[2024-01-24 11:43:25,072] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:25,076] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:25,076] [INFO] DQC Reference Directory: /var/lib/cwl/stg96e6980e-7176-46a7-b1e1-573ba4a76ed5/dqc_reference
[2024-01-24 11:43:30,063] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:30,064] [INFO] Task started: Prodigal
[2024-01-24 11:43:30,064] [INFO] Running command: gunzip -c /var/lib/cwl/stg61b693b5-36d2-4211-bf2d-cd2cfb0b0641/GCF_000685295.1_SOAPdenovo_v1.05_genomic.fna.gz | prodigal -d GCF_000685295.1_SOAPdenovo_v1.05_genomic.fna/cds.fna -a GCF_000685295.1_SOAPdenovo_v1.05_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:42,593] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:42,594] [INFO] Task started: HMMsearch
[2024-01-24 11:43:42,594] [INFO] Running command: hmmsearch --tblout GCF_000685295.1_SOAPdenovo_v1.05_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg96e6980e-7176-46a7-b1e1-573ba4a76ed5/dqc_reference/reference_markers.hmm GCF_000685295.1_SOAPdenovo_v1.05_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:42,881] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:42,883] [INFO] Found 6/6 markers.
[2024-01-24 11:43:42,921] [INFO] Query marker FASTA was written to GCF_000685295.1_SOAPdenovo_v1.05_genomic.fna/markers.fasta
[2024-01-24 11:43:42,922] [INFO] Task started: Blastn
[2024-01-24 11:43:42,922] [INFO] Running command: blastn -query GCF_000685295.1_SOAPdenovo_v1.05_genomic.fna/markers.fasta -db /var/lib/cwl/stg96e6980e-7176-46a7-b1e1-573ba4a76ed5/dqc_reference/reference_markers.fasta -out GCF_000685295.1_SOAPdenovo_v1.05_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:43,854] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:43,858] [INFO] Selected 14 target genomes.
[2024-01-24 11:43:43,859] [INFO] Target genome list was writen to GCF_000685295.1_SOAPdenovo_v1.05_genomic.fna/target_genomes.txt
[2024-01-24 11:43:43,865] [INFO] Task started: fastANI
[2024-01-24 11:43:43,865] [INFO] Running command: fastANI --query /var/lib/cwl/stg61b693b5-36d2-4211-bf2d-cd2cfb0b0641/GCF_000685295.1_SOAPdenovo_v1.05_genomic.fna.gz --refList GCF_000685295.1_SOAPdenovo_v1.05_genomic.fna/target_genomes.txt --output GCF_000685295.1_SOAPdenovo_v1.05_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:43:54,656] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:54,657] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg96e6980e-7176-46a7-b1e1-573ba4a76ed5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:43:54,657] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg96e6980e-7176-46a7-b1e1-573ba4a76ed5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:43:54,668] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:43:54,669] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:43:54,669] [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 oceanitis	strain=SCH89	GCA_000685295.1	81033	81033	type	True	100.0	1345	1349	95	conclusive
Hyphomonas chukchiensis	strain=BH-BN04-4	GCA_000682695.1	1280947	1280947	type	True	90.5143	1015	1349	95	below_threshold
Hyphomonas johnsonii	strain=MHS-2	GCA_000685275.1	81031	81031	type	True	81.4973	691	1349	95	below_threshold
Hyphomonas jannaschiana	strain=VP2	GCA_000685215.1	86	86	type	True	78.8557	485	1349	95	below_threshold
Hyphomonas adhaerens	strain=MHS-3	GCA_000685235.1	81029	81029	type	True	78.6704	462	1349	95	below_threshold
Hyphomonas beringensis	strain=25B14_1	GCA_000682755.1	1280946	1280946	type	True	78.5788	426	1349	95	below_threshold
Hyphomonas atlantica	strain=22II1-22F38	GCA_000682715.1	1280948	1280948	type	True	78.2804	368	1349	95	below_threshold
Hyphomonas pacifica	strain=T16B2	GCA_000682675.1	1280941	1280941	type	True	78.0774	410	1349	95	below_threshold
Hyphomonas sediminis	strain=WL0036	GCA_019679475.1	2866160	2866160	type	True	78.072	375	1349	95	below_threshold
Henriciella aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	77.759	316	1349	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	76.3509	57	1349	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	75.9499	76	1349	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	75.9321	69	1349	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	75.7486	75	1349	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:43:54,671] [INFO] DFAST Taxonomy check result was written to GCF_000685295.1_SOAPdenovo_v1.05_genomic.fna/tc_result.tsv
[2024-01-24 11:43:54,672] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:43:54,672] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:43:54,672] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg96e6980e-7176-46a7-b1e1-573ba4a76ed5/dqc_reference/checkm_data
[2024-01-24 11:43:54,673] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:43:54,712] [INFO] Task started: CheckM
[2024-01-24 11:43:54,713] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000685295.1_SOAPdenovo_v1.05_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000685295.1_SOAPdenovo_v1.05_genomic.fna/checkm_input GCF_000685295.1_SOAPdenovo_v1.05_genomic.fna/checkm_result
[2024-01-24 11:44:34,669] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:34,671] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:34,687] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:34,687] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:34,688] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000685295.1_SOAPdenovo_v1.05_genomic.fna/markers.fasta)
[2024-01-24 11:44:34,688] [INFO] Task started: Blastn
[2024-01-24 11:44:34,688] [INFO] Running command: blastn -query GCF_000685295.1_SOAPdenovo_v1.05_genomic.fna/markers.fasta -db /var/lib/cwl/stg96e6980e-7176-46a7-b1e1-573ba4a76ed5/dqc_reference/reference_markers_gtdb.fasta -out GCF_000685295.1_SOAPdenovo_v1.05_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:36,403] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:36,406] [INFO] Selected 7 target genomes.
[2024-01-24 11:44:36,407] [INFO] Target genome list was writen to GCF_000685295.1_SOAPdenovo_v1.05_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:36,411] [INFO] Task started: fastANI
[2024-01-24 11:44:36,412] [INFO] Running command: fastANI --query /var/lib/cwl/stg61b693b5-36d2-4211-bf2d-cd2cfb0b0641/GCF_000685295.1_SOAPdenovo_v1.05_genomic.fna.gz --refList GCF_000685295.1_SOAPdenovo_v1.05_genomic.fna/target_genomes_gtdb.txt --output GCF_000685295.1_SOAPdenovo_v1.05_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:42,470] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:42,482] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:42,483] [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_000685295.1	s__Hyphomonas oceanitis	100.0	1345	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000682695.1	s__Hyphomonas chukchiensis	90.4987	1016	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018827375.1	s__Hyphomonas sp018827375	87.2189	943	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.92	99.88	0.98	0.97	4	-
GCA_000961795.1	s__Hyphomonas sp000961795	83.3296	777	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018830285.1	s__Hyphomonas sp018830285	82.3251	741	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685275.1	s__Hyphomonas johnsonii	81.5015	690	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018819265.1	s__Filomicrobium sp018819265	75.7794	59	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Filomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:42,485] [INFO] GTDB search result was written to GCF_000685295.1_SOAPdenovo_v1.05_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:42,485] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:42,490] [INFO] DFAST_QC result json was written to GCF_000685295.1_SOAPdenovo_v1.05_genomic.fna/dqc_result.json
[2024-01-24 11:44:42,491] [INFO] DFAST_QC completed!
[2024-01-24 11:44:42,491] [INFO] Total running time: 0h1m17s