[2024-01-24 14:23:04,885] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:23:04,893] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:23:04,894] [INFO] DQC Reference Directory: /var/lib/cwl/stg9db2e4aa-b73c-4a9b-a85a-8822546d7110/dqc_reference
[2024-01-24 14:23:06,222] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:23:06,223] [INFO] Task started: Prodigal
[2024-01-24 14:23:06,223] [INFO] Running command: gunzip -c /var/lib/cwl/stg3db814b0-bba2-4756-a8da-d6de8aaa02ae/GCF_005049105.1_ASM504910v1_genomic.fna.gz | prodigal -d GCF_005049105.1_ASM504910v1_genomic.fna/cds.fna -a GCF_005049105.1_ASM504910v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:30,966] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:30,966] [INFO] Task started: HMMsearch
[2024-01-24 14:23:30,966] [INFO] Running command: hmmsearch --tblout GCF_005049105.1_ASM504910v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9db2e4aa-b73c-4a9b-a85a-8822546d7110/dqc_reference/reference_markers.hmm GCF_005049105.1_ASM504910v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:31,406] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:31,407] [INFO] Found 6/6 markers.
[2024-01-24 14:23:31,453] [INFO] Query marker FASTA was written to GCF_005049105.1_ASM504910v1_genomic.fna/markers.fasta
[2024-01-24 14:23:31,453] [INFO] Task started: Blastn
[2024-01-24 14:23:31,454] [INFO] Running command: blastn -query GCF_005049105.1_ASM504910v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9db2e4aa-b73c-4a9b-a85a-8822546d7110/dqc_reference/reference_markers.fasta -out GCF_005049105.1_ASM504910v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:32,086] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:32,089] [INFO] Selected 16 target genomes.
[2024-01-24 14:23:32,090] [INFO] Target genome list was writen to GCF_005049105.1_ASM504910v1_genomic.fna/target_genomes.txt
[2024-01-24 14:23:32,095] [INFO] Task started: fastANI
[2024-01-24 14:23:32,095] [INFO] Running command: fastANI --query /var/lib/cwl/stg3db814b0-bba2-4756-a8da-d6de8aaa02ae/GCF_005049105.1_ASM504910v1_genomic.fna.gz --refList GCF_005049105.1_ASM504910v1_genomic.fna/target_genomes.txt --output GCF_005049105.1_ASM504910v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:43,663] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:43,664] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9db2e4aa-b73c-4a9b-a85a-8822546d7110/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:43,664] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9db2e4aa-b73c-4a9b-a85a-8822546d7110/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:43,673] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:23:43,673] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:43,673] [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=Y3L14	GCA_005049105.1	1874115	1874115	type	True	100.0	1914	1915	95	conclusive
Sphingobacterium alkalisoli	strain=CGMCC 1.15782	GCA_014643675.1	1874115	1874115	type	True	99.9988	1914	1915	95	conclusive
Sphingobacterium olei	strain=HAL-9	GCA_005048855.1	2571155	2571155	type	True	87.5516	1183	1915	95	below_threshold
Sphingobacterium lumbrici	strain=1.3611	GCA_006476045.1	2559600	2559600	type	True	83.286	679	1915	95	below_threshold
Sphingobacterium composti Ten et al. 2007 non Yoo et al. 2007	strain=KCTC 12578	GCA_009829075.1	363260	363260	type	True	77.9558	165	1915	95	below_threshold
Sphingobacterium corticibacterium	strain=30C10-4-7	GCA_004208525.1	2484746	2484746	type	True	77.7492	167	1915	95	below_threshold
Sphingobacterium rhinopitheci	strain=WQ 047	GCA_022627575.1	2781960	2781960	type	True	77.7341	165	1915	95	below_threshold
Sphingobacterium prati	strain=arapr2	GCA_013167215.1	2737006	2737006	type	True	77.5303	138	1915	95	below_threshold
Sphingobacterium hungaricum	strain=KB22	GCA_015210005.1	2082723	2082723	type	True	77.4522	157	1915	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:43,675] [INFO] DFAST Taxonomy check result was written to GCF_005049105.1_ASM504910v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:43,676] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:43,676] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:43,676] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9db2e4aa-b73c-4a9b-a85a-8822546d7110/dqc_reference/checkm_data
[2024-01-24 14:23:43,678] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:43,738] [INFO] Task started: CheckM
[2024-01-24 14:23:43,738] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005049105.1_ASM504910v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005049105.1_ASM504910v1_genomic.fna/checkm_input GCF_005049105.1_ASM504910v1_genomic.fna/checkm_result
[2024-01-24 14:24:52,867] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:52,868] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:52,892] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:52,892] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:52,893] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005049105.1_ASM504910v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:52,893] [INFO] Task started: Blastn
[2024-01-24 14:24:52,893] [INFO] Running command: blastn -query GCF_005049105.1_ASM504910v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9db2e4aa-b73c-4a9b-a85a-8822546d7110/dqc_reference/reference_markers_gtdb.fasta -out GCF_005049105.1_ASM504910v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:53,664] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:53,668] [INFO] Selected 17 target genomes.
[2024-01-24 14:24:53,669] [INFO] Target genome list was writen to GCF_005049105.1_ASM504910v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:53,696] [INFO] Task started: fastANI
[2024-01-24 14:24:53,696] [INFO] Running command: fastANI --query /var/lib/cwl/stg3db814b0-bba2-4756-a8da-d6de8aaa02ae/GCF_005049105.1_ASM504910v1_genomic.fna.gz --refList GCF_005049105.1_ASM504910v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005049105.1_ASM504910v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:25:07,009] [INFO] Task succeeded: fastANI
[2024-01-24 14:25:07,021] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:25:07,021] [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	100.0	1914	1915	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	87.5721	1181	1915	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	84.3907	1069	1915	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	83.286	679	1915	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	78.1266	120	1915	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	77.9148	166	1915	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	77.8153	122	1915	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	77.5135	159	1915	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	77.2947	135	1915	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 14:25:07,023] [INFO] GTDB search result was written to GCF_005049105.1_ASM504910v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:25:07,023] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:25:07,027] [INFO] DFAST_QC result json was written to GCF_005049105.1_ASM504910v1_genomic.fna/dqc_result.json
[2024-01-24 14:25:07,028] [INFO] DFAST_QC completed!
[2024-01-24 14:25:07,028] [INFO] Total running time: 0h2m2s