[2024-01-24 15:17:49,680] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:17:49,682] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:17:49,682] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe6e2a6e-48d5-4d91-802e-6ae1163984f8/dqc_reference
[2024-01-24 15:17:51,533] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:17:51,535] [INFO] Task started: Prodigal
[2024-01-24 15:17:51,535] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b300686-0441-43d4-bb6f-af0912ed4c17/GCF_010500835.1_ASM1050083v1_genomic.fna.gz | prodigal -d GCF_010500835.1_ASM1050083v1_genomic.fna/cds.fna -a GCF_010500835.1_ASM1050083v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:04,663] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:04,664] [INFO] Task started: HMMsearch
[2024-01-24 15:18:04,664] [INFO] Running command: hmmsearch --tblout GCF_010500835.1_ASM1050083v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe6e2a6e-48d5-4d91-802e-6ae1163984f8/dqc_reference/reference_markers.hmm GCF_010500835.1_ASM1050083v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:04,984] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:04,986] [INFO] Found 6/6 markers.
[2024-01-24 15:18:05,059] [INFO] Query marker FASTA was written to GCF_010500835.1_ASM1050083v1_genomic.fna/markers.fasta
[2024-01-24 15:18:05,060] [INFO] Task started: Blastn
[2024-01-24 15:18:05,060] [INFO] Running command: blastn -query GCF_010500835.1_ASM1050083v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe6e2a6e-48d5-4d91-802e-6ae1163984f8/dqc_reference/reference_markers.fasta -out GCF_010500835.1_ASM1050083v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:06,197] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:06,200] [INFO] Selected 13 target genomes.
[2024-01-24 15:18:06,201] [INFO] Target genome list was writen to GCF_010500835.1_ASM1050083v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:06,211] [INFO] Task started: fastANI
[2024-01-24 15:18:06,211] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b300686-0441-43d4-bb6f-af0912ed4c17/GCF_010500835.1_ASM1050083v1_genomic.fna.gz --refList GCF_010500835.1_ASM1050083v1_genomic.fna/target_genomes.txt --output GCF_010500835.1_ASM1050083v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:20,879] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:20,880] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe6e2a6e-48d5-4d91-802e-6ae1163984f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:20,880] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe6e2a6e-48d5-4d91-802e-6ae1163984f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:20,893] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:18:20,893] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:20,893] [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
Aurantimonas aggregata	strain=KCTC 52919	GCA_010500835.1	2047720	2047720	type	True	100.0	1569	1576	95	conclusive
Aurantimonas endophytica	strain=DSM 103570	GCA_014196845.1	1522175	1522175	type	True	90.3174	1261	1576	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	90.2811	1263	1576	95	below_threshold
Aurantimonas manganoxydans	strain=SI85-9A1	GCA_000153465.1	651183	651183	type	True	82.5469	860	1576	95	below_threshold
Aurantimonas coralicida	strain=DSM 14790	GCA_001463825.1	182270	182270	type	True	82.4963	887	1576	95	below_threshold
Aurantimonas manganoxydans	strain=DSM 21871	GCA_001463865.1	651183	651183	type	True	82.4949	852	1576	95	below_threshold
Jiella endophytica	strain=CBS5Q-3	GCA_004519335.1	2558362	2558362	type	True	81.0173	780	1576	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	80.8569	793	1576	95	below_threshold
Jiella pacifica	strain=40Bstr34	GCA_010500815.1	2696469	2696469	type	True	80.713	809	1576	95	below_threshold
Aurantimonas marina	strain=SW136	GCA_017183135.1	2780508	2780508	type	True	80.683	750	1576	95	below_threshold
Aureimonas leprariae	strain=YIM 132180	GCA_008802405.1	2615207	2615207	type	True	79.4313	589	1576	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	77.9328	321	1576	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	76.9727	425	1576	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:20,895] [INFO] DFAST Taxonomy check result was written to GCF_010500835.1_ASM1050083v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:20,895] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:20,896] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:20,896] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe6e2a6e-48d5-4d91-802e-6ae1163984f8/dqc_reference/checkm_data
[2024-01-24 15:18:20,897] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:20,946] [INFO] Task started: CheckM
[2024-01-24 15:18:20,946] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010500835.1_ASM1050083v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010500835.1_ASM1050083v1_genomic.fna/checkm_input GCF_010500835.1_ASM1050083v1_genomic.fna/checkm_result
[2024-01-24 15:19:01,654] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:01,655] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:01,689] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:01,690] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:01,690] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010500835.1_ASM1050083v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:01,691] [INFO] Task started: Blastn
[2024-01-24 15:19:01,691] [INFO] Running command: blastn -query GCF_010500835.1_ASM1050083v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe6e2a6e-48d5-4d91-802e-6ae1163984f8/dqc_reference/reference_markers_gtdb.fasta -out GCF_010500835.1_ASM1050083v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:04,112] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:04,116] [INFO] Selected 11 target genomes.
[2024-01-24 15:19:04,117] [INFO] Target genome list was writen to GCF_010500835.1_ASM1050083v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:04,126] [INFO] Task started: fastANI
[2024-01-24 15:19:04,127] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b300686-0441-43d4-bb6f-af0912ed4c17/GCF_010500835.1_ASM1050083v1_genomic.fna.gz --refList GCF_010500835.1_ASM1050083v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010500835.1_ASM1050083v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:17,641] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:17,654] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:17,654] [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_010500835.1	s__Aurantimonas aggregata	100.0	1569	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014196845.1	s__Aurantimonas endophytica	90.3098	1261	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421645.1	s__Aurantimonas coralicida	82.5553	897	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.4342	97.41	96.44	0.92	0.87	5	-
GCF_000153465.1	s__Aurantimonas manganoxydans	82.5113	863	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.4342	99.99	99.99	1.00	1.00	2	-
GCF_002088275.1	s__Jiella sp002088275	81.2685	836	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700095.1	s__Jiella sp002700095	81.0171	807	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050685.1	s__Aurantimonas coralicida_A	80.9715	746	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	99.96	99.96	0.91	0.91	2	-
GCF_017353515.1	s__Jiella sp017353515	80.8256	798	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017183135.1	s__Aurantimonas sp017183135	80.7064	748	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017815135.1	s__Jiella sp017815135	80.2934	730	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008802405.1	s__Aureimonas_A leprariae	79.4148	591	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:17,655] [INFO] GTDB search result was written to GCF_010500835.1_ASM1050083v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:17,656] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:17,659] [INFO] DFAST_QC result json was written to GCF_010500835.1_ASM1050083v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:17,660] [INFO] DFAST_QC completed!
[2024-01-24 15:19:17,660] [INFO] Total running time: 0h1m28s