[2024-01-24 13:18:27,357] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:27,359] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:27,360] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c560771-df9a-4944-97bd-af0214f3335f/dqc_reference
[2024-01-24 13:18:28,656] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:28,657] [INFO] Task started: Prodigal
[2024-01-24 13:18:28,657] [INFO] Running command: gunzip -c /var/lib/cwl/stg4066fcd8-b115-44a4-bc87-24cb16bf025b/GCF_009828935.2_ASM982893v2_genomic.fna.gz | prodigal -d GCF_009828935.2_ASM982893v2_genomic.fna/cds.fna -a GCF_009828935.2_ASM982893v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:39,155] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:39,156] [INFO] Task started: HMMsearch
[2024-01-24 13:18:39,156] [INFO] Running command: hmmsearch --tblout GCF_009828935.2_ASM982893v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c560771-df9a-4944-97bd-af0214f3335f/dqc_reference/reference_markers.hmm GCF_009828935.2_ASM982893v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:39,463] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:39,465] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4066fcd8-b115-44a4-bc87-24cb16bf025b/GCF_009828935.2_ASM982893v2_genomic.fna.gz]
[2024-01-24 13:18:39,500] [INFO] Query marker FASTA was written to GCF_009828935.2_ASM982893v2_genomic.fna/markers.fasta
[2024-01-24 13:18:39,500] [INFO] Task started: Blastn
[2024-01-24 13:18:39,501] [INFO] Running command: blastn -query GCF_009828935.2_ASM982893v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c560771-df9a-4944-97bd-af0214f3335f/dqc_reference/reference_markers.fasta -out GCF_009828935.2_ASM982893v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:40,582] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:40,586] [INFO] Selected 16 target genomes.
[2024-01-24 13:18:40,587] [INFO] Target genome list was writen to GCF_009828935.2_ASM982893v2_genomic.fna/target_genomes.txt
[2024-01-24 13:18:40,615] [INFO] Task started: fastANI
[2024-01-24 13:18:40,616] [INFO] Running command: fastANI --query /var/lib/cwl/stg4066fcd8-b115-44a4-bc87-24cb16bf025b/GCF_009828935.2_ASM982893v2_genomic.fna.gz --refList GCF_009828935.2_ASM982893v2_genomic.fna/target_genomes.txt --output GCF_009828935.2_ASM982893v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:55,007] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:55,007] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c560771-df9a-4944-97bd-af0214f3335f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:55,008] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c560771-df9a-4944-97bd-af0214f3335f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:55,025] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:18:55,026] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:18:55,026] [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 fraxinea	strain=D4P002	GCA_021233355.1	2901869	2901869	type	True	85.0746	887	1194	95	below_threshold
Luteimonas terrae	strain=THG-MD21	GCA_004358165.1	1530191	1530191	type	True	84.4437	866	1194	95	below_threshold
Luteimonas deserti	strain=SJ-16	GCA_013425765.1	2752306	2752306	type	True	83.7041	863	1194	95	below_threshold
Luteimonas chenhongjianii	strain=100111	GCA_002327105.1	2006110	2006110	type	True	83.5456	826	1194	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	82.2975	717	1194	95	below_threshold
Luteimonas huabeiensis	strain=HB2	GCA_000559025.1	1244513	1244513	type	True	81.958	717	1194	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	81.5875	726	1194	95	below_threshold
Luteimonas mephitis	strain=DSM 12574	GCA_000422305.1	83615	83615	type	True	81.4849	615	1194	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	81.4507	746	1194	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	81.4331	610	1194	95	below_threshold
Luteimonas aestuarii	strain=B9	GCA_004357985.1	453837	453837	type	True	81.1899	649	1194	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	81.0464	636	1194	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	80.9509	558	1194	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	80.8481	686	1194	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	80.7718	524	1194	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	80.291	667	1194	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:55,028] [INFO] DFAST Taxonomy check result was written to GCF_009828935.2_ASM982893v2_genomic.fna/tc_result.tsv
[2024-01-24 13:18:55,028] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:55,028] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:55,028] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c560771-df9a-4944-97bd-af0214f3335f/dqc_reference/checkm_data
[2024-01-24 13:18:55,029] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:55,075] [INFO] Task started: CheckM
[2024-01-24 13:18:55,076] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009828935.2_ASM982893v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009828935.2_ASM982893v2_genomic.fna/checkm_input GCF_009828935.2_ASM982893v2_genomic.fna/checkm_result
[2024-01-24 13:19:46,728] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:46,730] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.02%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:46,754] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:46,754] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:46,755] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009828935.2_ASM982893v2_genomic.fna/markers.fasta)
[2024-01-24 13:19:46,755] [INFO] Task started: Blastn
[2024-01-24 13:19:46,755] [INFO] Running command: blastn -query GCF_009828935.2_ASM982893v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c560771-df9a-4944-97bd-af0214f3335f/dqc_reference/reference_markers_gtdb.fasta -out GCF_009828935.2_ASM982893v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:48,643] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:48,647] [INFO] Selected 9 target genomes.
[2024-01-24 13:19:48,647] [INFO] Target genome list was writen to GCF_009828935.2_ASM982893v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:48,674] [INFO] Task started: fastANI
[2024-01-24 13:19:48,674] [INFO] Running command: fastANI --query /var/lib/cwl/stg4066fcd8-b115-44a4-bc87-24cb16bf025b/GCF_009828935.2_ASM982893v2_genomic.fna.gz --refList GCF_009828935.2_ASM982893v2_genomic.fna/target_genomes_gtdb.txt --output GCF_009828935.2_ASM982893v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:56,853] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:56,868] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:56,868] [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_002849595.1	s__Luteimonas sp002849595	99.9744	1183	1194	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.97	99.97	0.99	0.99	2	conclusive
GCF_902506295.1	s__Luteimonas sp902506295	85.2454	867	1194	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002324875.1	s__Luteimonas sp002324875	84.7046	867	1194	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.99	99.99	0.99	0.99	3	-
GCF_004358165.1	s__Luteimonas terrae	84.4411	866	1194	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	96.65	96.65	0.95	0.95	2	-
GCF_001014645.1	s__Luteimonas sp001014645	84.3488	835	1194	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013425765.1	s__Luteimonas sp013425765	83.7167	862	1194	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002327105.1	s__Luteimonas chenhongjianii	83.5473	826	1194	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	98.75	98.75	0.95	0.95	2	-
GCF_014192745.1	s__Luteimonas sp014192745	83.2779	807	1194	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002240395.1	s__Luteimonas citri_A	82.9699	813	1194	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:56,870] [INFO] GTDB search result was written to GCF_009828935.2_ASM982893v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:56,871] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:56,874] [INFO] DFAST_QC result json was written to GCF_009828935.2_ASM982893v2_genomic.fna/dqc_result.json
[2024-01-24 13:19:56,875] [INFO] DFAST_QC completed!
[2024-01-24 13:19:56,875] [INFO] Total running time: 0h1m30s