[2024-01-24 12:36:35,609] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:35,612] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:35,612] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0611f6d-d020-4fb4-b49c-640a03518464/dqc_reference
[2024-01-24 12:36:36,826] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:36,827] [INFO] Task started: Prodigal
[2024-01-24 12:36:36,827] [INFO] Running command: gunzip -c /var/lib/cwl/stg13edc5d7-a027-40ac-a308-693d5fe79ca4/GCF_014643775.1_ASM1464377v1_genomic.fna.gz | prodigal -d GCF_014643775.1_ASM1464377v1_genomic.fna/cds.fna -a GCF_014643775.1_ASM1464377v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:45,821] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:45,822] [INFO] Task started: HMMsearch
[2024-01-24 12:36:45,822] [INFO] Running command: hmmsearch --tblout GCF_014643775.1_ASM1464377v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0611f6d-d020-4fb4-b49c-640a03518464/dqc_reference/reference_markers.hmm GCF_014643775.1_ASM1464377v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:46,116] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:46,118] [INFO] Found 6/6 markers.
[2024-01-24 12:36:46,147] [INFO] Query marker FASTA was written to GCF_014643775.1_ASM1464377v1_genomic.fna/markers.fasta
[2024-01-24 12:36:46,148] [INFO] Task started: Blastn
[2024-01-24 12:36:46,148] [INFO] Running command: blastn -query GCF_014643775.1_ASM1464377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0611f6d-d020-4fb4-b49c-640a03518464/dqc_reference/reference_markers.fasta -out GCF_014643775.1_ASM1464377v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:47,182] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:47,187] [INFO] Selected 10 target genomes.
[2024-01-24 12:36:47,188] [INFO] Target genome list was writen to GCF_014643775.1_ASM1464377v1_genomic.fna/target_genomes.txt
[2024-01-24 12:36:47,222] [INFO] Task started: fastANI
[2024-01-24 12:36:47,223] [INFO] Running command: fastANI --query /var/lib/cwl/stg13edc5d7-a027-40ac-a308-693d5fe79ca4/GCF_014643775.1_ASM1464377v1_genomic.fna.gz --refList GCF_014643775.1_ASM1464377v1_genomic.fna/target_genomes.txt --output GCF_014643775.1_ASM1464377v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:36:54,696] [INFO] Task succeeded: fastANI
[2024-01-24 12:36:54,696] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0611f6d-d020-4fb4-b49c-640a03518464/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:36:54,697] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0611f6d-d020-4fb4-b49c-640a03518464/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:36:54,708] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:36:54,709] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:36:54,709] [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
Arenimonas soli	strain=CGMCC 1.15905	GCA_014643775.1	2269504	2269504	type	True	100.0	994	994	95	conclusive
Arenimonas donghaensis	strain=HO3-R19	GCA_000743535.1	375061	375061	type	True	88.4421	816	994	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	86.8672	730	994	95	below_threshold
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	86.8453	715	994	95	below_threshold
Arenimonas metalli	strain=CF5-1	GCA_000747155.1	948077	948077	type	True	85.0531	721	994	95	below_threshold
Arenimonas terrae	strain=R29	GCA_006265115.1	2546226	2546226	type	True	84.7308	766	994	95	below_threshold
Pseudoxanthomonas koreensis	strain=KCTC 12208	GCA_010093225.1	266061	266061	type	True	80.2207	486	994	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	80.1841	429	994	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	79.738	486	994	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	79.335	497	994	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:36:54,711] [INFO] DFAST Taxonomy check result was written to GCF_014643775.1_ASM1464377v1_genomic.fna/tc_result.tsv
[2024-01-24 12:36:54,711] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:36:54,712] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:36:54,712] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0611f6d-d020-4fb4-b49c-640a03518464/dqc_reference/checkm_data
[2024-01-24 12:36:54,713] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:36:54,750] [INFO] Task started: CheckM
[2024-01-24 12:36:54,751] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014643775.1_ASM1464377v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014643775.1_ASM1464377v1_genomic.fna/checkm_input GCF_014643775.1_ASM1464377v1_genomic.fna/checkm_result
[2024-01-24 12:37:27,668] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:27,670] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:27,692] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:27,692] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:27,693] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014643775.1_ASM1464377v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:27,693] [INFO] Task started: Blastn
[2024-01-24 12:37:27,694] [INFO] Running command: blastn -query GCF_014643775.1_ASM1464377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0611f6d-d020-4fb4-b49c-640a03518464/dqc_reference/reference_markers_gtdb.fasta -out GCF_014643775.1_ASM1464377v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:29,605] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:29,610] [INFO] Selected 9 target genomes.
[2024-01-24 12:37:29,610] [INFO] Target genome list was writen to GCF_014643775.1_ASM1464377v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:29,632] [INFO] Task started: fastANI
[2024-01-24 12:37:29,633] [INFO] Running command: fastANI --query /var/lib/cwl/stg13edc5d7-a027-40ac-a308-693d5fe79ca4/GCF_014643775.1_ASM1464377v1_genomic.fna.gz --refList GCF_014643775.1_ASM1464377v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014643775.1_ASM1464377v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:37:36,452] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:36,464] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:37:36,464] [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_014643775.1	s__Arenimonas soli	100.0	994	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000743535.1	s__Arenimonas donghaensis	88.4324	816	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724815.1	s__Arenimonas sp001724815	86.9066	744	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000747075.1	s__Arenimonas malthae	86.8767	713	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003024235.1	s__Arenimonas caeni	86.8672	730	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003497545.1	s__Arenimonas sp003497545	86.0351	559	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	99.43	99.43	0.81	0.81	2	-
GCF_006265115.1	s__Arenimonas terrae	84.7188	768	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007993735.1	s__Arenimonas daejeonensis	84.6797	725	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241895.1	s__Arenimonas sp003241895	83.9736	685	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:37:36,466] [INFO] GTDB search result was written to GCF_014643775.1_ASM1464377v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:37:36,467] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:37:36,470] [INFO] DFAST_QC result json was written to GCF_014643775.1_ASM1464377v1_genomic.fna/dqc_result.json
[2024-01-24 12:37:36,471] [INFO] DFAST_QC completed!
[2024-01-24 12:37:36,471] [INFO] Total running time: 0h1m1s