[2024-01-25 19:53:20,677] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:53:20,678] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:53:20,678] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b74cf4a-ea42-4f91-8013-b5badd1e4147/dqc_reference
[2024-01-25 19:53:21,787] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:53:21,787] [INFO] Task started: Prodigal
[2024-01-25 19:53:21,787] [INFO] Running command: gunzip -c /var/lib/cwl/stg9997ad32-f604-49e1-bd89-56bd024443a6/GCF_000284415.1_ASM28441v2_genomic.fna.gz | prodigal -d GCF_000284415.1_ASM28441v2_genomic.fna/cds.fna -a GCF_000284415.1_ASM28441v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:53:34,002] [INFO] Task succeeded: Prodigal
[2024-01-25 19:53:34,002] [INFO] Task started: HMMsearch
[2024-01-25 19:53:34,002] [INFO] Running command: hmmsearch --tblout GCF_000284415.1_ASM28441v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b74cf4a-ea42-4f91-8013-b5badd1e4147/dqc_reference/reference_markers.hmm GCF_000284415.1_ASM28441v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:53:34,252] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:53:34,253] [INFO] Found 6/6 markers.
[2024-01-25 19:53:34,286] [INFO] Query marker FASTA was written to GCF_000284415.1_ASM28441v2_genomic.fna/markers.fasta
[2024-01-25 19:53:34,286] [INFO] Task started: Blastn
[2024-01-25 19:53:34,286] [INFO] Running command: blastn -query GCF_000284415.1_ASM28441v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b74cf4a-ea42-4f91-8013-b5badd1e4147/dqc_reference/reference_markers.fasta -out GCF_000284415.1_ASM28441v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:53:35,107] [INFO] Task succeeded: Blastn
[2024-01-25 19:53:35,109] [INFO] Selected 17 target genomes.
[2024-01-25 19:53:35,110] [INFO] Target genome list was writen to GCF_000284415.1_ASM28441v2_genomic.fna/target_genomes.txt
[2024-01-25 19:53:35,123] [INFO] Task started: fastANI
[2024-01-25 19:53:35,124] [INFO] Running command: fastANI --query /var/lib/cwl/stg9997ad32-f604-49e1-bd89-56bd024443a6/GCF_000284415.1_ASM28441v2_genomic.fna.gz --refList GCF_000284415.1_ASM28441v2_genomic.fna/target_genomes.txt --output GCF_000284415.1_ASM28441v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:53:49,743] [INFO] Task succeeded: fastANI
[2024-01-25 19:53:49,744] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b74cf4a-ea42-4f91-8013-b5badd1e4147/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:53:49,744] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b74cf4a-ea42-4f91-8013-b5badd1e4147/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:53:49,761] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:53:49,762] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:53:49,762] [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
Pararhodospirillum photometricum	strain=DSM 122	GCA_000284415.2	1084	1084	type	True	100.0	1292	1292	95	conclusive
Pararhodospirillum oryzae	strain=NBRC 107573	GCA_007992075.1	478448	478448	type	True	79.7225	531	1292	95	below_threshold
Rhodospirillum rubrum	strain=DSM 467	GCA_019134555.1	1085	1085	type	True	78.2397	361	1292	95	below_threshold
Rhodospirillum rubrum	strain=ATCC 11170	GCA_000013085.1	1085	1085	type	True	78.2349	358	1292	95	below_threshold
Phaeovibrio sulfidiphilus	strain=DSM 23193	GCA_014861485.1	1220600	1220600	type	True	77.5707	175	1292	95	below_threshold
Roseospira navarrensis	strain=DSM 15114	GCA_009601025.1	140058	140058	type	True	77.3126	241	1292	95	below_threshold
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	77.076	255	1292	95	below_threshold
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	77.0553	231	1292	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.8219	202	1292	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	76.4234	78	1292	95	below_threshold
Methylobacterium goesingense	strain=DSM 21331	GCA_022179225.1	243690	243690	type	True	76.3209	107	1292	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	76.251	142	1292	95	below_threshold
Methylobacterium adhaesivum	strain=DSM 17169	GCA_022179065.1	333297	333297	type	True	76.223	97	1292	95	below_threshold
Caulobacter soli	strain=Ji-3-8	GCA_011045195.1	2708539	2708539	type	True	75.963	149	1292	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	75.9237	90	1292	95	below_threshold
Methylobacterium segetis	strain=17J42-1	GCA_004348265.1	2488750	2488750	type	True	75.7276	109	1292	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:53:49,764] [INFO] DFAST Taxonomy check result was written to GCF_000284415.1_ASM28441v2_genomic.fna/tc_result.tsv
[2024-01-25 19:53:49,764] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:53:49,764] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:53:49,765] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b74cf4a-ea42-4f91-8013-b5badd1e4147/dqc_reference/checkm_data
[2024-01-25 19:53:49,766] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:53:49,808] [INFO] Task started: CheckM
[2024-01-25 19:53:49,808] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000284415.1_ASM28441v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000284415.1_ASM28441v2_genomic.fna/checkm_input GCF_000284415.1_ASM28441v2_genomic.fna/checkm_result
[2024-01-25 19:54:32,195] [INFO] Task succeeded: CheckM
[2024-01-25 19:54:32,196] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:54:32,215] [INFO] ===== Completeness check finished =====
[2024-01-25 19:54:32,215] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:54:32,216] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000284415.1_ASM28441v2_genomic.fna/markers.fasta)
[2024-01-25 19:54:32,216] [INFO] Task started: Blastn
[2024-01-25 19:54:32,216] [INFO] Running command: blastn -query GCF_000284415.1_ASM28441v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b74cf4a-ea42-4f91-8013-b5badd1e4147/dqc_reference/reference_markers_gtdb.fasta -out GCF_000284415.1_ASM28441v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:54:33,816] [INFO] Task succeeded: Blastn
[2024-01-25 19:54:33,819] [INFO] Selected 15 target genomes.
[2024-01-25 19:54:33,819] [INFO] Target genome list was writen to GCF_000284415.1_ASM28441v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:54:33,830] [INFO] Task started: fastANI
[2024-01-25 19:54:33,830] [INFO] Running command: fastANI --query /var/lib/cwl/stg9997ad32-f604-49e1-bd89-56bd024443a6/GCF_000284415.1_ASM28441v2_genomic.fna.gz --refList GCF_000284415.1_ASM28441v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000284415.1_ASM28441v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:54:45,271] [INFO] Task succeeded: fastANI
[2024-01-25 19:54:45,280] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:54:45,281] [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_000284415.1	s__Pararhodospirillum photometricum	100.0	1292	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Pararhodospirillum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007992075.1	s__Pararhodospirillum oryzae	79.7145	531	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Pararhodospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013085.1	s__Rhodospirillum rubrum	78.2287	359	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospirillum	95.0	98.74	96.31	0.98	0.96	7	-
GCF_014861485.1	s__Phaeovibrio sulfidiphilus	77.5879	174	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Phaeovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000961745.1	s__BRH-c57 sp000961745	77.3372	166	1292	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_009601025.1	s__Rhodospira navarrensis	77.3247	240	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184795.1	s__Phaeospirillum sp900184795	77.2596	237	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100455.1	s__Roseospirillum parvum	77.096	253	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Roseospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197795.1	s__Rhodospira goensis	77.0274	235	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101965.1	s__Rhodospira trueperi	77.0201	213	1292	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	76.9801	262	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Caenispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650635.1	s__Magnetospirillum moscoviense	76.8553	198	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	96.81	95.25	0.84	0.84	3	-
GCF_001427825.1	s__Brevundimonas sp001427825	76.5134	95	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348265.1	s__Methylobacterium segetis	75.7276	109	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003165275.1	s__BOG-935 sp003165275	75.2732	92	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__BOG-935	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:54:45,282] [INFO] GTDB search result was written to GCF_000284415.1_ASM28441v2_genomic.fna/result_gtdb.tsv
[2024-01-25 19:54:45,283] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:54:45,286] [INFO] DFAST_QC result json was written to GCF_000284415.1_ASM28441v2_genomic.fna/dqc_result.json
[2024-01-25 19:54:45,286] [INFO] DFAST_QC completed!
[2024-01-25 19:54:45,286] [INFO] Total running time: 0h1m25s