[2024-01-24 13:31:35,358] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:35,361] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:35,361] [INFO] DQC Reference Directory: /var/lib/cwl/stg3b02c5a4-d662-4814-93d9-e2a90f7e7332/dqc_reference
[2024-01-24 13:31:36,797] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:36,798] [INFO] Task started: Prodigal
[2024-01-24 13:31:36,799] [INFO] Running command: gunzip -c /var/lib/cwl/stge9d0852d-df83-4019-b235-b39fa53f0eab/GCF_005239095.1_ASM523909v1_genomic.fna.gz | prodigal -d GCF_005239095.1_ASM523909v1_genomic.fna/cds.fna -a GCF_005239095.1_ASM523909v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:48,709] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:48,710] [INFO] Task started: HMMsearch
[2024-01-24 13:31:48,710] [INFO] Running command: hmmsearch --tblout GCF_005239095.1_ASM523909v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3b02c5a4-d662-4814-93d9-e2a90f7e7332/dqc_reference/reference_markers.hmm GCF_005239095.1_ASM523909v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:49,061] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:49,062] [INFO] Found 6/6 markers.
[2024-01-24 13:31:49,099] [INFO] Query marker FASTA was written to GCF_005239095.1_ASM523909v1_genomic.fna/markers.fasta
[2024-01-24 13:31:49,100] [INFO] Task started: Blastn
[2024-01-24 13:31:49,100] [INFO] Running command: blastn -query GCF_005239095.1_ASM523909v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b02c5a4-d662-4814-93d9-e2a90f7e7332/dqc_reference/reference_markers.fasta -out GCF_005239095.1_ASM523909v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:50,171] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:50,174] [INFO] Selected 22 target genomes.
[2024-01-24 13:31:50,174] [INFO] Target genome list was writen to GCF_005239095.1_ASM523909v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:50,182] [INFO] Task started: fastANI
[2024-01-24 13:31:50,182] [INFO] Running command: fastANI --query /var/lib/cwl/stge9d0852d-df83-4019-b235-b39fa53f0eab/GCF_005239095.1_ASM523909v1_genomic.fna.gz --refList GCF_005239095.1_ASM523909v1_genomic.fna/target_genomes.txt --output GCF_005239095.1_ASM523909v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:10,117] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:10,117] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3b02c5a4-d662-4814-93d9-e2a90f7e7332/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:10,118] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3b02c5a4-d662-4814-93d9-e2a90f7e7332/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:10,135] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:10,135] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:10,136] [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 gilva	strain=H23	GCA_005239095.1	2572684	2572684	type	True	100.0	1208	1209	95	conclusive
Luteimonas cucumeris	strain=CGMCC 1.10821	GCA_007830035.1	985012	985012	type	True	83.342	813	1209	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	81.8323	591	1209	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	81.7679	726	1209	95	below_threshold
Luteimonas mephitis	strain=DSM 12574	GCA_000422305.1	83615	83615	type	True	81.5914	638	1209	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	81.525	595	1209	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	81.3069	643	1209	95	below_threshold
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	81.2679	661	1209	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	81.2585	695	1209	95	below_threshold
Lysobacter enzymogenes	strain=ATCC 29487	GCA_900106525.1	69	69	suspected-type	True	81.1216	759	1209	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	80.9392	629	1209	95	below_threshold
Luteimonas arsenica	strain=26-35	GCA_004352825.1	1586242	1586242	type	True	80.8868	553	1209	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	80.7625	503	1209	95	below_threshold
Pseudoxanthomonas yeongjuensis	strain=DSM 18204	GCA_010093345.1	377616	377616	type	True	80.4432	633	1209	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	80.4322	623	1209	95	below_threshold
Xanthomonas sacchari	strain=CFBP4641	GCA_002940085.1	56458	56458	suspected-type	True	80.3701	612	1209	95	below_threshold
Lysobacter dokdonensis	strain=DS-58	GCA_000770795.1	414050	414050	type	True	80.3447	545	1209	95	below_threshold
Pseudoxanthomonas wuyuanensis	strain=CGMCC 1.10978	GCA_900215535.1	1073196	1073196	type	True	80.2946	626	1209	95	below_threshold
Lysobacter psychrotolerans	strain=ZS60	GCA_003719825.1	1327343	1327343	type	True	80.0488	561	1209	95	below_threshold
Stenotrophomonas acidaminiphila	strain=JCM 13310	GCA_001431595.1	128780	128780	type	True	79.9414	528	1209	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	79.9388	543	1209	95	below_threshold
Stenotrophomonas bentonitica	strain=DSM 103927	GCA_013185915.1	1450134	1450134	type	True	79.6492	515	1209	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:10,138] [INFO] DFAST Taxonomy check result was written to GCF_005239095.1_ASM523909v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:10,139] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:10,139] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:10,139] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3b02c5a4-d662-4814-93d9-e2a90f7e7332/dqc_reference/checkm_data
[2024-01-24 13:32:10,140] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:10,179] [INFO] Task started: CheckM
[2024-01-24 13:32:10,179] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005239095.1_ASM523909v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005239095.1_ASM523909v1_genomic.fna/checkm_input GCF_005239095.1_ASM523909v1_genomic.fna/checkm_result
[2024-01-24 13:32:46,161] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:46,162] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:46,180] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:46,181] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:46,181] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005239095.1_ASM523909v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:46,182] [INFO] Task started: Blastn
[2024-01-24 13:32:46,182] [INFO] Running command: blastn -query GCF_005239095.1_ASM523909v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b02c5a4-d662-4814-93d9-e2a90f7e7332/dqc_reference/reference_markers_gtdb.fasta -out GCF_005239095.1_ASM523909v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:48,193] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:48,198] [INFO] Selected 19 target genomes.
[2024-01-24 13:32:48,199] [INFO] Target genome list was writen to GCF_005239095.1_ASM523909v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:48,216] [INFO] Task started: fastANI
[2024-01-24 13:32:48,216] [INFO] Running command: fastANI --query /var/lib/cwl/stge9d0852d-df83-4019-b235-b39fa53f0eab/GCF_005239095.1_ASM523909v1_genomic.fna.gz --refList GCF_005239095.1_ASM523909v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005239095.1_ASM523909v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:07,811] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:07,828] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:07,828] [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_005239095.1	s__Luteimonas_C gilva	100.0	1208	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902825775.1	s__Luteimonas_C sp902825775	84.6199	910	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830035.1	s__Luteimonas_C cucumeris	83.3312	814	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003416885.1	s__Luteimonas_B sp003416885	81.8324	591	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422305.1	s__Luteimonas mephitis	81.5859	639	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006337105.1	s__Thermomonas sp006337105	81.5201	596	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114355.1	s__Lysobacter sp900114355	81.3639	743	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489475.1	s__Lysobacter solisilvae	81.308	630	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859325.1	s__Luteimonas marina	81.2949	643	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017939625.1	s__Pseudoxanthomonas_A helianthi	80.9025	633	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011526085.1	s__SCMT01 sp011526085	80.7059	613	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__SCMT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362405.1	s__JABFWF01 sp013362405	80.5298	440	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__JABFWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093345.1	s__Pseudoxanthomonas_A yeongjuensis	80.4431	633	1209	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_000770795.1	s__Lysobacter_A dokdonensis	80.3229	547	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216795.1	s__Stenotrophomonas_A sp004216795	80.3102	554	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003719825.1	s__Lysobacter psychrotolerans	80.0545	560	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002429615.1	s__Stenotrophomonas_A sp002429615	79.898	480	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004284655.1	s__Pseudoxanthomonas_A spadix_A	79.8802	559	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	98.46	98.41	0.91	0.91	3	-
GCF_002893095.1	s__Stenotrophomonas sp002893095	79.654	514	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.47	97.41	0.90	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:07,829] [INFO] GTDB search result was written to GCF_005239095.1_ASM523909v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:07,830] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:07,834] [INFO] DFAST_QC result json was written to GCF_005239095.1_ASM523909v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:07,834] [INFO] DFAST_QC completed!
[2024-01-24 13:33:07,834] [INFO] Total running time: 0h1m32s