[2024-01-24 12:14:35,723] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:35,726] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:35,726] [INFO] DQC Reference Directory: /var/lib/cwl/stg7868ab3b-cca0-4006-b6a8-4d8fe9b405c0/dqc_reference
[2024-01-24 12:14:37,050] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:37,051] [INFO] Task started: Prodigal
[2024-01-24 12:14:37,051] [INFO] Running command: gunzip -c /var/lib/cwl/stg7a883d5a-f2f9-4a7b-9153-dc5b3915397a/GCF_014643675.1_ASM1464367v1_genomic.fna.gz | prodigal -d GCF_014643675.1_ASM1464367v1_genomic.fna/cds.fna -a GCF_014643675.1_ASM1464367v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:02,284] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:02,285] [INFO] Task started: HMMsearch
[2024-01-24 12:15:02,285] [INFO] Running command: hmmsearch --tblout GCF_014643675.1_ASM1464367v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7868ab3b-cca0-4006-b6a8-4d8fe9b405c0/dqc_reference/reference_markers.hmm GCF_014643675.1_ASM1464367v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:02,637] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:02,638] [INFO] Found 6/6 markers.
[2024-01-24 12:15:02,687] [INFO] Query marker FASTA was written to GCF_014643675.1_ASM1464367v1_genomic.fna/markers.fasta
[2024-01-24 12:15:02,688] [INFO] Task started: Blastn
[2024-01-24 12:15:02,688] [INFO] Running command: blastn -query GCF_014643675.1_ASM1464367v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7868ab3b-cca0-4006-b6a8-4d8fe9b405c0/dqc_reference/reference_markers.fasta -out GCF_014643675.1_ASM1464367v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:03,289] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:03,295] [INFO] Selected 16 target genomes.
[2024-01-24 12:15:03,295] [INFO] Target genome list was writen to GCF_014643675.1_ASM1464367v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:03,304] [INFO] Task started: fastANI
[2024-01-24 12:15:03,305] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a883d5a-f2f9-4a7b-9153-dc5b3915397a/GCF_014643675.1_ASM1464367v1_genomic.fna.gz --refList GCF_014643675.1_ASM1464367v1_genomic.fna/target_genomes.txt --output GCF_014643675.1_ASM1464367v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:14,890] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:14,891] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7868ab3b-cca0-4006-b6a8-4d8fe9b405c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:14,891] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7868ab3b-cca0-4006-b6a8-4d8fe9b405c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:14,899] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:15:14,899] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:14,900] [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
Sphingobacterium alkalisoli	strain=CGMCC 1.15782	GCA_014643675.1	1874115	1874115	type	True	100.0	1929	1930	95	conclusive
Sphingobacterium alkalisoli	strain=Y3L14	GCA_005049105.1	1874115	1874115	type	True	99.9993	1914	1930	95	conclusive
Sphingobacterium olei	strain=HAL-9	GCA_005048855.1	2571155	2571155	type	True	87.4967	1202	1930	95	below_threshold
Sphingobacterium lumbrici	strain=1.3611	GCA_006476045.1	2559600	2559600	type	True	83.1669	680	1930	95	below_threshold
Sphingobacterium composti Ten et al. 2007 non Yoo et al. 2007	strain=KCTC 12578	GCA_009829075.1	363260	363260	type	True	77.9035	163	1930	95	below_threshold
Sphingobacterium rhinopitheci	strain=WQ 047	GCA_022627575.1	2781960	2781960	type	True	77.7795	157	1930	95	below_threshold
Sphingobacterium corticibacterium	strain=30C10-4-7	GCA_004208525.1	2484746	2484746	type	True	77.7406	156	1930	95	below_threshold
Sphingobacterium prati	strain=arapr2	GCA_013167215.1	2737006	2737006	type	True	77.5767	136	1930	95	below_threshold
Sphingobacterium hungaricum	strain=KB22	GCA_015210005.1	2082723	2082723	type	True	77.5397	148	1930	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:14,903] [INFO] DFAST Taxonomy check result was written to GCF_014643675.1_ASM1464367v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:14,903] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:14,903] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:14,904] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7868ab3b-cca0-4006-b6a8-4d8fe9b405c0/dqc_reference/checkm_data
[2024-01-24 12:15:14,904] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:14,958] [INFO] Task started: CheckM
[2024-01-24 12:15:14,958] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014643675.1_ASM1464367v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014643675.1_ASM1464367v1_genomic.fna/checkm_input GCF_014643675.1_ASM1464367v1_genomic.fna/checkm_result
[2024-01-24 12:16:22,980] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:22,981] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:22,999] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:22,999] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:23,000] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014643675.1_ASM1464367v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:23,000] [INFO] Task started: Blastn
[2024-01-24 12:16:23,000] [INFO] Running command: blastn -query GCF_014643675.1_ASM1464367v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7868ab3b-cca0-4006-b6a8-4d8fe9b405c0/dqc_reference/reference_markers_gtdb.fasta -out GCF_014643675.1_ASM1464367v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:23,754] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:23,757] [INFO] Selected 17 target genomes.
[2024-01-24 12:16:23,758] [INFO] Target genome list was writen to GCF_014643675.1_ASM1464367v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:23,769] [INFO] Task started: fastANI
[2024-01-24 12:16:23,770] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a883d5a-f2f9-4a7b-9153-dc5b3915397a/GCF_014643675.1_ASM1464367v1_genomic.fna.gz --refList GCF_014643675.1_ASM1464367v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014643675.1_ASM1464367v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:36,872] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:36,881] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:36,881] [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_005049105.1	s__Sphingobacterium alkalisoli	99.9993	1914	1930	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_005048855.1	s__Sphingobacterium olei	87.5055	1202	1930	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015209965.1	s__Sphingobacterium sp015209965	84.3572	1072	1930	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006476045.1	s__Sphingobacterium lumbrici	83.1816	678	1930	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002354335.1	s__Sphingobacterium sp002354335	77.9995	118	1930	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009829075.1	s__Sphingobacterium composti	77.9028	160	1930	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000747525.1	s__Sphingobacterium sp000747525	77.7909	120	1930	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015210005.1	s__Sphingobacterium sp015210005	77.5845	150	1930	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002933815.1	s__Sphingobacterium sp002933815	77.4857	132	1930	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:36,883] [INFO] GTDB search result was written to GCF_014643675.1_ASM1464367v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:36,883] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:36,886] [INFO] DFAST_QC result json was written to GCF_014643675.1_ASM1464367v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:36,886] [INFO] DFAST_QC completed!
[2024-01-24 12:16:36,886] [INFO] Total running time: 0h2m1s