[2023-06-29 10:06:20,621] [INFO] DFAST_QC pipeline started.
[2023-06-29 10:06:20,624] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 10:06:20,624] [INFO] DQC Reference Directory: /var/lib/cwl/stg44c0ba2f-c5a0-468d-a3e8-10b2e7702362/dqc_reference
[2023-06-29 10:06:22,223] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 10:06:22,224] [INFO] Task started: Prodigal
[2023-06-29 10:06:22,225] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d0288cd-631c-49e9-85a4-c98f00977b67/GCA_020201235.1_ASM2020123v1_genomic.fna.gz | prodigal -d GCA_020201235.1_ASM2020123v1_genomic.fna/cds.fna -a GCA_020201235.1_ASM2020123v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 10:06:29,413] [INFO] Task succeeded: Prodigal
[2023-06-29 10:06:29,413] [INFO] Task started: HMMsearch
[2023-06-29 10:06:29,413] [INFO] Running command: hmmsearch --tblout GCA_020201235.1_ASM2020123v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44c0ba2f-c5a0-468d-a3e8-10b2e7702362/dqc_reference/reference_markers.hmm GCA_020201235.1_ASM2020123v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 10:06:29,663] [INFO] Task succeeded: HMMsearch
[2023-06-29 10:06:29,665] [INFO] Found 6/6 markers.
[2023-06-29 10:06:29,695] [INFO] Query marker FASTA was written to GCA_020201235.1_ASM2020123v1_genomic.fna/markers.fasta
[2023-06-29 10:06:29,696] [INFO] Task started: Blastn
[2023-06-29 10:06:29,696] [INFO] Running command: blastn -query GCA_020201235.1_ASM2020123v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44c0ba2f-c5a0-468d-a3e8-10b2e7702362/dqc_reference/reference_markers.fasta -out GCA_020201235.1_ASM2020123v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 10:06:30,552] [INFO] Task succeeded: Blastn
[2023-06-29 10:06:30,557] [INFO] Selected 31 target genomes.
[2023-06-29 10:06:30,558] [INFO] Target genome list was writen to GCA_020201235.1_ASM2020123v1_genomic.fna/target_genomes.txt
[2023-06-29 10:06:30,565] [INFO] Task started: fastANI
[2023-06-29 10:06:30,565] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d0288cd-631c-49e9-85a4-c98f00977b67/GCA_020201235.1_ASM2020123v1_genomic.fna.gz --refList GCA_020201235.1_ASM2020123v1_genomic.fna/target_genomes.txt --output GCA_020201235.1_ASM2020123v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 10:06:53,395] [INFO] Task succeeded: fastANI
[2023-06-29 10:06:53,396] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44c0ba2f-c5a0-468d-a3e8-10b2e7702362/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 10:06:53,396] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44c0ba2f-c5a0-468d-a3e8-10b2e7702362/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 10:06:53,407] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 10:06:53,407] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 10:06:53,407] [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
Wenzhouxiangella sediminis	strain=XDB06	GCA_003410055.1	1792836	1792836	type	True	76.7548	125	740	95	below_threshold
Wenzhouxiangella marina	strain=KCTC 42284	GCA_001187785.1	1579979	1579979	type	True	76.6535	108	740	95	below_threshold
Wenzhouxiangella marina	strain=DSM 103414	GCA_014203035.1	1579979	1579979	type	True	76.5996	109	740	95	below_threshold
Pseudoxanthomonas winnipegensis	strain=NML 130738	GCA_004283755.1	2480810	2480810	type	True	75.6283	62	740	95	below_threshold
Oleiagrimonas soli	strain=3.5X	GCA_000761445.1	1543381	1543381	type	True	75.6134	60	740	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	75.4967	62	740	95	below_threshold
Oleiagrimonas soli	strain=DSM 107085	GCA_014201555.1	1543381	1543381	type	True	75.4887	61	740	95	below_threshold
Tahibacter aquaticus	strain=DSM 21667	GCA_004363655.1	520092	520092	type	True	75.4337	71	740	95	below_threshold
Pseudomonas citronellolis	strain=LMG 18378	GCA_900112375.1	53408	53408	type	True	75.0281	58	740	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	74.9963	56	740	95	below_threshold
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	74.903	51	740	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 10:06:53,410] [INFO] DFAST Taxonomy check result was written to GCA_020201235.1_ASM2020123v1_genomic.fna/tc_result.tsv
[2023-06-29 10:06:53,410] [INFO] ===== Taxonomy check completed =====
[2023-06-29 10:06:53,410] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 10:06:53,410] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44c0ba2f-c5a0-468d-a3e8-10b2e7702362/dqc_reference/checkm_data
[2023-06-29 10:06:53,412] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 10:06:53,449] [INFO] Task started: CheckM
[2023-06-29 10:06:53,449] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020201235.1_ASM2020123v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020201235.1_ASM2020123v1_genomic.fna/checkm_input GCA_020201235.1_ASM2020123v1_genomic.fna/checkm_result
[2023-06-29 10:07:20,356] [INFO] Task succeeded: CheckM
[2023-06-29 10:07:20,358] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.02%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 10:07:20,380] [INFO] ===== Completeness check finished =====
[2023-06-29 10:07:20,380] [INFO] ===== Start GTDB Search =====
[2023-06-29 10:07:20,381] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020201235.1_ASM2020123v1_genomic.fna/markers.fasta)
[2023-06-29 10:07:20,381] [INFO] Task started: Blastn
[2023-06-29 10:07:20,381] [INFO] Running command: blastn -query GCA_020201235.1_ASM2020123v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44c0ba2f-c5a0-468d-a3e8-10b2e7702362/dqc_reference/reference_markers_gtdb.fasta -out GCA_020201235.1_ASM2020123v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 10:07:21,968] [INFO] Task succeeded: Blastn
[2023-06-29 10:07:21,974] [INFO] Selected 23 target genomes.
[2023-06-29 10:07:21,974] [INFO] Target genome list was writen to GCA_020201235.1_ASM2020123v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 10:07:22,018] [INFO] Task started: fastANI
[2023-06-29 10:07:22,019] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d0288cd-631c-49e9-85a4-c98f00977b67/GCA_020201235.1_ASM2020123v1_genomic.fna.gz --refList GCA_020201235.1_ASM2020123v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020201235.1_ASM2020123v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 10:07:33,226] [INFO] Task succeeded: fastANI
[2023-06-29 10:07:33,243] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 10:07:33,244] [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
GCA_002722315.1	s__GCA-2722315 sp002722315	78.0038	221	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__GCA-2722315	95.0	99.66	99.66	0.81	0.81	2	-
GCA_018334995.1	s__GCA-2722315 sp018334995	77.8206	252	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__GCA-2722315	95.0	99.60	99.60	0.94	0.94	3	-
GCF_012272825.1	s__GCA-2722315 sp012272825	77.444	229	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__GCA-2722315	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010499265.1	s__Wenzhouxiangella sp010499265	77.1206	130	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__Wenzhouxiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003565625.1	s__Wenzhouxiangella sp003565625	76.8616	85	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__Wenzhouxiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014725735.1	s__Wenzhouxiangella sp014725735	76.8521	108	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__Wenzhouxiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003560975.1	s__Wenzhouxiangella sp003560975	76.7022	125	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__Wenzhouxiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001187785.1	s__Wenzhouxiangella marina	76.6535	108	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__Wenzhouxiangella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011008905.1	s__Wenzhouxiangella sp011008905	76.5958	109	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__Wenzhouxiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007695005.1	s__Wenzhouxiangella sp007695005	76.4516	74	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__Wenzhouxiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007118895.1	s__SKQS01 sp007118895	76.4026	102	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__SKQS01	95.0	99.66	99.62	0.88	0.86	3	-
GCA_007121485.1	s__Wenzhouxiangella sp007121485	76.3927	67	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__Wenzhouxiangella	95.0	99.57	99.47	0.88	0.87	3	-
GCF_003417465.1	s__Wenzhouxiangella sp003417465	76.3657	105	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__Wenzhouxiangella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_007694885.1	s__Wenzhouxiangella sp007694885	76.2924	89	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__Wenzhouxiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007119095.1	s__Wenzhouxiangella sp007119095	76.2311	54	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__Wenzhouxiangella	95.0	99.63	99.55	0.87	0.85	3	-
GCA_007123575.1	s__Wenzhouxiangella sp007123575	76.2121	84	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__Wenzhouxiangella	95.0	99.55	99.36	0.82	0.75	4	-
GCA_007116585.1	s__Wenzhouxiangella sp007116585	76.1908	60	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__Wenzhouxiangella	95.0	98.00	98.00	0.65	0.65	2	-
--------------------------------------------------------------------------------
[2023-06-29 10:07:33,246] [INFO] GTDB search result was written to GCA_020201235.1_ASM2020123v1_genomic.fna/result_gtdb.tsv
[2023-06-29 10:07:33,246] [INFO] ===== GTDB Search completed =====
[2023-06-29 10:07:33,250] [INFO] DFAST_QC result json was written to GCA_020201235.1_ASM2020123v1_genomic.fna/dqc_result.json
[2023-06-29 10:07:33,250] [INFO] DFAST_QC completed!
[2023-06-29 10:07:33,250] [INFO] Total running time: 0h1m13s