[2024-01-24 12:44:10,551] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:10,553] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:10,553] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a38d5fb-840a-4ce3-a0ca-381ad23d042b/dqc_reference
[2024-01-24 12:44:11,995] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:11,996] [INFO] Task started: Prodigal
[2024-01-24 12:44:11,997] [INFO] Running command: gunzip -c /var/lib/cwl/stga56f0c5e-ac6c-4048-be73-76f5b213aab8/GCF_024195285.1_ASM2419528v1_genomic.fna.gz | prodigal -d GCF_024195285.1_ASM2419528v1_genomic.fna/cds.fna -a GCF_024195285.1_ASM2419528v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:22,509] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:22,509] [INFO] Task started: HMMsearch
[2024-01-24 12:44:22,510] [INFO] Running command: hmmsearch --tblout GCF_024195285.1_ASM2419528v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a38d5fb-840a-4ce3-a0ca-381ad23d042b/dqc_reference/reference_markers.hmm GCF_024195285.1_ASM2419528v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:22,847] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:22,849] [INFO] Found 6/6 markers.
[2024-01-24 12:44:22,884] [INFO] Query marker FASTA was written to GCF_024195285.1_ASM2419528v1_genomic.fna/markers.fasta
[2024-01-24 12:44:22,884] [INFO] Task started: Blastn
[2024-01-24 12:44:22,884] [INFO] Running command: blastn -query GCF_024195285.1_ASM2419528v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a38d5fb-840a-4ce3-a0ca-381ad23d042b/dqc_reference/reference_markers.fasta -out GCF_024195285.1_ASM2419528v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:23,874] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:23,879] [INFO] Selected 15 target genomes.
[2024-01-24 12:44:23,879] [INFO] Target genome list was writen to GCF_024195285.1_ASM2419528v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:23,893] [INFO] Task started: fastANI
[2024-01-24 12:44:23,894] [INFO] Running command: fastANI --query /var/lib/cwl/stga56f0c5e-ac6c-4048-be73-76f5b213aab8/GCF_024195285.1_ASM2419528v1_genomic.fna.gz --refList GCF_024195285.1_ASM2419528v1_genomic.fna/target_genomes.txt --output GCF_024195285.1_ASM2419528v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:37,533] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:37,533] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a38d5fb-840a-4ce3-a0ca-381ad23d042b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:37,534] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a38d5fb-840a-4ce3-a0ca-381ad23d042b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:37,548] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:44:37,548] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:44:37,548] [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 marina	strain=SW136	GCA_017183135.1	2780508	2780508	type	True	90.8209	1061	1209	95	below_threshold
Aurantimonas manganoxydans	strain=SI85-9A1	GCA_000153465.1	651183	651183	type	True	81.3248	756	1209	95	below_threshold
Aurantimonas coralicida	strain=DSM 14790	GCA_000421645.1	182270	182270	type	True	81.3211	761	1209	95	below_threshold
Aurantimonas coralicida	strain=DSM 14790	GCA_001463825.1	182270	182270	type	True	81.2609	759	1209	95	below_threshold
Aurantimonas aggregata	strain=KCTC 52919	GCA_010500835.1	2047720	2047720	type	True	80.8543	696	1209	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	80.5721	704	1209	95	below_threshold
Aurantimonas endophytica	strain=DSM 103570	GCA_014196845.1	1522175	1522175	type	True	80.5035	711	1209	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	79.979	612	1209	95	below_threshold
Jiella endophytica	strain=CBS5Q-3	GCA_004519335.1	2558362	2558362	type	True	79.9352	613	1209	95	below_threshold
Jiella pacifica	strain=40Bstr34	GCA_010500815.1	2696469	2696469	type	True	79.7659	608	1209	95	below_threshold
Consotaella salsifontis	strain=USBA 369	GCA_900167365.1	1365950	1365950	type	True	77.9333	352	1209	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	77.2195	282	1209	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	77.2176	283	1209	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	77.2082	256	1209	95	below_threshold
Martelella lutilitoris	strain=GH2-6	GCA_005924265.1	2583532	2583532	type	True	77.0326	234	1209	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:37,551] [INFO] DFAST Taxonomy check result was written to GCF_024195285.1_ASM2419528v1_genomic.fna/tc_result.tsv
[2024-01-24 12:44:37,552] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:37,553] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:37,553] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a38d5fb-840a-4ce3-a0ca-381ad23d042b/dqc_reference/checkm_data
[2024-01-24 12:44:37,554] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:37,601] [INFO] Task started: CheckM
[2024-01-24 12:44:37,601] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024195285.1_ASM2419528v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024195285.1_ASM2419528v1_genomic.fna/checkm_input GCF_024195285.1_ASM2419528v1_genomic.fna/checkm_result
[2024-01-24 12:45:12,081] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:12,083] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:12,107] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:12,108] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:12,108] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024195285.1_ASM2419528v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:12,109] [INFO] Task started: Blastn
[2024-01-24 12:45:12,109] [INFO] Running command: blastn -query GCF_024195285.1_ASM2419528v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a38d5fb-840a-4ce3-a0ca-381ad23d042b/dqc_reference/reference_markers_gtdb.fasta -out GCF_024195285.1_ASM2419528v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:14,026] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:14,030] [INFO] Selected 14 target genomes.
[2024-01-24 12:45:14,030] [INFO] Target genome list was writen to GCF_024195285.1_ASM2419528v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:14,055] [INFO] Task started: fastANI
[2024-01-24 12:45:14,056] [INFO] Running command: fastANI --query /var/lib/cwl/stga56f0c5e-ac6c-4048-be73-76f5b213aab8/GCF_024195285.1_ASM2419528v1_genomic.fna.gz --refList GCF_024195285.1_ASM2419528v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024195285.1_ASM2419528v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:27,160] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:27,171] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:45:27,172] [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_017183135.1	s__Aurantimonas sp017183135	90.8362	1060	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050685.1	s__Aurantimonas coralicida_A	89.2249	1004	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	99.96	99.96	0.91	0.91	2	-
GCF_000421645.1	s__Aurantimonas coralicida	81.3202	762	1209	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	81.3194	756	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.4342	99.99	99.99	1.00	1.00	2	-
GCF_010500835.1	s__Aurantimonas aggregata	80.8535	696	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196845.1	s__Aurantimonas endophytica	80.5008	711	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002088275.1	s__Jiella sp002088275	80.0614	633	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017353515.1	s__Jiella sp017353515	79.9918	611	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004519335.1	s__Jiella endophytica	79.9448	614	1209	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	79.8929	607	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500815.1	s__Jiella pacifica	79.7573	608	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017815135.1	s__Jiella sp017815135	79.5613	577	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643375.1	s__Aureimonas_A glaciei	79.3827	564	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000192745.1	s__Polymorphum gilvum	77.3999	307	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Polymorphum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:27,173] [INFO] GTDB search result was written to GCF_024195285.1_ASM2419528v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:27,174] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:27,178] [INFO] DFAST_QC result json was written to GCF_024195285.1_ASM2419528v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:27,178] [INFO] DFAST_QC completed!
[2024-01-24 12:45:27,178] [INFO] Total running time: 0h1m17s