[2024-01-24 15:26:47,959] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:47,960] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:47,960] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a13e17b-66d3-4d97-9d3c-f6a136092bf6/dqc_reference
[2024-01-24 15:26:49,164] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:49,165] [INFO] Task started: Prodigal
[2024-01-24 15:26:49,165] [INFO] Running command: gunzip -c /var/lib/cwl/stg9e288a34-f014-417b-8d85-bffb395ba96d/GCF_014652535.1_ASM1465253v1_genomic.fna.gz | prodigal -d GCF_014652535.1_ASM1465253v1_genomic.fna/cds.fna -a GCF_014652535.1_ASM1465253v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:00,646] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:00,647] [INFO] Task started: HMMsearch
[2024-01-24 15:27:00,647] [INFO] Running command: hmmsearch --tblout GCF_014652535.1_ASM1465253v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a13e17b-66d3-4d97-9d3c-f6a136092bf6/dqc_reference/reference_markers.hmm GCF_014652535.1_ASM1465253v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:00,930] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:00,932] [INFO] Found 6/6 markers.
[2024-01-24 15:27:00,977] [INFO] Query marker FASTA was written to GCF_014652535.1_ASM1465253v1_genomic.fna/markers.fasta
[2024-01-24 15:27:00,978] [INFO] Task started: Blastn
[2024-01-24 15:27:00,978] [INFO] Running command: blastn -query GCF_014652535.1_ASM1465253v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a13e17b-66d3-4d97-9d3c-f6a136092bf6/dqc_reference/reference_markers.fasta -out GCF_014652535.1_ASM1465253v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:01,683] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:01,686] [INFO] Selected 23 target genomes.
[2024-01-24 15:27:01,687] [INFO] Target genome list was writen to GCF_014652535.1_ASM1465253v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:01,697] [INFO] Task started: fastANI
[2024-01-24 15:27:01,697] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e288a34-f014-417b-8d85-bffb395ba96d/GCF_014652535.1_ASM1465253v1_genomic.fna.gz --refList GCF_014652535.1_ASM1465253v1_genomic.fna/target_genomes.txt --output GCF_014652535.1_ASM1465253v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:17,433] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:17,434] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a13e17b-66d3-4d97-9d3c-f6a136092bf6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:17,434] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a13e17b-66d3-4d97-9d3c-f6a136092bf6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:17,441] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:17,442] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:17,442] [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 zantedeschiae	strain=KCTC 32239	GCA_014652535.1	1237077	1237077	type	True	100.0	1416	1417	95	conclusive
Cellvibrio polysaccharolyticus	strain=Ka43	GCA_015182315.1	2082724	2082724	type	True	77.4347	138	1417	95	below_threshold
Cellvibrio japonicus	strain=Ueda107	GCA_000019225.1	155077	155077	type	True	77.3718	147	1417	95	below_threshold
Pseudoteredinibacter isoporae	strain=LMG 25246	GCA_011602085.1	570281	570281	type	True	76.7253	52	1417	95	below_threshold
Pseudoteredinibacter isoporae	strain=DSM 22368	GCA_014207695.1	570281	570281	type	True	76.6406	51	1417	95	below_threshold
Gilvimarinus polysaccharolyticus	strain=YN3	GCA_001187555.1	863921	863921	type	True	76.2738	66	1417	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:17,443] [INFO] DFAST Taxonomy check result was written to GCF_014652535.1_ASM1465253v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:17,444] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:17,444] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:17,444] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a13e17b-66d3-4d97-9d3c-f6a136092bf6/dqc_reference/checkm_data
[2024-01-24 15:27:17,446] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:17,487] [INFO] Task started: CheckM
[2024-01-24 15:27:17,487] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014652535.1_ASM1465253v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014652535.1_ASM1465253v1_genomic.fna/checkm_input GCF_014652535.1_ASM1465253v1_genomic.fna/checkm_result
[2024-01-24 15:27:55,565] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:55,566] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:55,583] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:55,583] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:55,584] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014652535.1_ASM1465253v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:55,584] [INFO] Task started: Blastn
[2024-01-24 15:27:55,584] [INFO] Running command: blastn -query GCF_014652535.1_ASM1465253v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a13e17b-66d3-4d97-9d3c-f6a136092bf6/dqc_reference/reference_markers_gtdb.fasta -out GCF_014652535.1_ASM1465253v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:56,738] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:56,742] [INFO] Selected 13 target genomes.
[2024-01-24 15:27:56,742] [INFO] Target genome list was writen to GCF_014652535.1_ASM1465253v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:56,758] [INFO] Task started: fastANI
[2024-01-24 15:27:56,758] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e288a34-f014-417b-8d85-bffb395ba96d/GCF_014652535.1_ASM1465253v1_genomic.fna.gz --refList GCF_014652535.1_ASM1465253v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014652535.1_ASM1465253v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:09,114] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:09,126] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:09,126] [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_014652535.1	s__Cellvibrio zantedeschiae	100.0	1416	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004172865.1	s__Cellvibrio sp004172865	79.7277	599	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005801205.1	s__Cellvibrio sp005801205	79.2067	465	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004173475.1	s__Cellvibrio sp004173475	79.0963	468	1417	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	78.3448	266	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008806955.1	s__Cellvibrio sp000263355	78.2459	258	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	98.02	97.81	0.88	0.84	3	-
GCF_002007605.1	s__Cellvibrio sp002007605	78.2349	242	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	97.66	97.66	0.90	0.90	2	-
GCF_000953825.1	s__Cellvibrio sp000953825	78.0956	266	1417	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	77.9241	274	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008806975.1	s__Cellvibrio sp008806975	77.8887	248	1417	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	77.7307	269	1417	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	77.7168	277	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:09,128] [INFO] GTDB search result was written to GCF_014652535.1_ASM1465253v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:09,128] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:09,132] [INFO] DFAST_QC result json was written to GCF_014652535.1_ASM1465253v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:09,133] [INFO] DFAST_QC completed!
[2024-01-24 15:28:09,133] [INFO] Total running time: 0h1m21s