[2024-01-24 11:34:40,445] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:40,447] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:40,447] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e808741-11b1-43e8-9987-52c608d93b80/dqc_reference
[2024-01-24 11:34:41,769] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:41,770] [INFO] Task started: Prodigal
[2024-01-24 11:34:41,770] [INFO] Running command: gunzip -c /var/lib/cwl/stg17a37bbf-4a06-41d0-9428-be652c69ab2b/GCF_008244685.1_ASM824468v1_genomic.fna.gz | prodigal -d GCF_008244685.1_ASM824468v1_genomic.fna/cds.fna -a GCF_008244685.1_ASM824468v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:54,151] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:54,151] [INFO] Task started: HMMsearch
[2024-01-24 11:34:54,151] [INFO] Running command: hmmsearch --tblout GCF_008244685.1_ASM824468v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e808741-11b1-43e8-9987-52c608d93b80/dqc_reference/reference_markers.hmm GCF_008244685.1_ASM824468v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:54,480] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:54,481] [INFO] Found 6/6 markers.
[2024-01-24 11:34:54,524] [INFO] Query marker FASTA was written to GCF_008244685.1_ASM824468v1_genomic.fna/markers.fasta
[2024-01-24 11:34:54,525] [INFO] Task started: Blastn
[2024-01-24 11:34:54,525] [INFO] Running command: blastn -query GCF_008244685.1_ASM824468v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e808741-11b1-43e8-9987-52c608d93b80/dqc_reference/reference_markers.fasta -out GCF_008244685.1_ASM824468v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:55,605] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:55,608] [INFO] Selected 13 target genomes.
[2024-01-24 11:34:55,609] [INFO] Target genome list was writen to GCF_008244685.1_ASM824468v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:55,614] [INFO] Task started: fastANI
[2024-01-24 11:34:55,614] [INFO] Running command: fastANI --query /var/lib/cwl/stg17a37bbf-4a06-41d0-9428-be652c69ab2b/GCF_008244685.1_ASM824468v1_genomic.fna.gz --refList GCF_008244685.1_ASM824468v1_genomic.fna/target_genomes.txt --output GCF_008244685.1_ASM824468v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:07,444] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:07,445] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e808741-11b1-43e8-9987-52c608d93b80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:07,445] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e808741-11b1-43e8-9987-52c608d93b80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:07,457] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:07,457] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:07,457] [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 viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	100.0	1386	1386	95	conclusive
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	91.2175	1192	1386	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	86.9672	969	1386	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	85.0249	911	1386	95	below_threshold
Luteimonas aestuarii	strain=B9	GCA_004357985.1	453837	453837	type	True	82.8597	794	1386	95	below_threshold
Luteimonas arsenica	strain=26-35	GCA_004352825.1	1586242	1586242	type	True	82.554	696	1386	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	82.4421	665	1386	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	82.2235	686	1386	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	82.0367	716	1386	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	81.947	623	1386	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	81.4339	630	1386	95	below_threshold
Thermomonas haemolytica	strain=LMG 19653	GCA_006352395.1	141949	141949	type	True	81.2307	540	1386	95	below_threshold
Thermomonas haemolytica	strain=DSM 13605	GCA_004346265.1	141949	141949	type	True	81.1921	562	1386	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:07,459] [INFO] DFAST Taxonomy check result was written to GCF_008244685.1_ASM824468v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:07,459] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:07,459] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:07,459] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e808741-11b1-43e8-9987-52c608d93b80/dqc_reference/checkm_data
[2024-01-24 11:35:07,461] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:07,514] [INFO] Task started: CheckM
[2024-01-24 11:35:07,514] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008244685.1_ASM824468v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008244685.1_ASM824468v1_genomic.fna/checkm_input GCF_008244685.1_ASM824468v1_genomic.fna/checkm_result
[2024-01-24 11:36:14,036] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:14,037] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:14,054] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:14,054] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:14,055] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008244685.1_ASM824468v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:14,055] [INFO] Task started: Blastn
[2024-01-24 11:36:14,055] [INFO] Running command: blastn -query GCF_008244685.1_ASM824468v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e808741-11b1-43e8-9987-52c608d93b80/dqc_reference/reference_markers_gtdb.fasta -out GCF_008244685.1_ASM824468v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:16,059] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:16,062] [INFO] Selected 9 target genomes.
[2024-01-24 11:36:16,062] [INFO] Target genome list was writen to GCF_008244685.1_ASM824468v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:16,068] [INFO] Task started: fastANI
[2024-01-24 11:36:16,068] [INFO] Running command: fastANI --query /var/lib/cwl/stg17a37bbf-4a06-41d0-9428-be652c69ab2b/GCF_008244685.1_ASM824468v1_genomic.fna.gz --refList GCF_008244685.1_ASM824468v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008244685.1_ASM824468v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:25,233] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:25,241] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:25,242] [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_008244685.1	s__Luteimonas sp008244685	100.0	1386	1386	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_016774335.1	s__Luteimonas sp016774335	91.2175	1192	1386	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	86.98	968	1386	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	85.1315	914	1386	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	85.0289	910	1386	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	82.8724	792	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652935.1	s__Luteimonas padinae	82.4622	663	1386	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	82.2351	685	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004346265.1	s__Thermomonas haemolytica	81.1549	564	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	99.99	99.99	0.99	0.99	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:25,247] [INFO] GTDB search result was written to GCF_008244685.1_ASM824468v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:25,248] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:25,251] [INFO] DFAST_QC result json was written to GCF_008244685.1_ASM824468v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:25,251] [INFO] DFAST_QC completed!
[2024-01-24 11:36:25,251] [INFO] Total running time: 0h1m45s