[2024-01-24 11:59:13,613] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:13,615] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:13,615] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a877a1c-183a-4e35-a4e3-089a5c6e47d1/dqc_reference
[2024-01-24 11:59:14,893] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:14,894] [INFO] Task started: Prodigal
[2024-01-24 11:59:14,894] [INFO] Running command: gunzip -c /var/lib/cwl/stg9b78e737-b9a8-497d-b05a-9186959fdddc/GCF_024105745.1_ASM2410574v1_genomic.fna.gz | prodigal -d GCF_024105745.1_ASM2410574v1_genomic.fna/cds.fna -a GCF_024105745.1_ASM2410574v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:29,704] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:29,704] [INFO] Task started: HMMsearch
[2024-01-24 11:59:29,704] [INFO] Running command: hmmsearch --tblout GCF_024105745.1_ASM2410574v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a877a1c-183a-4e35-a4e3-089a5c6e47d1/dqc_reference/reference_markers.hmm GCF_024105745.1_ASM2410574v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:30,094] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:30,095] [INFO] Found 6/6 markers.
[2024-01-24 11:59:30,139] [INFO] Query marker FASTA was written to GCF_024105745.1_ASM2410574v1_genomic.fna/markers.fasta
[2024-01-24 11:59:30,140] [INFO] Task started: Blastn
[2024-01-24 11:59:30,140] [INFO] Running command: blastn -query GCF_024105745.1_ASM2410574v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a877a1c-183a-4e35-a4e3-089a5c6e47d1/dqc_reference/reference_markers.fasta -out GCF_024105745.1_ASM2410574v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:31,271] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:31,275] [INFO] Selected 11 target genomes.
[2024-01-24 11:59:31,276] [INFO] Target genome list was writen to GCF_024105745.1_ASM2410574v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:31,280] [INFO] Task started: fastANI
[2024-01-24 11:59:31,280] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b78e737-b9a8-497d-b05a-9186959fdddc/GCF_024105745.1_ASM2410574v1_genomic.fna.gz --refList GCF_024105745.1_ASM2410574v1_genomic.fna/target_genomes.txt --output GCF_024105745.1_ASM2410574v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:44,152] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:44,152] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a877a1c-183a-4e35-a4e3-089a5c6e47d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:44,153] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a877a1c-183a-4e35-a4e3-089a5c6e47d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:44,164] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:59:44,165] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:44,165] [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 endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	100.0	1675	1676	95	conclusive
Aurantimonas endophytica	strain=DSM 103570	GCA_014196845.1	1522175	1522175	type	True	99.9995	1672	1676	95	conclusive
Aurantimonas aggregata	strain=KCTC 52919	GCA_010500835.1	2047720	2047720	type	True	90.3537	1250	1676	95	below_threshold
Aurantimonas manganoxydans	strain=DSM 21871	GCA_001463865.1	651183	651183	type	True	82.2779	868	1676	95	below_threshold
Aurantimonas manganoxydans	strain=SI85-9A1	GCA_000153465.1	651183	651183	type	True	82.2489	874	1676	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	80.9565	783	1676	95	below_threshold
Jiella endophytica	strain=CBS5Q-3	GCA_004519335.1	2558362	2558362	type	True	80.8196	826	1676	95	below_threshold
Jiella pacifica	strain=40Bstr34	GCA_010500815.1	2696469	2696469	type	True	80.6848	812	1676	95	below_threshold
Aurantimonas marina	strain=SW136	GCA_017183135.1	2780508	2780508	type	True	80.6765	734	1676	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	78.0461	448	1676	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	77.9827	368	1676	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:44,167] [INFO] DFAST Taxonomy check result was written to GCF_024105745.1_ASM2410574v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:44,168] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:44,168] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:44,168] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a877a1c-183a-4e35-a4e3-089a5c6e47d1/dqc_reference/checkm_data
[2024-01-24 11:59:44,170] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:44,219] [INFO] Task started: CheckM
[2024-01-24 11:59:44,220] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024105745.1_ASM2410574v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024105745.1_ASM2410574v1_genomic.fna/checkm_input GCF_024105745.1_ASM2410574v1_genomic.fna/checkm_result
[2024-01-24 12:00:27,075] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:27,076] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:27,100] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:27,101] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:27,101] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024105745.1_ASM2410574v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:27,102] [INFO] Task started: Blastn
[2024-01-24 12:00:27,102] [INFO] Running command: blastn -query GCF_024105745.1_ASM2410574v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a877a1c-183a-4e35-a4e3-089a5c6e47d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_024105745.1_ASM2410574v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:29,416] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:29,420] [INFO] Selected 14 target genomes.
[2024-01-24 12:00:29,420] [INFO] Target genome list was writen to GCF_024105745.1_ASM2410574v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:29,432] [INFO] Task started: fastANI
[2024-01-24 12:00:29,432] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b78e737-b9a8-497d-b05a-9186959fdddc/GCF_024105745.1_ASM2410574v1_genomic.fna.gz --refList GCF_024105745.1_ASM2410574v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024105745.1_ASM2410574v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:44,361] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:44,378] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:44,378] [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_014196845.1	s__Aurantimonas endophytica	99.9995	1672	1676	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_010500835.1	s__Aurantimonas aggregata	90.3348	1252	1676	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	82.3776	895	1676	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	82.234	876	1676	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	81.215	862	1676	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	80.9648	782	1676	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	80.912	824	1676	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	80.8012	827	1676	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	80.7699	730	1676	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	99.96	99.96	0.91	0.91	2	-
GCF_017183135.1	s__Aurantimonas sp017183135	80.702	731	1676	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500815.1	s__Jiella pacifica	80.6846	812	1676	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196835.1	s__Aureimonas pseudogalii	79.6494	633	1676	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765365.1	s__VTOM01 sp009765365	79.6395	685	1676	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__VTOM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008802405.1	s__Aureimonas_A leprariae	79.4148	574	1676	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 12:00:44,380] [INFO] GTDB search result was written to GCF_024105745.1_ASM2410574v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:44,380] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:44,384] [INFO] DFAST_QC result json was written to GCF_024105745.1_ASM2410574v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:44,384] [INFO] DFAST_QC completed!
[2024-01-24 12:00:44,384] [INFO] Total running time: 0h1m31s