[2024-01-24 13:17:05,405] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:05,407] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:05,408] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0efb7ba-8e1b-4f6e-a247-5794c272654a/dqc_reference
[2024-01-24 13:17:06,950] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:06,951] [INFO] Task started: Prodigal
[2024-01-24 13:17:06,952] [INFO] Running command: gunzip -c /var/lib/cwl/stgf32f7688-7ba5-4b43-bd1c-f95b32c3ccef/GCF_021730435.1_ASM2173043v1_genomic.fna.gz | prodigal -d GCF_021730435.1_ASM2173043v1_genomic.fna/cds.fna -a GCF_021730435.1_ASM2173043v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:23,098] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:23,098] [INFO] Task started: HMMsearch
[2024-01-24 13:17:23,098] [INFO] Running command: hmmsearch --tblout GCF_021730435.1_ASM2173043v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0efb7ba-8e1b-4f6e-a247-5794c272654a/dqc_reference/reference_markers.hmm GCF_021730435.1_ASM2173043v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:23,473] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:23,474] [INFO] Found 6/6 markers.
[2024-01-24 13:17:23,517] [INFO] Query marker FASTA was written to GCF_021730435.1_ASM2173043v1_genomic.fna/markers.fasta
[2024-01-24 13:17:23,518] [INFO] Task started: Blastn
[2024-01-24 13:17:23,518] [INFO] Running command: blastn -query GCF_021730435.1_ASM2173043v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0efb7ba-8e1b-4f6e-a247-5794c272654a/dqc_reference/reference_markers.fasta -out GCF_021730435.1_ASM2173043v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:24,525] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:24,528] [INFO] Selected 9 target genomes.
[2024-01-24 13:17:24,528] [INFO] Target genome list was writen to GCF_021730435.1_ASM2173043v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:24,534] [INFO] Task started: fastANI
[2024-01-24 13:17:24,534] [INFO] Running command: fastANI --query /var/lib/cwl/stgf32f7688-7ba5-4b43-bd1c-f95b32c3ccef/GCF_021730435.1_ASM2173043v1_genomic.fna.gz --refList GCF_021730435.1_ASM2173043v1_genomic.fna/target_genomes.txt --output GCF_021730435.1_ASM2173043v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:34,900] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:34,901] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0efb7ba-8e1b-4f6e-a247-5794c272654a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:34,901] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0efb7ba-8e1b-4f6e-a247-5794c272654a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:34,911] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:34,911] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:34,911] [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
Xanthobacter agilis	strain=LMG 16336	GCA_021730435.1	47492	47492	type	True	100.0	1570	1572	95	conclusive
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	82.5649	888	1572	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	82.2331	889	1572	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	82.1163	885	1572	95	below_threshold
Xanthobacter autotrophicus	strain=DSM 432	GCA_005871085.1	280	280	type	True	82.0092	860	1572	95	below_threshold
Xanthobacter tagetidis	strain=ATCC 700314	GCA_003667445.1	60216	60216	type	True	81.4881	758	1572	95	below_threshold
Xanthobacter tagetidis	strain=DSM 11105	GCA_014206845.1	60216	60216	type	True	81.4605	765	1572	95	below_threshold
Azorhizobium caulinodans	strain=ORS 571	GCA_000010525.1	7	7	type	True	80.0916	663	1572	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	77.5477	252	1572	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:34,913] [INFO] DFAST Taxonomy check result was written to GCF_021730435.1_ASM2173043v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:34,914] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:34,914] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:34,914] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0efb7ba-8e1b-4f6e-a247-5794c272654a/dqc_reference/checkm_data
[2024-01-24 13:17:34,916] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:34,965] [INFO] Task started: CheckM
[2024-01-24 13:17:34,966] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021730435.1_ASM2173043v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021730435.1_ASM2173043v1_genomic.fna/checkm_input GCF_021730435.1_ASM2173043v1_genomic.fna/checkm_result
[2024-01-24 13:18:27,713] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:27,715] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:27,736] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:27,737] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:27,737] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021730435.1_ASM2173043v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:27,738] [INFO] Task started: Blastn
[2024-01-24 13:18:27,738] [INFO] Running command: blastn -query GCF_021730435.1_ASM2173043v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0efb7ba-8e1b-4f6e-a247-5794c272654a/dqc_reference/reference_markers_gtdb.fasta -out GCF_021730435.1_ASM2173043v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:29,544] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:29,548] [INFO] Selected 11 target genomes.
[2024-01-24 13:18:29,548] [INFO] Target genome list was writen to GCF_021730435.1_ASM2173043v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:29,567] [INFO] Task started: fastANI
[2024-01-24 13:18:29,568] [INFO] Running command: fastANI --query /var/lib/cwl/stgf32f7688-7ba5-4b43-bd1c-f95b32c3ccef/GCF_021730435.1_ASM2173043v1_genomic.fna.gz --refList GCF_021730435.1_ASM2173043v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021730435.1_ASM2173043v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:41,214] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:41,226] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:18:41,227] [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_016807805.1	s__Xanthobacter sp016807805	82.5005	895	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000017645.1	s__Xanthobacter autotrophicus	82.3303	869	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008364685.1	s__Xanthobacter sp008364685	82.2625	885	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017849325.1	s__Xanthobacter autotrophicus_B	82.1018	545	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005871085.1	s__Xanthobacter autotrophicus_A	82.0363	857	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932745.1	s__Xanthobacter sp012932745	82.0178	848	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	97.23	97.23	0.90	0.90	2	-
GCF_012275355.1	s__Xanthobacter sp012275355	81.9613	865	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000702385.1	s__Xanthobacter sp000702385	81.8494	880	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	96.09	96.09	0.89	0.89	2	-
GCF_017875275.1	s__Xanthobacter flavus	81.7508	853	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667445.1	s__Xanthobacter tagetidis	81.4235	765	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000010525.1	s__Azorhizobium caulinodans	80.0964	663	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Azorhizobium	95.0	97.54	97.54	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:41,228] [INFO] GTDB search result was written to GCF_021730435.1_ASM2173043v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:41,229] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:41,232] [INFO] DFAST_QC result json was written to GCF_021730435.1_ASM2173043v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:41,232] [INFO] DFAST_QC completed!
[2024-01-24 13:18:41,233] [INFO] Total running time: 0h1m36s