[2024-01-24 12:47:26,373] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:26,375] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:26,375] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ddacaba-5e60-47ce-a656-ef8007793af1/dqc_reference
[2024-01-24 12:47:27,697] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:27,698] [INFO] Task started: Prodigal
[2024-01-24 12:47:27,698] [INFO] Running command: gunzip -c /var/lib/cwl/stg50d864f6-7592-4d7e-99a3-4a677b962560/GCF_900100455.1_IMG-taxon_2675903017_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900100455.1_IMG-taxon_2675903017_annotated_assembly_genomic.fna/cds.fna -a GCF_900100455.1_IMG-taxon_2675903017_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:37,978] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:37,978] [INFO] Task started: HMMsearch
[2024-01-24 12:47:37,978] [INFO] Running command: hmmsearch --tblout GCF_900100455.1_IMG-taxon_2675903017_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ddacaba-5e60-47ce-a656-ef8007793af1/dqc_reference/reference_markers.hmm GCF_900100455.1_IMG-taxon_2675903017_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:38,250] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:38,251] [INFO] Found 6/6 markers.
[2024-01-24 12:47:38,282] [INFO] Query marker FASTA was written to GCF_900100455.1_IMG-taxon_2675903017_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:47:38,283] [INFO] Task started: Blastn
[2024-01-24 12:47:38,283] [INFO] Running command: blastn -query GCF_900100455.1_IMG-taxon_2675903017_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ddacaba-5e60-47ce-a656-ef8007793af1/dqc_reference/reference_markers.fasta -out GCF_900100455.1_IMG-taxon_2675903017_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:39,294] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:39,297] [INFO] Selected 20 target genomes.
[2024-01-24 12:47:39,298] [INFO] Target genome list was writen to GCF_900100455.1_IMG-taxon_2675903017_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:47:39,304] [INFO] Task started: fastANI
[2024-01-24 12:47:39,304] [INFO] Running command: fastANI --query /var/lib/cwl/stg50d864f6-7592-4d7e-99a3-4a677b962560/GCF_900100455.1_IMG-taxon_2675903017_annotated_assembly_genomic.fna.gz --refList GCF_900100455.1_IMG-taxon_2675903017_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900100455.1_IMG-taxon_2675903017_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:59,578] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:59,579] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ddacaba-5e60-47ce-a656-ef8007793af1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:59,579] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ddacaba-5e60-47ce-a656-ef8007793af1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:59,594] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:59,595] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:59,595] [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
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	100.0	1144	1146	95	conclusive
Roseospira navarrensis	strain=DSM 15114	GCA_009601025.1	140058	140058	type	True	78.5295	414	1146	95	below_threshold
Roseospira goensis	strain=JA135	GCA_014197795.1	391922	391922	type	True	78.187	484	1146	95	below_threshold
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	78.0704	450	1146	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	77.9381	393	1146	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	77.7168	339	1146	95	below_threshold
Rhodospirillum rubrum	strain=ATCC 11170	GCA_000013085.1	1085	1085	type	True	77.5907	328	1146	95	below_threshold
Rhodospirillum rubrum	strain=DSM 467	GCA_019134555.1	1085	1085	type	True	77.571	330	1146	95	below_threshold
Pararhodospirillum oryzae	strain=NBRC 107573	GCA_007992075.1	478448	478448	type	True	77.5513	323	1146	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	77.2572	430	1146	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	77.2201	430	1146	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	77.1569	433	1146	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	77.0148	432	1146	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	76.9967	349	1146	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.839	209	1146	95	below_threshold
Novispirillum itersonii subsp. itersonii	strain=ATCC 12639	GCA_000381985.1	180199	189	type	True	76.6794	196	1146	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.6454	294	1146	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	76.5466	175	1146	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	76.3887	276	1146	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	76.1847	126	1146	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:59,597] [INFO] DFAST Taxonomy check result was written to GCF_900100455.1_IMG-taxon_2675903017_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:47:59,597] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:59,597] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:59,598] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ddacaba-5e60-47ce-a656-ef8007793af1/dqc_reference/checkm_data
[2024-01-24 12:47:59,599] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:59,635] [INFO] Task started: CheckM
[2024-01-24 12:47:59,635] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900100455.1_IMG-taxon_2675903017_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900100455.1_IMG-taxon_2675903017_annotated_assembly_genomic.fna/checkm_input GCF_900100455.1_IMG-taxon_2675903017_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:48:53,331] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:53,332] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:53,355] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:53,356] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:53,356] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900100455.1_IMG-taxon_2675903017_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:48:53,356] [INFO] Task started: Blastn
[2024-01-24 12:48:53,357] [INFO] Running command: blastn -query GCF_900100455.1_IMG-taxon_2675903017_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ddacaba-5e60-47ce-a656-ef8007793af1/dqc_reference/reference_markers_gtdb.fasta -out GCF_900100455.1_IMG-taxon_2675903017_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:55,275] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:55,279] [INFO] Selected 16 target genomes.
[2024-01-24 12:48:55,280] [INFO] Target genome list was writen to GCF_900100455.1_IMG-taxon_2675903017_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:55,291] [INFO] Task started: fastANI
[2024-01-24 12:48:55,291] [INFO] Running command: fastANI --query /var/lib/cwl/stg50d864f6-7592-4d7e-99a3-4a677b962560/GCF_900100455.1_IMG-taxon_2675903017_annotated_assembly_genomic.fna.gz --refList GCF_900100455.1_IMG-taxon_2675903017_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900100455.1_IMG-taxon_2675903017_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:49:09,285] [INFO] Task succeeded: fastANI
[2024-01-24 12:49:09,309] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:49:09,309] [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_900100455.1	s__Roseospirillum parvum	100.0	1144	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Roseospirillum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900101965.1	s__Rhodospira trueperi	78.7747	402	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009601025.1	s__Rhodospira navarrensis	78.5903	409	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197915.1	s__Rhodospira visakhapatnamensis	78.3315	429	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900230255.1	s__Caenispirillum bisanense	78.306	503	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Caenispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197795.1	s__Rhodospira goensis	78.1888	484	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902729435.1	s__Magnetospirillum sp902729435	78.1636	426	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197855.1	s__Rhodospira marina	78.1353	357	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	100.00	99.99	1.00	1.00	3	-
GCA_000961745.1	s__BRH-c57 sp000961745	78.115	306	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__BRH-c57	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002105535.1	s__Phaeospirillum sp002105535	77.9473	364	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013085.1	s__Rhodospirillum rubrum	77.6277	324	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospirillum	95.0	98.74	96.31	0.98	0.96	7	-
GCF_007992075.1	s__Pararhodospirillum oryzae	77.5323	325	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Pararhodospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003246625.1	s__Alpha-05 sp003246625	77.3821	281	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Alpha-05	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	77.2027	433	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014205675.1	s__Novispirillum itersonii_A	76.9571	252	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Novispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381985.1	s__Novispirillum itersonii	76.6962	197	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Novispirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:49:09,311] [INFO] GTDB search result was written to GCF_900100455.1_IMG-taxon_2675903017_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:49:09,312] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:49:09,315] [INFO] DFAST_QC result json was written to GCF_900100455.1_IMG-taxon_2675903017_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:49:09,316] [INFO] DFAST_QC completed!
[2024-01-24 12:49:09,316] [INFO] Total running time: 0h1m43s