[2024-01-25 18:52:35,650] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:52:35,652] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:52:35,652] [INFO] DQC Reference Directory: /var/lib/cwl/stg84eb750e-a37e-4be9-ae6c-51c34cc0617f/dqc_reference
[2024-01-25 18:52:36,774] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:52:36,774] [INFO] Task started: Prodigal
[2024-01-25 18:52:36,775] [INFO] Running command: gunzip -c /var/lib/cwl/stg20d6b2fe-4619-45bf-a978-ae22036205ae/GCF_014651575.1_ASM1465157v1_genomic.fna.gz | prodigal -d GCF_014651575.1_ASM1465157v1_genomic.fna/cds.fna -a GCF_014651575.1_ASM1465157v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:52:48,927] [INFO] Task succeeded: Prodigal
[2024-01-25 18:52:48,927] [INFO] Task started: HMMsearch
[2024-01-25 18:52:48,927] [INFO] Running command: hmmsearch --tblout GCF_014651575.1_ASM1465157v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84eb750e-a37e-4be9-ae6c-51c34cc0617f/dqc_reference/reference_markers.hmm GCF_014651575.1_ASM1465157v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:52:49,202] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:52:49,203] [INFO] Found 6/6 markers.
[2024-01-25 18:52:49,240] [INFO] Query marker FASTA was written to GCF_014651575.1_ASM1465157v1_genomic.fna/markers.fasta
[2024-01-25 18:52:49,241] [INFO] Task started: Blastn
[2024-01-25 18:52:49,241] [INFO] Running command: blastn -query GCF_014651575.1_ASM1465157v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84eb750e-a37e-4be9-ae6c-51c34cc0617f/dqc_reference/reference_markers.fasta -out GCF_014651575.1_ASM1465157v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:52:50,025] [INFO] Task succeeded: Blastn
[2024-01-25 18:52:50,034] [INFO] Selected 13 target genomes.
[2024-01-25 18:52:50,034] [INFO] Target genome list was writen to GCF_014651575.1_ASM1465157v1_genomic.fna/target_genomes.txt
[2024-01-25 18:52:50,044] [INFO] Task started: fastANI
[2024-01-25 18:52:50,044] [INFO] Running command: fastANI --query /var/lib/cwl/stg20d6b2fe-4619-45bf-a978-ae22036205ae/GCF_014651575.1_ASM1465157v1_genomic.fna.gz --refList GCF_014651575.1_ASM1465157v1_genomic.fna/target_genomes.txt --output GCF_014651575.1_ASM1465157v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:53:01,393] [INFO] Task succeeded: fastANI
[2024-01-25 18:53:01,393] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84eb750e-a37e-4be9-ae6c-51c34cc0617f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:53:01,394] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84eb750e-a37e-4be9-ae6c-51c34cc0617f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:53:01,402] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:53:01,402] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:53:01,402] [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
Halomonas lutea	strain=KCTC 12847	GCA_014651575.1	453962	453962	type	True	100.0	1493	1494	95	conclusive
Halomonas lutea	strain=DSM 23508	GCA_000378505.1	453962	453962	type	True	99.9858	1475	1494	95	conclusive
Halomonas xianhensis	strain=CGMCC 1.6848	GCA_900113605.1	442341	442341	type	True	83.3662	1018	1494	95	below_threshold
Halomonas zincidurans	strain=B6	GCA_000731955.1	1178777	1178777	type	True	79.8247	552	1494	95	below_threshold
Halomonas muralis	strain=DSM 14789	GCA_900102945.1	119000	119000	type	True	79.5218	526	1494	95	below_threshold
Halomonas ilicicola	strain=DSM 19980	GCA_900128925.1	480814	480814	type	True	79.2145	501	1494	95	below_threshold
Halomonas salipaludis	strain=WRN001	GCA_002286975.1	2032625	2032625	type	True	78.8809	476	1494	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	78.8514	443	1494	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	78.8212	414	1494	95	below_threshold
Halomonas sulfidivorans	strain=MCCC 1A13718	GCA_017868935.1	2733488	2733488	type	True	78.7186	427	1494	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	78.6959	434	1494	95	below_threshold
Halomonas antri	strain=Y3S6	GCA_019430905.1	2846777	2846777	type	True	78.6795	413	1494	95	below_threshold
Halomonas gudaonensis	strain=CGMCC 1.6133	GCA_900100195.1	376427	376427	type	True	78.3537	389	1494	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:53:01,404] [INFO] DFAST Taxonomy check result was written to GCF_014651575.1_ASM1465157v1_genomic.fna/tc_result.tsv
[2024-01-25 18:53:01,404] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:53:01,404] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:53:01,404] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84eb750e-a37e-4be9-ae6c-51c34cc0617f/dqc_reference/checkm_data
[2024-01-25 18:53:01,405] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:53:01,448] [INFO] Task started: CheckM
[2024-01-25 18:53:01,448] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014651575.1_ASM1465157v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014651575.1_ASM1465157v1_genomic.fna/checkm_input GCF_014651575.1_ASM1465157v1_genomic.fna/checkm_result
[2024-01-25 18:53:40,041] [INFO] Task succeeded: CheckM
[2024-01-25 18:53:40,042] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:53:40,062] [INFO] ===== Completeness check finished =====
[2024-01-25 18:53:40,063] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:53:40,063] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014651575.1_ASM1465157v1_genomic.fna/markers.fasta)
[2024-01-25 18:53:40,063] [INFO] Task started: Blastn
[2024-01-25 18:53:40,063] [INFO] Running command: blastn -query GCF_014651575.1_ASM1465157v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84eb750e-a37e-4be9-ae6c-51c34cc0617f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014651575.1_ASM1465157v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:53:41,436] [INFO] Task succeeded: Blastn
[2024-01-25 18:53:41,438] [INFO] Selected 13 target genomes.
[2024-01-25 18:53:41,438] [INFO] Target genome list was writen to GCF_014651575.1_ASM1465157v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:53:41,448] [INFO] Task started: fastANI
[2024-01-25 18:53:41,448] [INFO] Running command: fastANI --query /var/lib/cwl/stg20d6b2fe-4619-45bf-a978-ae22036205ae/GCF_014651575.1_ASM1465157v1_genomic.fna.gz --refList GCF_014651575.1_ASM1465157v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014651575.1_ASM1465157v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:53:52,176] [INFO] Task succeeded: fastANI
[2024-01-25 18:53:52,191] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:53:52,191] [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_000378505.1	s__Halomonas_C lutea	99.9858	1475	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_900113605.1	s__Halomonas_C xianhensis	83.3606	1018	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	96.25	96.25	0.87	0.87	2	-
GCF_900961225.1	s__Halomonas_C sp900961225	79.8859	592	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000731955.1	s__Halomonas_C zincidurans	79.8351	550	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001577635.1	s__Halomonas_C sp001577635	79.688	513	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993675.1	s__Halomonas_C sp010993675	79.6586	514	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102945.1	s__Halomonas_C muralis	79.531	525	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004117855.1	s__Halomonas_C coralii	79.3432	557	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128925.1	s__Halomonas_C ilicicola	79.2241	500	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010977575.1	s__Halomonas_B socia	78.9943	458	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002879645.1	s__Halomonas heilongjiangensis	78.9888	442	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002286975.1	s__Halomonas_B sp002286975	78.8873	476	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013349955.1	s__Halomonas_E taeanensis_B	78.7239	378	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:53:52,192] [INFO] GTDB search result was written to GCF_014651575.1_ASM1465157v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:53:52,193] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:53:52,195] [INFO] DFAST_QC result json was written to GCF_014651575.1_ASM1465157v1_genomic.fna/dqc_result.json
[2024-01-25 18:53:52,195] [INFO] DFAST_QC completed!
[2024-01-25 18:53:52,196] [INFO] Total running time: 0h1m17s