775.2_ASM778577v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0edf26e2-81b0-406c-82f3-53bf4e7191eb/dqc_reference/reference_markers.hmm GCF_007785775.2_ASM778577v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:58:18,052] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:58:18,054] [INFO] Found 6/6 markers.
[2024-01-24 12:58:18,089] [INFO] Query marker FASTA was written to GCF_007785775.2_ASM778577v2_genomic.fna/markers.fasta
[2024-01-24 12:58:18,089] [INFO] Task started: Blastn
[2024-01-24 12:58:18,090] [INFO] Running command: blastn -query GCF_007785775.2_ASM778577v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg0edf26e2-81b0-406c-82f3-53bf4e7191eb/dqc_reference/reference_markers.fasta -out GCF_007785775.2_ASM778577v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:58:18,668] [INFO] Task succeeded: Blastn
[2024-01-24 12:58:18,671] [INFO] Selected 8 target genomes.
[2024-01-24 12:58:18,672] [INFO] Target genome list was writen to GCF_007785775.2_ASM778577v2_genomic.fna/target_genomes.txt
[2024-01-24 12:58:18,675] [INFO] Task started: fastANI
[2024-01-24 12:58:18,675] [INFO] Running command: fastANI --query /var/lib/cwl/stg756bd795-44bc-4b6f-b4fd-8e24498ec373/GCF_007785775.2_ASM778577v2_genomic.fna.gz --refList GCF_007785775.2_ASM778577v2_genomic.fna/target_genomes.txt --output GCF_007785775.2_ASM778577v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:58:25,361] [INFO] Task succeeded: fastANI
[2024-01-24 12:58:25,362] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0edf26e2-81b0-406c-82f3-53bf4e7191eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:58:25,362] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0edf26e2-81b0-406c-82f3-53bf4e7191eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:58:25,370] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:58:25,370] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:58:25,370] [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
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	100.0	1330	1334	95	conclusive
Muricauda amoyensis	strain=GCL-11	GCA_003058265.1	2169401	2169401	type	True	90.5609	1065	1334	95	below_threshold
Muricauda taeanensis	strain=JCM 17757	GCA_003584105.1	1005926	1005926	type	True	89.4486	1048	1334	95	below_threshold
Muricauda antarctica	strain=DSM 26351	GCA_900112295.1	1055723	1055723	type	True	89.4076	1045	1334	95	below_threshold
Muricauda antarctica	strain=CGMCC 1.12174	GCA_900142405.1	1055723	1055723	type	True	89.3662	1048	1334	95	below_threshold
Muricauda aurea	strain=BC31-1-A7	GCA_017313785.1	2915619	2915619	type	True	80.5141	572	1334	95	below_threshold
Muricauda profundi	strain=BC31-3-A3	GCA_017313275.1	2915620	2915620	type	True	79.3261	488	1334	95	below_threshold
Muricauda hymeniacidonis	strain=176CP4-71	GCA_004296335.1	2517819	2517819	type	True	77.4301	197	1334	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:58:25,372] [INFO] DFAST Taxonomy check result was written to GCF_007785775.2_ASM778577v2_genomic.fna/tc_result.tsv
[2024-01-24 12:58:25,373] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:58:25,373] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:58:25,373] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0edf26e2-81b0-406c-82f3-53bf4e7191eb/dqc_reference/checkm_data
[2024-01-24 12:58:25,374] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:58:25,413] [INFO] Task started: CheckM
[2024-01-24 12:58:25,413] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007785775.2_ASM778577v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007785775.2_ASM778577v2_genomic.fna/checkm_input GCF_007785775.2_ASM778577v2_genomic.fna/checkm_result
[2024-01-24 12:59:36,903] [INFO] Task succeeded: CheckM
[2024-01-24 12:59:36,904] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:59:36,922] [INFO] ===== Completeness check finished =====
[2024-01-24 12:59:36,922] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:59:36,922] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007785775.2_ASM778577v2_genomic.fna/markers.fasta)
[2024-01-24 12:59:36,923] [INFO] Task started: Blastn
[2024-01-24 12:59:36,923] [INFO] Running command: blastn -query GCF_007785775.2_ASM778577v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg0edf26e2-81b0-406c-82f3-53bf4e7191eb/dqc_reference/reference_markers_gtdb.fasta -out GCF_007785775.2_ASM778577v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:59:37,699] [INFO] Task succeeded: Blastn
[2024-01-24 12:59:37,702] [INFO] Selected 11 target genomes.
[2024-01-24 12:59:37,703] [INFO] Target genome list was writen to GCF_007785775.2_ASM778577v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:59:37,725] [INFO] Task started: fastANI
[2024-01-24 12:59:37,726] [INFO] Running command: fastANI --query /var/lib/cwl/stg756bd795-44bc-4b6f-b4fd-8e24498ec373/GCF_007785775.2_ASM778577v2_genomic.fna.gz --refList GCF_007785775.2_ASM778577v2_genomic.fna/target_genomes_gtdb.txt --output GCF_007785775.2_ASM778577v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:59:46,509] [INFO] Task succeeded: fastANI
[2024-01-24 12:59:46,519] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:59:46,519] [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_007785775.2	s__Muricauda sp003973595	100.0	1330	1334	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	98.36	98.36	0.87	0.87	2	conclusive
GCF_003058265.1	s__Muricauda sp003058265	90.5708	1064	1334	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584105.1	s__Muricauda taeanensis	89.44	1048	1334	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.68	97.68	0.85	0.85	3	-
GCF_003584135.1	s__Muricauda sp003584135	81.8105	726	1334	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	0.99	0.99	2	-
GCF_010500845.1	s__Muricauda sediminis	81.1082	668	1334	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745185.1	s__Muricauda sp000745185	80.6959	547	1334	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584165.1	s__Muricauda sp003584165	80.6626	690	1334	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001683915.1	s__Muricauda sp001683915	79.7617	543	1334	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.66	99.66	0.95	0.95	2	-
GCF_003992615.1	s__Muricauda beolgyonensis	79.2379	537	1334	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385855.1	s__Muricauda sp003385855	78.9342	519	1334	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.98	97.98	0.89	0.89	2	-
GCF_009184425.1	s__Muricauda olearia	78.902	510	1334	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.52	96.52	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:59:46,520] [INFO] GTDB search result was written to GCF_007785775.2_ASM778577v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:59:46,521] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:59:46,524] [INFO] DFAST_QC result json was written to GCF_007785775.2_ASM778577v2_genomic.fna/dqc_result.json
[2024-01-24 12:59:46,524] [INFO] DFAST_QC completed!
[2024-01-24 12:59:46,524] [INFO] Total running time: 0h1m56s