[2024-01-25 17:52:35,316] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:52:35,318] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:52:35,318] [INFO] DQC Reference Directory: /var/lib/cwl/stg73e3fcd4-4c99-4df8-b294-87fe8c0fc9b6/dqc_reference
[2024-01-25 17:52:36,464] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:52:36,465] [INFO] Task started: Prodigal
[2024-01-25 17:52:36,465] [INFO] Running command: gunzip -c /var/lib/cwl/stgd1a96767-475e-4ba2-b21b-9d4a7cd13ac8/GCF_013185915.1_ASM1318591v1_genomic.fna.gz | prodigal -d GCF_013185915.1_ASM1318591v1_genomic.fna/cds.fna -a GCF_013185915.1_ASM1318591v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:52:49,418] [INFO] Task succeeded: Prodigal
[2024-01-25 17:52:49,418] [INFO] Task started: HMMsearch
[2024-01-25 17:52:49,418] [INFO] Running command: hmmsearch --tblout GCF_013185915.1_ASM1318591v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg73e3fcd4-4c99-4df8-b294-87fe8c0fc9b6/dqc_reference/reference_markers.hmm GCF_013185915.1_ASM1318591v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:52:49,664] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:52:49,668] [INFO] Found 6/6 markers.
[2024-01-25 17:52:49,704] [INFO] Query marker FASTA was written to GCF_013185915.1_ASM1318591v1_genomic.fna/markers.fasta
[2024-01-25 17:52:49,705] [INFO] Task started: Blastn
[2024-01-25 17:52:49,705] [INFO] Running command: blastn -query GCF_013185915.1_ASM1318591v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg73e3fcd4-4c99-4df8-b294-87fe8c0fc9b6/dqc_reference/reference_markers.fasta -out GCF_013185915.1_ASM1318591v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:50,593] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:50,598] [INFO] Selected 21 target genomes.
[2024-01-25 17:52:50,598] [INFO] Target genome list was writen to GCF_013185915.1_ASM1318591v1_genomic.fna/target_genomes.txt
[2024-01-25 17:52:50,611] [INFO] Task started: fastANI
[2024-01-25 17:52:50,612] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1a96767-475e-4ba2-b21b-9d4a7cd13ac8/GCF_013185915.1_ASM1318591v1_genomic.fna.gz --refList GCF_013185915.1_ASM1318591v1_genomic.fna/target_genomes.txt --output GCF_013185915.1_ASM1318591v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:53:10,092] [INFO] Task succeeded: fastANI
[2024-01-25 17:53:10,093] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg73e3fcd4-4c99-4df8-b294-87fe8c0fc9b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:53:10,093] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg73e3fcd4-4c99-4df8-b294-87fe8c0fc9b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:53:10,105] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:53:10,106] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:53:10,106] [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
Stenotrophomonas bentonitica	strain=DSM 103927	GCA_013185915.1	1450134	1450134	type	True	100.0	1466	1466	95	conclusive
Stenotrophomonas rhizophila	strain=DSM14405	GCA_000661955.1	216778	216778	suspected-type	True	87.3751	1042	1466	95	below_threshold
Stenotrophomonas nematodicola	strain=CPCC 101271	GCA_009467805.1	2656746	2656746	type	True	86.6415	1012	1466	95	below_threshold
Stenotrophomonas pavanii	strain=LMG 25348	GCA_900101175.1	487698	487698	type	True	85.0826	944	1466	95	below_threshold
Stenotrophomonas pavanii	strain=DSM 25135	GCA_001431565.1	487698	487698	type	True	85.025	926	1466	95	below_threshold
Stenotrophomonas maltophilia	strain=MTCC 434	GCA_000597745.1	40324	40324	type	True	84.925	882	1466	95	below_threshold
Stenotrophomonas maltophilia	strain=ATCC 13637	GCA_001997185.1	40324	40324	type	True	84.9027	936	1466	95	below_threshold
Stenotrophomonas maltophilia	strain=NBRC 14161	GCA_001591205.1	40324	40324	type	True	84.886	937	1466	95	below_threshold
Stenotrophomonas lactitubi	strain=M15	GCA_002803515.1	2045214	2045214	type	True	84.8405	982	1466	95	below_threshold
Stenotrophomonas chelatiphaga	strain=DSM 21508	GCA_001431535.1	517011	517011	type	True	84.3322	886	1466	95	below_threshold
Stenotrophomonas pennii	strain=Sa5BUN4	GCA_014836545.1	2762239	2762239	type	True	83.9956	919	1466	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	83.8995	795	1466	95	below_threshold
Stenotrophomonas tumulicola	strain=JCM 30961	GCA_014117215.1	1685415	1685415	type	True	83.55	868	1466	95	below_threshold
Stenotrophomonas pictorum	strain=JCM 9942	GCA_001310775.1	86184	86184	type	True	83.4027	512	1466	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	83.0264	839	1466	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	82.9121	700	1466	95	below_threshold
Pseudoxanthomonas taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	81.7655	611	1466	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_014202435.1	83619	83619	type	True	81.4632	651	1466	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_010093165.1	83619	83619	type	True	81.4325	652	1466	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	79.9989	591	1466	95	below_threshold
Brevundimonas bacteroides	strain=DSM 4726	GCA_000701445.1	74311	74311	type	True	75.7161	74	1466	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:53:10,107] [INFO] DFAST Taxonomy check result was written to GCF_013185915.1_ASM1318591v1_genomic.fna/tc_result.tsv
[2024-01-25 17:53:10,109] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:53:10,109] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:53:10,109] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg73e3fcd4-4c99-4df8-b294-87fe8c0fc9b6/dqc_reference/checkm_data
[2024-01-25 17:53:10,110] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:53:10,150] [INFO] Task started: CheckM
[2024-01-25 17:53:10,151] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013185915.1_ASM1318591v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013185915.1_ASM1318591v1_genomic.fna/checkm_input GCF_013185915.1_ASM1318591v1_genomic.fna/checkm_result
[2024-01-25 17:54:03,497] [INFO] Task succeeded: CheckM
[2024-01-25 17:54:03,498] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:54:03,514] [INFO] ===== Completeness check finished =====
[2024-01-25 17:54:03,514] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:54:03,515] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013185915.1_ASM1318591v1_genomic.fna/markers.fasta)
[2024-01-25 17:54:03,515] [INFO] Task started: Blastn
[2024-01-25 17:54:03,515] [INFO] Running command: blastn -query GCF_013185915.1_ASM1318591v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg73e3fcd4-4c99-4df8-b294-87fe8c0fc9b6/dqc_reference/reference_markers_gtdb.fasta -out GCF_013185915.1_ASM1318591v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:54:05,136] [INFO] Task succeeded: Blastn
[2024-01-25 17:54:05,140] [INFO] Selected 12 target genomes.
[2024-01-25 17:54:05,140] [INFO] Target genome list was writen to GCF_013185915.1_ASM1318591v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:54:05,168] [INFO] Task started: fastANI
[2024-01-25 17:54:05,168] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1a96767-475e-4ba2-b21b-9d4a7cd13ac8/GCF_013185915.1_ASM1318591v1_genomic.fna.gz --refList GCF_013185915.1_ASM1318591v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013185915.1_ASM1318591v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:54:17,933] [INFO] Task succeeded: fastANI
[2024-01-25 17:54:17,941] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:54:17,941] [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_013185915.1	s__Stenotrophomonas bentonitica	100.0	1466	1466	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_002893095.1	s__Stenotrophomonas sp002893095	94.7047	1224	1466	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.47	97.41	0.90	0.90	3	-
GCF_007667275.1	s__Stenotrophomonas maltophilia_AE	89.6554	1161	1466	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.01	98.01	0.93	0.93	2	-
GCF_018612915.1	s__Stenotrophomonas sp018612915	89.2672	788	1466	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002386405.1	s__Stenotrophomonas maltophilia_AD	89.25	886	1466	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001704155.1	s__Stenotrophomonas rhizophila_A	89.2107	1160	1466	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.53	97.30	0.92	0.89	10	-
GCA_002435595.1	s__Stenotrophomonas maltophilia_AC	87.2685	945	1466	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	99.01	98.85	0.95	0.92	3	-
GCF_002887735.1	s__Stenotrophomonas bentonitica_A	86.5825	996	1466	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.97	97.41	0.91	0.87	8	-
GCF_003935715.1	s__Stenotrophomonas maltophilia_AH	86.3428	949	1466	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.89	97.89	0.86	0.86	2	-
GCF_001431665.1	s__Stenotrophomonas maltophilia_K	85.0589	916	1466	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348115.1	s__Stenotrophomonas sp004348115	83.9268	812	1466	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.00	98.00	0.94	0.94	2	-
GCF_014117215.1	s__Stenotrophomonas tumulicola	83.55	868	1466	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:54:17,945] [INFO] GTDB search result was written to GCF_013185915.1_ASM1318591v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:54:17,946] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:54:17,949] [INFO] DFAST_QC result json was written to GCF_013185915.1_ASM1318591v1_genomic.fna/dqc_result.json
[2024-01-25 17:54:17,950] [INFO] DFAST_QC completed!
[2024-01-25 17:54:17,950] [INFO] Total running time: 0h1m43s