[2024-01-24 12:14:35,736] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:35,738] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:35,739] [INFO] DQC Reference Directory: /var/lib/cwl/stg66f00ef0-3d95-45ac-80d6-49471ea90a73/dqc_reference
[2024-01-24 12:14:37,136] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:37,137] [INFO] Task started: Prodigal
[2024-01-24 12:14:37,138] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ce5867f-4b45-4c4e-83ad-e3c9d01a5d69/GCF_010093235.1_ASM1009323v1_genomic.fna.gz | prodigal -d GCF_010093235.1_ASM1009323v1_genomic.fna/cds.fna -a GCF_010093235.1_ASM1009323v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:47,448] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:47,449] [INFO] Task started: HMMsearch
[2024-01-24 12:14:47,449] [INFO] Running command: hmmsearch --tblout GCF_010093235.1_ASM1009323v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg66f00ef0-3d95-45ac-80d6-49471ea90a73/dqc_reference/reference_markers.hmm GCF_010093235.1_ASM1009323v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:47,663] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:47,665] [INFO] Found 6/6 markers.
[2024-01-24 12:14:47,705] [INFO] Query marker FASTA was written to GCF_010093235.1_ASM1009323v1_genomic.fna/markers.fasta
[2024-01-24 12:14:47,705] [INFO] Task started: Blastn
[2024-01-24 12:14:47,706] [INFO] Running command: blastn -query GCF_010093235.1_ASM1009323v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66f00ef0-3d95-45ac-80d6-49471ea90a73/dqc_reference/reference_markers.fasta -out GCF_010093235.1_ASM1009323v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:48,712] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:48,717] [INFO] Selected 15 target genomes.
[2024-01-24 12:14:48,717] [INFO] Target genome list was writen to GCF_010093235.1_ASM1009323v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:48,724] [INFO] Task started: fastANI
[2024-01-24 12:14:48,724] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ce5867f-4b45-4c4e-83ad-e3c9d01a5d69/GCF_010093235.1_ASM1009323v1_genomic.fna.gz --refList GCF_010093235.1_ASM1009323v1_genomic.fna/target_genomes.txt --output GCF_010093235.1_ASM1009323v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:01,989] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:01,990] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg66f00ef0-3d95-45ac-80d6-49471ea90a73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:01,990] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg66f00ef0-3d95-45ac-80d6-49471ea90a73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:02,002] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:02,002] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:02,002] [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
Pseudoxanthomonas suwonensis	strain=DSM 17175	GCA_010093235.1	314722	314722	suspected-type	True	100.0	1106	1111	95	conclusive
Pseudoxanthomonas taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	86.9856	759	1111	95	below_threshold
Pseudoxanthomonas jiangsuensis	strain=DSM 22398	GCA_010093185.1	619688	619688	type	True	86.6816	856	1111	95	below_threshold
Pseudoxanthomonas koreensis	strain=KCTC 12208	GCA_010093225.1	266061	266061	type	True	86.0153	727	1111	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_010093165.1	83619	83619	type	True	85.9262	782	1111	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_014202435.1	83619	83619	type	True	85.9046	787	1111	95	below_threshold
Pseudoxanthomonas kaohsiungensis	strain=DSM 17583	GCA_010211765.1	283923	283923	type	True	85.7496	840	1111	95	below_threshold
Stenotrophomonas acidaminiphila	strain=JCM 13310	GCA_001431595.1	128780	128780	type	True	83.0313	667	1111	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	83.0185	703	1111	95	below_threshold
Xanthomonas sacchari	strain=CFBP4641	GCA_002940085.1	56458	56458	suspected-type	True	82.7351	739	1111	95	below_threshold
Stenotrophomonas maltophilia	strain=NBRC 14161	GCA_001591205.1	40324	40324	type	True	81.7521	653	1111	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	81.7007	561	1111	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	81.5895	630	1111	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	81.0623	672	1111	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	80.9067	512	1111	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:02,005] [INFO] DFAST Taxonomy check result was written to GCF_010093235.1_ASM1009323v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:02,007] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:02,007] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:02,007] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg66f00ef0-3d95-45ac-80d6-49471ea90a73/dqc_reference/checkm_data
[2024-01-24 12:15:02,008] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:02,043] [INFO] Task started: CheckM
[2024-01-24 12:15:02,043] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010093235.1_ASM1009323v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010093235.1_ASM1009323v1_genomic.fna/checkm_input GCF_010093235.1_ASM1009323v1_genomic.fna/checkm_result
[2024-01-24 12:15:39,225] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:39,226] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:39,246] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:39,247] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:39,247] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010093235.1_ASM1009323v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:39,247] [INFO] Task started: Blastn
[2024-01-24 12:15:39,247] [INFO] Running command: blastn -query GCF_010093235.1_ASM1009323v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66f00ef0-3d95-45ac-80d6-49471ea90a73/dqc_reference/reference_markers_gtdb.fasta -out GCF_010093235.1_ASM1009323v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:41,309] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:41,313] [INFO] Selected 9 target genomes.
[2024-01-24 12:15:41,313] [INFO] Target genome list was writen to GCF_010093235.1_ASM1009323v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:41,319] [INFO] Task started: fastANI
[2024-01-24 12:15:41,320] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ce5867f-4b45-4c4e-83ad-e3c9d01a5d69/GCF_010093235.1_ASM1009323v1_genomic.fna.gz --refList GCF_010093235.1_ASM1009323v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010093235.1_ASM1009323v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:49,439] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:49,448] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:49,448] [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_010093235.1	s__Pseudoxanthomonas suwonensis	100.0	1106	1111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000510725.1	s__Pseudoxanthomonas sp000510725	91.4412	951	1111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.33	99.13	0.95	0.92	5	-
GCF_000185965.1	s__Pseudoxanthomonas suwonensis_A	91.2477	960	1111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513955.1	s__Pseudoxanthomonas suwonensis_C	87.2043	849	1111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	98.37	96.94	0.95	0.91	3	-
GCF_000513995.1	s__Pseudoxanthomonas sp000513995	87.1321	838	1111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093135.1	s__Pseudoxanthomonas taiwanensis	86.9851	759	1111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.04	99.04	0.90	0.90	2	-
GCF_010093185.1	s__Pseudoxanthomonas jiangsuensis	86.6673	857	1111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202435.1	s__Pseudoxanthomonas broegbernensis	85.9046	787	1111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCA_014654535.1	s__Pseudomonas_S boreopolis	83.0725	728	1111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudomonas_S	95.0	98.68	98.68	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:49,450] [INFO] GTDB search result was written to GCF_010093235.1_ASM1009323v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:49,451] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:49,455] [INFO] DFAST_QC result json was written to GCF_010093235.1_ASM1009323v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:49,455] [INFO] DFAST_QC completed!
[2024-01-24 12:15:49,455] [INFO] Total running time: 0h1m14s