[2023-06-29 16:35:07,311] [INFO] DFAST_QC pipeline started.
[2023-06-29 16:35:07,313] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 16:35:07,314] [INFO] DQC Reference Directory: /var/lib/cwl/stg1df0abf3-786f-448c-b95b-5cfae40d0fd3/dqc_reference
[2023-06-29 16:35:08,673] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 16:35:08,674] [INFO] Task started: Prodigal
[2023-06-29 16:35:08,674] [INFO] Running command: gunzip -c /var/lib/cwl/stge1b7522a-f8bd-4a1c-b5f7-9c668a7540ea/GCA_021151615.1_ASM2115161v1_genomic.fna.gz | prodigal -d GCA_021151615.1_ASM2115161v1_genomic.fna/cds.fna -a GCA_021151615.1_ASM2115161v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 16:35:22,220] [INFO] Task succeeded: Prodigal
[2023-06-29 16:35:22,220] [INFO] Task started: HMMsearch
[2023-06-29 16:35:22,221] [INFO] Running command: hmmsearch --tblout GCA_021151615.1_ASM2115161v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1df0abf3-786f-448c-b95b-5cfae40d0fd3/dqc_reference/reference_markers.hmm GCA_021151615.1_ASM2115161v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 16:35:22,562] [INFO] Task succeeded: HMMsearch
[2023-06-29 16:35:22,564] [INFO] Found 6/6 markers.
[2023-06-29 16:35:22,616] [INFO] Query marker FASTA was written to GCA_021151615.1_ASM2115161v1_genomic.fna/markers.fasta
[2023-06-29 16:35:22,616] [INFO] Task started: Blastn
[2023-06-29 16:35:22,616] [INFO] Running command: blastn -query GCA_021151615.1_ASM2115161v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1df0abf3-786f-448c-b95b-5cfae40d0fd3/dqc_reference/reference_markers.fasta -out GCA_021151615.1_ASM2115161v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:35:23,251] [INFO] Task succeeded: Blastn
[2023-06-29 16:35:23,255] [INFO] Selected 30 target genomes.
[2023-06-29 16:35:23,255] [INFO] Target genome list was writen to GCA_021151615.1_ASM2115161v1_genomic.fna/target_genomes.txt
[2023-06-29 16:35:23,260] [INFO] Task started: fastANI
[2023-06-29 16:35:23,260] [INFO] Running command: fastANI --query /var/lib/cwl/stge1b7522a-f8bd-4a1c-b5f7-9c668a7540ea/GCA_021151615.1_ASM2115161v1_genomic.fna.gz --refList GCA_021151615.1_ASM2115161v1_genomic.fna/target_genomes.txt --output GCA_021151615.1_ASM2115161v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 16:35:46,594] [INFO] Task succeeded: fastANI
[2023-06-29 16:35:46,594] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1df0abf3-786f-448c-b95b-5cfae40d0fd3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 16:35:46,595] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1df0abf3-786f-448c-b95b-5cfae40d0fd3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 16:35:46,610] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 16:35:46,610] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 16:35:46,610] [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
Cellvibrio japonicus	strain=Ueda107	GCA_000019225.1	155077	155077	type	True	77.6466	322	1391	95	below_threshold
Cellvibrio zantedeschiae	strain=KCTC 32239	GCA_014652535.1	1237077	1237077	type	True	77.6007	228	1391	95	below_threshold
Cellvibrio polysaccharolyticus	strain=Ka43	GCA_015182315.1	2082724	2082724	type	True	76.7189	173	1391	95	below_threshold
Gilvimarinus chinensis	strain=DSM 19667	GCA_000377745.1	396005	396005	type	True	76.6078	60	1391	95	below_threshold
Gilvimarinus polysaccharolyticus	strain=YN3	GCA_001187555.1	863921	863921	type	True	75.975	59	1391	95	below_threshold
Marinimicrobium alkaliphilum	strain=SW121	GCA_003259155.1	2202654	2202654	type	True	75.7357	61	1391	95	below_threshold
Pseudoteredinibacter isoporae	strain=DSM 22368	GCA_011683895.1	570281	570281	type	True	75.5178	53	1391	95	below_threshold
Pseudoteredinibacter isoporae	strain=LMG 25246	GCA_011602085.1	570281	570281	type	True	75.5178	53	1391	95	below_threshold
Pseudoteredinibacter isoporae	strain=DSM 22368	GCA_014207695.1	570281	570281	type	True	75.5178	53	1391	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 16:35:46,612] [INFO] DFAST Taxonomy check result was written to GCA_021151615.1_ASM2115161v1_genomic.fna/tc_result.tsv
[2023-06-29 16:35:46,613] [INFO] ===== Taxonomy check completed =====
[2023-06-29 16:35:46,613] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 16:35:46,613] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1df0abf3-786f-448c-b95b-5cfae40d0fd3/dqc_reference/checkm_data
[2023-06-29 16:35:46,614] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 16:35:46,668] [INFO] Task started: CheckM
[2023-06-29 16:35:46,668] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021151615.1_ASM2115161v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021151615.1_ASM2115161v1_genomic.fna/checkm_input GCA_021151615.1_ASM2115161v1_genomic.fna/checkm_result
[2023-06-29 16:36:28,169] [INFO] Task succeeded: CheckM
[2023-06-29 16:36:28,170] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.40%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 16:36:28,195] [INFO] ===== Completeness check finished =====
[2023-06-29 16:36:28,195] [INFO] ===== Start GTDB Search =====
[2023-06-29 16:36:28,196] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021151615.1_ASM2115161v1_genomic.fna/markers.fasta)
[2023-06-29 16:36:28,196] [INFO] Task started: Blastn
[2023-06-29 16:36:28,197] [INFO] Running command: blastn -query GCA_021151615.1_ASM2115161v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1df0abf3-786f-448c-b95b-5cfae40d0fd3/dqc_reference/reference_markers_gtdb.fasta -out GCA_021151615.1_ASM2115161v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:36:29,077] [INFO] Task succeeded: Blastn
[2023-06-29 16:36:29,082] [INFO] Selected 16 target genomes.
[2023-06-29 16:36:29,082] [INFO] Target genome list was writen to GCA_021151615.1_ASM2115161v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 16:36:29,087] [INFO] Task started: fastANI
[2023-06-29 16:36:29,087] [INFO] Running command: fastANI --query /var/lib/cwl/stge1b7522a-f8bd-4a1c-b5f7-9c668a7540ea/GCA_021151615.1_ASM2115161v1_genomic.fna.gz --refList GCA_021151615.1_ASM2115161v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021151615.1_ASM2115161v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 16:36:41,882] [INFO] Task succeeded: fastANI
[2023-06-29 16:36:41,895] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 16:36:41,896] [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_008806975.1	s__Cellvibrio sp008806975	86.4232	1148	1391	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003056245.1	s__Cellvibrio sp003056245	80.3933	726	1391	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000766945.1	s__Cellvibrio mixtus_A	80.3351	754	1391	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001183545.1	s__Cellvibrio sp001183545	79.3216	519	1391	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483365.1	s__Cellvibrio sp002483365	79.1383	521	1391	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483145.1	s__Cellvibrio sp002483145	79.1163	594	1391	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363885.1	s__Cellvibrio sp004363885	79.0948	516	1391	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903858205.1	s__Cellvibrio sp903858205	79.0794	409	1391	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002007605.1	s__Cellvibrio sp002007605	78.6296	468	1391	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	97.66	97.66	0.90	0.90	2	-
GCF_008806955.1	s__Cellvibrio sp000263355	78.4826	482	1391	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	98.02	97.81	0.88	0.84	3	-
GCF_014652535.1	s__Cellvibrio zantedeschiae	77.6087	226	1391	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 16:36:41,898] [INFO] GTDB search result was written to GCA_021151615.1_ASM2115161v1_genomic.fna/result_gtdb.tsv
[2023-06-29 16:36:41,899] [INFO] ===== GTDB Search completed =====
[2023-06-29 16:36:41,902] [INFO] DFAST_QC result json was written to GCA_021151615.1_ASM2115161v1_genomic.fna/dqc_result.json
[2023-06-29 16:36:41,903] [INFO] DFAST_QC completed!
[2023-06-29 16:36:41,903] [INFO] Total running time: 0h1m35s