[2023-06-28 16:34:01,107] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:34:01,109] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:34:01,109] [INFO] DQC Reference Directory: /var/lib/cwl/stgc292cdd0-5349-4336-8587-f734a194cb12/dqc_reference
[2023-06-28 16:34:02,271] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:34:02,272] [INFO] Task started: Prodigal
[2023-06-28 16:34:02,272] [INFO] Running command: gunzip -c /var/lib/cwl/stgd4401a06-a4f1-477c-bb38-fcf1a324cc2a/GCA_017995095.1_ASM1799509v1_genomic.fna.gz | prodigal -d GCA_017995095.1_ASM1799509v1_genomic.fna/cds.fna -a GCA_017995095.1_ASM1799509v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:34:08,813] [INFO] Task succeeded: Prodigal
[2023-06-28 16:34:08,813] [INFO] Task started: HMMsearch
[2023-06-28 16:34:08,813] [INFO] Running command: hmmsearch --tblout GCA_017995095.1_ASM1799509v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc292cdd0-5349-4336-8587-f734a194cb12/dqc_reference/reference_markers.hmm GCA_017995095.1_ASM1799509v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:34:09,011] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:34:09,012] [INFO] Found 6/6 markers.
[2023-06-28 16:34:09,036] [INFO] Query marker FASTA was written to GCA_017995095.1_ASM1799509v1_genomic.fna/markers.fasta
[2023-06-28 16:34:09,037] [INFO] Task started: Blastn
[2023-06-28 16:34:09,037] [INFO] Running command: blastn -query GCA_017995095.1_ASM1799509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc292cdd0-5349-4336-8587-f734a194cb12/dqc_reference/reference_markers.fasta -out GCA_017995095.1_ASM1799509v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:34:09,957] [INFO] Task succeeded: Blastn
[2023-06-28 16:34:09,961] [INFO] Selected 16 target genomes.
[2023-06-28 16:34:09,961] [INFO] Target genome list was writen to GCA_017995095.1_ASM1799509v1_genomic.fna/target_genomes.txt
[2023-06-28 16:34:09,963] [INFO] Task started: fastANI
[2023-06-28 16:34:09,963] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4401a06-a4f1-477c-bb38-fcf1a324cc2a/GCA_017995095.1_ASM1799509v1_genomic.fna.gz --refList GCA_017995095.1_ASM1799509v1_genomic.fna/target_genomes.txt --output GCA_017995095.1_ASM1799509v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:34:21,484] [INFO] Task succeeded: fastANI
[2023-06-28 16:34:21,485] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc292cdd0-5349-4336-8587-f734a194cb12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:34:21,485] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc292cdd0-5349-4336-8587-f734a194cb12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:34:21,495] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:34:21,495] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 16:34:21,496] [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
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	87.3199	638	779	95	below_threshold
Thermomonas carbonis	strain=KCTC 42013	GCA_014396975.1	1463158	1463158	type	True	84.4978	612	779	95	below_threshold
Thermomonas carbonis	strain=KCTC 42013	GCA_014652775.1	1463158	1463158	type	True	84.4952	609	779	95	below_threshold
Thermomonas fusca	strain=DSM 15424	GCA_000423885.1	215690	215690	type	True	84.3598	573	779	95	below_threshold
Thermomonas haemolytica	strain=LMG 19653	GCA_006352395.1	141949	141949	type	True	84.1733	515	779	95	below_threshold
Thermomonas haemolytica	strain=DSM 13605	GCA_004346265.1	141949	141949	type	True	84.1176	528	779	95	below_threshold
Luteimonas huabeiensis	strain=HB2	GCA_000559025.1	1244513	1244513	type	True	81.837	509	779	95	below_threshold
Luteimonas mephitis	strain=DSM 12574	GCA_000422305.1	83615	83615	type	True	81.7991	516	779	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	81.5932	508	779	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	81.5633	488	779	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	81.5464	497	779	95	below_threshold
Luteimonas arsenica	strain=26-35	GCA_004352825.1	1586242	1586242	type	True	81.537	479	779	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	81.321	512	779	95	below_threshold
Luteimonas aestuarii	strain=B9	GCA_004357985.1	453837	453837	type	True	81.2729	476	779	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	81.2673	492	779	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	81.2206	513	779	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 16:34:21,497] [INFO] DFAST Taxonomy check result was written to GCA_017995095.1_ASM1799509v1_genomic.fna/tc_result.tsv
[2023-06-28 16:34:21,498] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:34:21,498] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:34:21,498] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc292cdd0-5349-4336-8587-f734a194cb12/dqc_reference/checkm_data
[2023-06-28 16:34:21,499] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:34:21,525] [INFO] Task started: CheckM
[2023-06-28 16:34:21,526] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017995095.1_ASM1799509v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017995095.1_ASM1799509v1_genomic.fna/checkm_input GCA_017995095.1_ASM1799509v1_genomic.fna/checkm_result
[2023-06-28 16:34:50,784] [INFO] Task succeeded: CheckM
[2023-06-28 16:34:50,785] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.91%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 16:34:50,802] [INFO] ===== Completeness check finished =====
[2023-06-28 16:34:50,802] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:34:50,804] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017995095.1_ASM1799509v1_genomic.fna/markers.fasta)
[2023-06-28 16:34:50,804] [INFO] Task started: Blastn
[2023-06-28 16:34:50,804] [INFO] Running command: blastn -query GCA_017995095.1_ASM1799509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc292cdd0-5349-4336-8587-f734a194cb12/dqc_reference/reference_markers_gtdb.fasta -out GCA_017995095.1_ASM1799509v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:34:52,637] [INFO] Task succeeded: Blastn
[2023-06-28 16:34:52,639] [INFO] Selected 13 target genomes.
[2023-06-28 16:34:52,640] [INFO] Target genome list was writen to GCA_017995095.1_ASM1799509v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:34:52,650] [INFO] Task started: fastANI
[2023-06-28 16:34:52,650] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4401a06-a4f1-477c-bb38-fcf1a324cc2a/GCA_017995095.1_ASM1799509v1_genomic.fna.gz --refList GCA_017995095.1_ASM1799509v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017995095.1_ASM1799509v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:35:01,647] [INFO] Task succeeded: fastANI
[2023-06-28 16:35:01,656] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 16:35:01,656] [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
GCA_016720345.1	s__Thermomonas sp016720345	99.5482	726	779	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	99.48	99.08	0.97	0.93	11	conclusive
GCF_006337105.1	s__Thermomonas sp006337105	87.3199	638	779	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011302915.1	s__Thermomonas sp011302915	85.5226	594	779	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302075.1	s__Thermomonas sp017302075	85.2104	527	779	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302095.1	s__Thermomonas sp017302095	84.6397	402	779	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014395425.1	s__Thermomonas brevis	84.5519	568	779	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014396975.1	s__Thermomonas carbonis	84.4978	612	779	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000423885.1	s__Thermomonas fusca	84.3713	573	779	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	96.57	96.57	0.92	0.92	2	-
GCF_014678725.1	s__Thermomonas sp014678725	84.162	565	779	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004346265.1	s__Thermomonas haemolytica	84.1229	528	779	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	99.99	99.99	0.99	0.99	3	-
GCA_017305095.1	s__Thermomonas sp017305095	83.8533	545	779	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000472505.1	s__Luteimonas sp000472505	81.3181	490	779	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.95	99.95	0.99	0.99	2	-
GCF_016774335.1	s__Luteimonas sp016774335	81.238	512	779	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 16:35:01,658] [INFO] GTDB search result was written to GCA_017995095.1_ASM1799509v1_genomic.fna/result_gtdb.tsv
[2023-06-28 16:35:01,659] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:35:01,663] [INFO] DFAST_QC result json was written to GCA_017995095.1_ASM1799509v1_genomic.fna/dqc_result.json
[2023-06-28 16:35:01,663] [INFO] DFAST_QC completed!
[2023-06-28 16:35:01,663] [INFO] Total running time: 0h1m1s