[2023-06-19 02:11:45,006] [INFO] DFAST_QC pipeline started.
[2023-06-19 02:11:45,009] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 02:11:45,009] [INFO] DQC Reference Directory: /var/lib/cwl/stg6fb86e77-9526-438d-b82c-77c67ea33689/dqc_reference
[2023-06-19 02:11:46,281] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 02:11:46,282] [INFO] Task started: Prodigal
[2023-06-19 02:11:46,282] [INFO] Running command: gunzip -c /var/lib/cwl/stg591bd004-f326-4d68-a3d1-44a04f143d5a/GCA_018900135.1_ASM1890013v1_genomic.fna.gz | prodigal -d GCA_018900135.1_ASM1890013v1_genomic.fna/cds.fna -a GCA_018900135.1_ASM1890013v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 02:11:57,580] [INFO] Task succeeded: Prodigal
[2023-06-19 02:11:57,580] [INFO] Task started: HMMsearch
[2023-06-19 02:11:57,580] [INFO] Running command: hmmsearch --tblout GCA_018900135.1_ASM1890013v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6fb86e77-9526-438d-b82c-77c67ea33689/dqc_reference/reference_markers.hmm GCA_018900135.1_ASM1890013v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 02:11:57,868] [INFO] Task succeeded: HMMsearch
[2023-06-19 02:11:57,869] [INFO] Found 6/6 markers.
[2023-06-19 02:11:57,909] [INFO] Query marker FASTA was written to GCA_018900135.1_ASM1890013v1_genomic.fna/markers.fasta
[2023-06-19 02:11:57,910] [INFO] Task started: Blastn
[2023-06-19 02:11:57,910] [INFO] Running command: blastn -query GCA_018900135.1_ASM1890013v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fb86e77-9526-438d-b82c-77c67ea33689/dqc_reference/reference_markers.fasta -out GCA_018900135.1_ASM1890013v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 02:11:58,895] [INFO] Task succeeded: Blastn
[2023-06-19 02:11:58,900] [INFO] Selected 12 target genomes.
[2023-06-19 02:11:58,901] [INFO] Target genome list was writen to GCA_018900135.1_ASM1890013v1_genomic.fna/target_genomes.txt
[2023-06-19 02:11:58,903] [INFO] Task started: fastANI
[2023-06-19 02:11:58,903] [INFO] Running command: fastANI --query /var/lib/cwl/stg591bd004-f326-4d68-a3d1-44a04f143d5a/GCA_018900135.1_ASM1890013v1_genomic.fna.gz --refList GCA_018900135.1_ASM1890013v1_genomic.fna/target_genomes.txt --output GCA_018900135.1_ASM1890013v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 02:12:08,387] [INFO] Task succeeded: fastANI
[2023-06-19 02:12:08,388] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6fb86e77-9526-438d-b82c-77c67ea33689/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 02:12:08,388] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6fb86e77-9526-438d-b82c-77c67ea33689/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 02:12:08,399] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 02:12:08,400] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 02:12:08,400] [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
Hyphomonas polymorpha	strain=PS728	GCA_000685315.1	74319	74319	type	True	79.5652	570	1284	95	below_threshold
Hyphomonas sediminis	strain=WL0036	GCA_019679475.1	2866160	2866160	type	True	79.4392	529	1284	95	below_threshold
Hyphomonas johnsonii	strain=MHS-2	GCA_000685275.1	81031	81031	type	True	78.5341	435	1284	95	below_threshold
Hyphomonas chukchiensis	strain=BH-BN04-4	GCA_000682695.1	1280947	1280947	type	True	78.5182	436	1284	95	below_threshold
Hyphomonas jannaschiana	strain=VP2	GCA_000685215.1	86	86	type	True	78.3463	428	1284	95	below_threshold
Hyphomonas oceanitis	strain=SCH89	GCA_000685295.1	81033	81033	type	True	78.256	418	1284	95	below_threshold
Hyphomonas adhaerens	strain=MHS-3	GCA_000685235.1	81029	81029	type	True	78.2076	420	1284	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	76.3843	95	1284	95	below_threshold
Methylobacterium mesophilicum	strain=NBRC 15688	GCA_022179445.1	39956	39956	type	True	76.2034	113	1284	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	76.0525	162	1284	95	below_threshold
Pontivivens ytuae	strain=MT2928	GCA_015679265.1	2789856	2789856	type	True	75.841	101	1284	95	below_threshold
Chelatococcus reniformis	strain=CGMCC 1.12919	GCA_014640075.1	1494448	1494448	type	True	75.4558	143	1284	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 02:12:08,402] [INFO] DFAST Taxonomy check result was written to GCA_018900135.1_ASM1890013v1_genomic.fna/tc_result.tsv
[2023-06-19 02:12:08,402] [INFO] ===== Taxonomy check completed =====
[2023-06-19 02:12:08,402] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 02:12:08,403] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6fb86e77-9526-438d-b82c-77c67ea33689/dqc_reference/checkm_data
[2023-06-19 02:12:08,404] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 02:12:08,443] [INFO] Task started: CheckM
[2023-06-19 02:12:08,444] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018900135.1_ASM1890013v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018900135.1_ASM1890013v1_genomic.fna/checkm_input GCA_018900135.1_ASM1890013v1_genomic.fna/checkm_result
[2023-06-19 02:12:44,349] [INFO] Task succeeded: CheckM
[2023-06-19 02:12:44,350] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 02:12:44,367] [INFO] ===== Completeness check finished =====
[2023-06-19 02:12:44,368] [INFO] ===== Start GTDB Search =====
[2023-06-19 02:12:44,368] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018900135.1_ASM1890013v1_genomic.fna/markers.fasta)
[2023-06-19 02:12:44,368] [INFO] Task started: Blastn
[2023-06-19 02:12:44,368] [INFO] Running command: blastn -query GCA_018900135.1_ASM1890013v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fb86e77-9526-438d-b82c-77c67ea33689/dqc_reference/reference_markers_gtdb.fasta -out GCA_018900135.1_ASM1890013v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 02:12:46,266] [INFO] Task succeeded: Blastn
[2023-06-19 02:12:46,270] [INFO] Selected 7 target genomes.
[2023-06-19 02:12:46,270] [INFO] Target genome list was writen to GCA_018900135.1_ASM1890013v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 02:12:46,271] [INFO] Task started: fastANI
[2023-06-19 02:12:46,271] [INFO] Running command: fastANI --query /var/lib/cwl/stg591bd004-f326-4d68-a3d1-44a04f143d5a/GCA_018900135.1_ASM1890013v1_genomic.fna.gz --refList GCA_018900135.1_ASM1890013v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018900135.1_ASM1890013v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 02:12:51,795] [INFO] Task succeeded: fastANI
[2023-06-19 02:12:51,807] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 02:12:51,807] [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
GCA_013791775.1	s__Hyphomonas sp013791775	99.987	1275	1284	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.98	99.96	1.00	0.99	4	conclusive
GCA_016125515.1	s__Hyphomonas sp016125515	84.1761	820	1284	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464545.1	s__Hyphomonas sp001464545	83.0204	744	1284	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	98.95	98.95	0.94	0.94	2	-
GCA_016712445.1	s__Hyphomonas sp016712445	82.9462	811	1284	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124495.1	s__Hyphomonas sp016124495	82.1717	697	1284	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003486945.1	s__Hyphomonas sp003486945	81.7455	518	1284	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001767925.1	s__CV81 sp001767925	77.4706	95	1284	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__CV81	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 02:12:51,809] [INFO] GTDB search result was written to GCA_018900135.1_ASM1890013v1_genomic.fna/result_gtdb.tsv
[2023-06-19 02:12:51,810] [INFO] ===== GTDB Search completed =====
[2023-06-19 02:12:51,813] [INFO] DFAST_QC result json was written to GCA_018900135.1_ASM1890013v1_genomic.fna/dqc_result.json
[2023-06-19 02:12:51,813] [INFO] DFAST_QC completed!
[2023-06-19 02:12:51,813] [INFO] Total running time: 0h1m7s