[2024-01-24 12:29:39,465] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:39,467] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:39,467] [INFO] DQC Reference Directory: /var/lib/cwl/stgcfd33b81-3930-48b9-a889-1b78e5b34fc3/dqc_reference
[2024-01-24 12:29:42,404] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:42,405] [INFO] Task started: Prodigal
[2024-01-24 12:29:42,406] [INFO] Running command: gunzip -c /var/lib/cwl/stg40a3d2b4-ab47-4477-9666-78a59f4d1ce3/GCF_016774335.1_ASM1677433v1_genomic.fna.gz | prodigal -d GCF_016774335.1_ASM1677433v1_genomic.fna/cds.fna -a GCF_016774335.1_ASM1677433v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:56,115] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:56,116] [INFO] Task started: HMMsearch
[2024-01-24 12:29:56,116] [INFO] Running command: hmmsearch --tblout GCF_016774335.1_ASM1677433v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcfd33b81-3930-48b9-a889-1b78e5b34fc3/dqc_reference/reference_markers.hmm GCF_016774335.1_ASM1677433v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:56,386] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:56,388] [INFO] Found 6/6 markers.
[2024-01-24 12:29:56,427] [INFO] Query marker FASTA was written to GCF_016774335.1_ASM1677433v1_genomic.fna/markers.fasta
[2024-01-24 12:29:56,428] [INFO] Task started: Blastn
[2024-01-24 12:29:56,428] [INFO] Running command: blastn -query GCF_016774335.1_ASM1677433v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfd33b81-3930-48b9-a889-1b78e5b34fc3/dqc_reference/reference_markers.fasta -out GCF_016774335.1_ASM1677433v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:57,525] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:57,530] [INFO] Selected 11 target genomes.
[2024-01-24 12:29:57,530] [INFO] Target genome list was writen to GCF_016774335.1_ASM1677433v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:57,534] [INFO] Task started: fastANI
[2024-01-24 12:29:57,534] [INFO] Running command: fastANI --query /var/lib/cwl/stg40a3d2b4-ab47-4477-9666-78a59f4d1ce3/GCF_016774335.1_ASM1677433v1_genomic.fna.gz --refList GCF_016774335.1_ASM1677433v1_genomic.fna/target_genomes.txt --output GCF_016774335.1_ASM1677433v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:07,829] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:07,830] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcfd33b81-3930-48b9-a889-1b78e5b34fc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:07,830] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcfd33b81-3930-48b9-a889-1b78e5b34fc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:07,845] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:30:07,845] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:07,845] [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
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	100.0	1523	1523	95	conclusive
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	91.2312	1204	1523	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	86.7775	984	1523	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	84.9501	901	1523	95	below_threshold
Luteimonas aestuarii	strain=B9	GCA_004357985.1	453837	453837	type	True	82.8142	809	1523	95	below_threshold
Luteimonas arsenica	strain=26-35	GCA_004352825.1	1586242	1586242	type	True	82.2698	686	1523	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	82.1262	680	1523	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	81.9709	714	1523	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	81.6996	592	1523	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	80.8046	646	1523	95	below_threshold
Pseudoxanthomonas japonensis	strain=DSM 17109	GCA_010093445.1	69284	69284	type	True	80.53	713	1523	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:07,847] [INFO] DFAST Taxonomy check result was written to GCF_016774335.1_ASM1677433v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:07,848] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:07,848] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:07,848] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcfd33b81-3930-48b9-a889-1b78e5b34fc3/dqc_reference/checkm_data
[2024-01-24 12:30:07,849] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:07,894] [INFO] Task started: CheckM
[2024-01-24 12:30:07,895] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016774335.1_ASM1677433v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016774335.1_ASM1677433v1_genomic.fna/checkm_input GCF_016774335.1_ASM1677433v1_genomic.fna/checkm_result
[2024-01-24 12:30:58,241] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:58,244] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:58,277] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:58,278] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:58,279] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016774335.1_ASM1677433v1_genomic.fna/markers.fasta)
[2024-01-24 12:30:58,279] [INFO] Task started: Blastn
[2024-01-24 12:30:58,280] [INFO] Running command: blastn -query GCF_016774335.1_ASM1677433v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfd33b81-3930-48b9-a889-1b78e5b34fc3/dqc_reference/reference_markers_gtdb.fasta -out GCF_016774335.1_ASM1677433v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:00,291] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:00,296] [INFO] Selected 10 target genomes.
[2024-01-24 12:31:00,297] [INFO] Target genome list was writen to GCF_016774335.1_ASM1677433v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:00,305] [INFO] Task started: fastANI
[2024-01-24 12:31:00,305] [INFO] Running command: fastANI --query /var/lib/cwl/stg40a3d2b4-ab47-4477-9666-78a59f4d1ce3/GCF_016774335.1_ASM1677433v1_genomic.fna.gz --refList GCF_016774335.1_ASM1677433v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016774335.1_ASM1677433v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:10,524] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:10,537] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:10,538] [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_016774335.1	s__Luteimonas sp016774335	100.0	1523	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008244685.1	s__Luteimonas sp008244685	91.25	1202	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859325.1	s__Luteimonas marina	86.7776	984	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000472505.1	s__Luteimonas sp000472505	85.0519	916	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.95	99.95	0.99	0.99	2	-
GCF_007859305.1	s__Luteimonas wenzhouensis	84.9329	903	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.47	99.47	0.98	0.98	2	-
GCF_004357985.1	s__Luteimonas aestuarii	82.8167	809	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836665.1	s__Luteimonas sp014836665	82.1362	680	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014851815.1	s__Pseudoxanthomonas_A sp014851815	80.5922	684	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004284195.1	s__Pseudoxanthomonas_A sp004284195	80.4573	684	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	97.94	97.04	0.92	0.87	11	-
GCF_014851805.1	s__Pseudoxanthomonas_A sp014851805	80.3262	695	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:10,539] [INFO] GTDB search result was written to GCF_016774335.1_ASM1677433v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:10,540] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:10,543] [INFO] DFAST_QC result json was written to GCF_016774335.1_ASM1677433v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:10,543] [INFO] DFAST_QC completed!
[2024-01-24 12:31:10,544] [INFO] Total running time: 0h1m31s