[2024-01-25 19:39:21,002] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:39:21,004] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:39:21,004] [INFO] DQC Reference Directory: /var/lib/cwl/stg91e0cad3-446e-4211-964a-73f4c91d3fb9/dqc_reference
[2024-01-25 19:39:22,249] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:39:22,250] [INFO] Task started: Prodigal
[2024-01-25 19:39:22,250] [INFO] Running command: gunzip -c /var/lib/cwl/stg64be8093-eef7-4483-99f4-395ad7e668d3/GCF_025574465.1_ASM2557446v1_genomic.fna.gz | prodigal -d GCF_025574465.1_ASM2557446v1_genomic.fna/cds.fna -a GCF_025574465.1_ASM2557446v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:39:33,990] [INFO] Task succeeded: Prodigal
[2024-01-25 19:39:33,990] [INFO] Task started: HMMsearch
[2024-01-25 19:39:33,990] [INFO] Running command: hmmsearch --tblout GCF_025574465.1_ASM2557446v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg91e0cad3-446e-4211-964a-73f4c91d3fb9/dqc_reference/reference_markers.hmm GCF_025574465.1_ASM2557446v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:39:34,239] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:39:34,241] [INFO] Found 6/6 markers.
[2024-01-25 19:39:34,286] [INFO] Query marker FASTA was written to GCF_025574465.1_ASM2557446v1_genomic.fna/markers.fasta
[2024-01-25 19:39:34,287] [INFO] Task started: Blastn
[2024-01-25 19:39:34,287] [INFO] Running command: blastn -query GCF_025574465.1_ASM2557446v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg91e0cad3-446e-4211-964a-73f4c91d3fb9/dqc_reference/reference_markers.fasta -out GCF_025574465.1_ASM2557446v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:39:35,000] [INFO] Task succeeded: Blastn
[2024-01-25 19:39:35,003] [INFO] Selected 19 target genomes.
[2024-01-25 19:39:35,003] [INFO] Target genome list was writen to GCF_025574465.1_ASM2557446v1_genomic.fna/target_genomes.txt
[2024-01-25 19:39:35,010] [INFO] Task started: fastANI
[2024-01-25 19:39:35,011] [INFO] Running command: fastANI --query /var/lib/cwl/stg64be8093-eef7-4483-99f4-395ad7e668d3/GCF_025574465.1_ASM2557446v1_genomic.fna.gz --refList GCF_025574465.1_ASM2557446v1_genomic.fna/target_genomes.txt --output GCF_025574465.1_ASM2557446v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:39:48,725] [INFO] Task succeeded: fastANI
[2024-01-25 19:39:48,725] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg91e0cad3-446e-4211-964a-73f4c91d3fb9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:39:48,725] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg91e0cad3-446e-4211-964a-73f4c91d3fb9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:39:48,732] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:39:48,732] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:39:48,732] [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
Kordiimonas gwangyangensis	strain=DSM 19435	GCA_000375545.1	288022	288022	type	True	80.7291	790	1357	95	below_threshold
Kordiimonas gwangyangensis	strain=JCM 12864	GCA_000616065.1	288022	288022	type	True	80.6222	808	1357	95	below_threshold
Kordiimonas lipolytica	strain=M41	GCA_001550065.1	1662421	1662421	type	True	78.341	360	1357	95	below_threshold
Kordiimonas lacus	strain=S3-22	GCA_001550055.1	637679	637679	type	True	78.2476	378	1357	95	below_threshold
Kordiimonas lacus	strain=CGMCC 1.9109	GCA_900101935.1	637679	637679	type	True	78.1585	366	1357	95	below_threshold
Kordiimonas marina	strain=A6E486	GCA_023006325.1	2872312	2872312	type	True	77.8153	331	1357	95	below_threshold
Kordiimonas sediminis	strain=KCTC 42590	GCA_014656395.1	1735581	1735581	type	True	76.5241	77	1357	95	below_threshold
Eilatimonas milleporae	strain=DSM 25217	GCA_003688555.1	911205	911205	type	True	75.9413	105	1357	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:39:48,733] [INFO] DFAST Taxonomy check result was written to GCF_025574465.1_ASM2557446v1_genomic.fna/tc_result.tsv
[2024-01-25 19:39:48,734] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:39:48,734] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:39:48,734] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg91e0cad3-446e-4211-964a-73f4c91d3fb9/dqc_reference/checkm_data
[2024-01-25 19:39:48,735] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:39:48,778] [INFO] Task started: CheckM
[2024-01-25 19:39:48,779] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025574465.1_ASM2557446v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025574465.1_ASM2557446v1_genomic.fna/checkm_input GCF_025574465.1_ASM2557446v1_genomic.fna/checkm_result
[2024-01-25 19:40:24,915] [INFO] Task succeeded: CheckM
[2024-01-25 19:40:24,917] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:40:24,937] [INFO] ===== Completeness check finished =====
[2024-01-25 19:40:24,938] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:40:24,939] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025574465.1_ASM2557446v1_genomic.fna/markers.fasta)
[2024-01-25 19:40:24,939] [INFO] Task started: Blastn
[2024-01-25 19:40:24,939] [INFO] Running command: blastn -query GCF_025574465.1_ASM2557446v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg91e0cad3-446e-4211-964a-73f4c91d3fb9/dqc_reference/reference_markers_gtdb.fasta -out GCF_025574465.1_ASM2557446v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:40:26,028] [INFO] Task succeeded: Blastn
[2024-01-25 19:40:26,031] [INFO] Selected 16 target genomes.
[2024-01-25 19:40:26,031] [INFO] Target genome list was writen to GCF_025574465.1_ASM2557446v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:40:26,044] [INFO] Task started: fastANI
[2024-01-25 19:40:26,044] [INFO] Running command: fastANI --query /var/lib/cwl/stg64be8093-eef7-4483-99f4-395ad7e668d3/GCF_025574465.1_ASM2557446v1_genomic.fna.gz --refList GCF_025574465.1_ASM2557446v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025574465.1_ASM2557446v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:40:37,602] [INFO] Task succeeded: fastANI
[2024-01-25 19:40:37,609] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:40:37,609] [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_000375545.1	s__Kordiimonas gwangyangensis	80.7337	789	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	99.96	99.96	1.00	1.00	2	-
GCF_001550065.1	s__Kordiimonas lipolytica	78.2918	363	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001550055.1	s__Kordiimonas lacus	78.2109	376	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	98.68	97.35	0.95	0.90	3	-
GCA_006226495.1	s__Kordiimonas sp006226495	77.5956	373	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013372975.1	s__Kordiimonas sp013372975	77.3171	269	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013372925.1	s__Kordiimonas sp013372925	77.0329	230	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015485385.1	s__Kordiimonas sp015485385	76.6346	74	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656395.1	s__Kordiimonas sediminis	76.5241	77	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011088215.1	s__Kordiimonas sp011088215	76.0411	76	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:40:37,611] [INFO] GTDB search result was written to GCF_025574465.1_ASM2557446v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:40:37,611] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:40:37,614] [INFO] DFAST_QC result json was written to GCF_025574465.1_ASM2557446v1_genomic.fna/dqc_result.json
[2024-01-25 19:40:37,614] [INFO] DFAST_QC completed!
[2024-01-25 19:40:37,614] [INFO] Total running time: 0h1m17s