[2024-01-24 12:06:13,804] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:13,809] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:13,809] [INFO] DQC Reference Directory: /var/lib/cwl/stg75f56576-5cba-401d-8612-a260aec132d2/dqc_reference
[2024-01-24 12:06:15,343] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:15,344] [INFO] Task started: Prodigal
[2024-01-24 12:06:15,344] [INFO] Running command: gunzip -c /var/lib/cwl/stg9318ae4c-e670-4f78-bcfa-58194fd09d72/GCF_020005365.1_ASM2000536v1_genomic.fna.gz | prodigal -d GCF_020005365.1_ASM2000536v1_genomic.fna/cds.fna -a GCF_020005365.1_ASM2000536v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:22,229] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:22,229] [INFO] Task started: HMMsearch
[2024-01-24 12:06:22,229] [INFO] Running command: hmmsearch --tblout GCF_020005365.1_ASM2000536v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg75f56576-5cba-401d-8612-a260aec132d2/dqc_reference/reference_markers.hmm GCF_020005365.1_ASM2000536v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:22,509] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:22,510] [INFO] Found 6/6 markers.
[2024-01-24 12:06:22,538] [INFO] Query marker FASTA was written to GCF_020005365.1_ASM2000536v1_genomic.fna/markers.fasta
[2024-01-24 12:06:22,538] [INFO] Task started: Blastn
[2024-01-24 12:06:22,539] [INFO] Running command: blastn -query GCF_020005365.1_ASM2000536v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg75f56576-5cba-401d-8612-a260aec132d2/dqc_reference/reference_markers.fasta -out GCF_020005365.1_ASM2000536v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:23,248] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:23,252] [INFO] Selected 12 target genomes.
[2024-01-24 12:06:23,252] [INFO] Target genome list was writen to GCF_020005365.1_ASM2000536v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:23,278] [INFO] Task started: fastANI
[2024-01-24 12:06:23,279] [INFO] Running command: fastANI --query /var/lib/cwl/stg9318ae4c-e670-4f78-bcfa-58194fd09d72/GCF_020005365.1_ASM2000536v1_genomic.fna.gz --refList GCF_020005365.1_ASM2000536v1_genomic.fna/target_genomes.txt --output GCF_020005365.1_ASM2000536v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:32,382] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:32,383] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg75f56576-5cba-401d-8612-a260aec132d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:32,383] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg75f56576-5cba-401d-8612-a260aec132d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:32,391] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:32,392] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:32,392] [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
Kangiella shandongensis	strain=PI	GCA_020005365.1	2763258	2763258	type	True	100.0	920	923	95	conclusive
Kangiella sediminilitoris	strain=KCTC 23892	GCA_001708405.1	1144748	1144748	type	True	80.4329	444	923	95	below_threshold
Kangiella taiwanensis	strain=KT1	GCA_020005165.1	1079179	1079179	type	True	79.6754	336	923	95	below_threshold
Kangiella geojedonensis	strain=YCS-5	GCA_000981765.1	914150	914150	type	True	79.4982	319	923	95	below_threshold
Kangiella spongicola	strain=ATCC BAA-2076	GCA_003194565.2	796379	796379	type	True	79.111	297	923	95	below_threshold
Kangiella profundi	strain=CGMCC 1.12959	GCA_014640235.1	1561924	1561924	type	True	78.1496	166	923	95	below_threshold
Kangiella koreensis	strain=DSM 16069	GCA_000024085.1	261964	261964	type	True	77.576	190	923	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:32,394] [INFO] DFAST Taxonomy check result was written to GCF_020005365.1_ASM2000536v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:32,395] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:32,395] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:32,395] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg75f56576-5cba-401d-8612-a260aec132d2/dqc_reference/checkm_data
[2024-01-24 12:06:32,397] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:32,429] [INFO] Task started: CheckM
[2024-01-24 12:06:32,429] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020005365.1_ASM2000536v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020005365.1_ASM2000536v1_genomic.fna/checkm_input GCF_020005365.1_ASM2000536v1_genomic.fna/checkm_result
[2024-01-24 12:06:59,879] [INFO] Task succeeded: CheckM
[2024-01-24 12:06:59,880] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:06:59,898] [INFO] ===== Completeness check finished =====
[2024-01-24 12:06:59,899] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:06:59,899] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020005365.1_ASM2000536v1_genomic.fna/markers.fasta)
[2024-01-24 12:06:59,900] [INFO] Task started: Blastn
[2024-01-24 12:06:59,900] [INFO] Running command: blastn -query GCF_020005365.1_ASM2000536v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg75f56576-5cba-401d-8612-a260aec132d2/dqc_reference/reference_markers_gtdb.fasta -out GCF_020005365.1_ASM2000536v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:01,019] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:01,024] [INFO] Selected 17 target genomes.
[2024-01-24 12:07:01,025] [INFO] Target genome list was writen to GCF_020005365.1_ASM2000536v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:01,044] [INFO] Task started: fastANI
[2024-01-24 12:07:01,045] [INFO] Running command: fastANI --query /var/lib/cwl/stg9318ae4c-e670-4f78-bcfa-58194fd09d72/GCF_020005365.1_ASM2000536v1_genomic.fna.gz --refList GCF_020005365.1_ASM2000536v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020005365.1_ASM2000536v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:12,286] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:12,294] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:07:12,295] [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_001708405.1	s__Kangiella sediminilitoris	80.4194	445	923	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000981765.1	s__Kangiella geojedonensis	79.5188	319	923	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003194565.2	s__Kangiella spongicola	79.111	297	923	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	96.32	96.32	0.92	0.92	2	-
GCF_002838765.1	s__Kangiella profundi	78.119	167	923	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000374105.1	s__Kangiella aquimarina	77.757	157	923	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762745.1	s__Kangiella sp014762745	77.6763	161	923	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024085.1	s__Kangiella koreensis	77.5617	193	923	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013372875.1	s__Kangiella sp013372875	76.5177	51	923	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:12,296] [INFO] GTDB search result was written to GCF_020005365.1_ASM2000536v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:12,297] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:12,301] [INFO] DFAST_QC result json was written to GCF_020005365.1_ASM2000536v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:12,301] [INFO] DFAST_QC completed!
[2024-01-24 12:07:12,301] [INFO] Total running time: 0h0m58s