[2024-01-24 11:51:50,781] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:50,783] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:50,783] [INFO] DQC Reference Directory: /var/lib/cwl/stg09ba7ad0-eb30-41b5-b3e3-c9989522db6d/dqc_reference
[2024-01-24 11:51:51,978] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:51,979] [INFO] Task started: Prodigal
[2024-01-24 11:51:51,979] [INFO] Running command: gunzip -c /var/lib/cwl/stgf16a3e56-ca74-4f86-9ede-671985353594/GCF_021602025.1_ASM2160202v1_genomic.fna.gz | prodigal -d GCF_021602025.1_ASM2160202v1_genomic.fna/cds.fna -a GCF_021602025.1_ASM2160202v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:52:12,090] [INFO] Task succeeded: Prodigal
[2024-01-24 11:52:12,090] [INFO] Task started: HMMsearch
[2024-01-24 11:52:12,091] [INFO] Running command: hmmsearch --tblout GCF_021602025.1_ASM2160202v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09ba7ad0-eb30-41b5-b3e3-c9989522db6d/dqc_reference/reference_markers.hmm GCF_021602025.1_ASM2160202v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:52:12,399] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:52:12,401] [INFO] Found 6/6 markers.
[2024-01-24 11:52:12,452] [INFO] Query marker FASTA was written to GCF_021602025.1_ASM2160202v1_genomic.fna/markers.fasta
[2024-01-24 11:52:12,452] [INFO] Task started: Blastn
[2024-01-24 11:52:12,452] [INFO] Running command: blastn -query GCF_021602025.1_ASM2160202v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09ba7ad0-eb30-41b5-b3e3-c9989522db6d/dqc_reference/reference_markers.fasta -out GCF_021602025.1_ASM2160202v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:13,395] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:13,399] [INFO] Selected 18 target genomes.
[2024-01-24 11:52:13,400] [INFO] Target genome list was writen to GCF_021602025.1_ASM2160202v1_genomic.fna/target_genomes.txt
[2024-01-24 11:52:13,411] [INFO] Task started: fastANI
[2024-01-24 11:52:13,411] [INFO] Running command: fastANI --query /var/lib/cwl/stgf16a3e56-ca74-4f86-9ede-671985353594/GCF_021602025.1_ASM2160202v1_genomic.fna.gz --refList GCF_021602025.1_ASM2160202v1_genomic.fna/target_genomes.txt --output GCF_021602025.1_ASM2160202v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:35,620] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:35,621] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09ba7ad0-eb30-41b5-b3e3-c9989522db6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:35,621] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09ba7ad0-eb30-41b5-b3e3-c9989522db6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:35,635] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:52:35,635] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:35,635] [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
Pseudomonas ceruminis	strain=BML-PP028	GCA_021602025.1	2740516	2740516	type	True	100.0	2067	2070	95	conclusive
Pseudomonas ceruminis	strain=BML-PP028	GCA_013373895.1	2740516	2740516	type	True	99.9832	2014	2070	95	conclusive
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	88.2766	1314	2070	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	88.2458	1430	2070	95	below_threshold
Pseudomonas plecoglossicida	strain=DSM 15088	GCA_000688275.1	70775	70775	suspected-type	True	87.6859	1326	2070	95	below_threshold
Pseudomonas plecoglossicida	strain=NBRC 103162	GCA_000730665.1	70775	70775	suspected-type	True	87.6311	1311	2070	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	87.0641	1396	2070	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	87.0094	1370	2070	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	86.7904	1263	2070	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_000731675.1	1495066	1495066	type	True	86.7574	1377	2070	95	below_threshold
Pseudomonas anuradhapurensis	strain=RD8MR3	GCA_014269225.2	485870	485870	type	True	86.7514	1287	2070	95	below_threshold
Pseudomonas kermanshahensis	strain=SWRI100	GCA_014269205.2	2745482	2745482	type	True	86.5904	1351	2070	95	below_threshold
Pseudomonas oryzicola	strain=RD9SR1	GCA_014269185.2	485876	485876	type	True	86.4211	1284	2070	95	below_threshold
Pseudomonas muyukensis	strain=COW39	GCA_019139535.1	2842357	2842357	type	True	85.992	1268	2070	95	below_threshold
Pseudomonas defluvii	strain=WCHP16	GCA_001695625.1	1876757	1876757	type	True	82.0493	853	2070	95	below_threshold
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	80.6844	913	2070	95	below_threshold
Pseudomonas delhiensis	strain=RLD-1	GCA_900187975.1	366289	366289	type	True	80.6334	916	2070	95	below_threshold
Pseudomonas rhizoryzae	strain=RY24	GCA_005250615.1	2571129	2571129	type	True	79.0755	534	2070	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:35,637] [INFO] DFAST Taxonomy check result was written to GCF_021602025.1_ASM2160202v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:35,637] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:35,638] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:35,638] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09ba7ad0-eb30-41b5-b3e3-c9989522db6d/dqc_reference/checkm_data
[2024-01-24 11:52:35,639] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:35,694] [INFO] Task started: CheckM
[2024-01-24 11:52:35,695] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021602025.1_ASM2160202v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021602025.1_ASM2160202v1_genomic.fna/checkm_input GCF_021602025.1_ASM2160202v1_genomic.fna/checkm_result
[2024-01-24 11:53:34,040] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:34,042] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:34,067] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:34,067] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:34,067] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021602025.1_ASM2160202v1_genomic.fna/markers.fasta)
[2024-01-24 11:53:34,068] [INFO] Task started: Blastn
[2024-01-24 11:53:34,068] [INFO] Running command: blastn -query GCF_021602025.1_ASM2160202v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09ba7ad0-eb30-41b5-b3e3-c9989522db6d/dqc_reference/reference_markers_gtdb.fasta -out GCF_021602025.1_ASM2160202v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:35,677] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:35,680] [INFO] Selected 22 target genomes.
[2024-01-24 11:53:35,681] [INFO] Target genome list was writen to GCF_021602025.1_ASM2160202v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:35,699] [INFO] Task started: fastANI
[2024-01-24 11:53:35,699] [INFO] Running command: fastANI --query /var/lib/cwl/stgf16a3e56-ca74-4f86-9ede-671985353594/GCF_021602025.1_ASM2160202v1_genomic.fna.gz --refList GCF_021602025.1_ASM2160202v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021602025.1_ASM2160202v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:54:04,881] [INFO] Task succeeded: fastANI
[2024-01-24 11:54:04,902] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:54:04,902] [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_001320525.1	s__Pseudomonas_E sp001320525	98.7077	1808	2070	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.10	98.78	0.89	0.86	10	conclusive
GCF_013373935.1	s__Pseudomonas_E sp002438125	88.2661	1315	2070	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.14	98.14	0.84	0.84	2	-
GCF_000282535.1	s__Pseudomonas_E sp000282535	87.8191	1249	2070	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000730665.1	s__Pseudomonas_E plecoglossicida	87.6276	1312	2070	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.81	99.74	0.97	0.95	6	-
GCF_002112505.1	s__Pseudomonas_E sp002112505	87.5971	1408	2070	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	0.99	6	-
GCA_003428805.1	s__Pseudomonas_E sp003428805	87.4921	1482	2070	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.29	96.05	0.90	0.83	9	-
GCF_000019445.1	s__Pseudomonas_E putida_E	87.3982	1403	2070	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.71	96.19	0.87	0.82	12	-
GCF_000935045.1	s__Pseudomonas_E sp000935045	87.0518	1358	2070	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002165135.1	s__Pseudomonas_E sp002165135	86.8067	1297	2070	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000731675.1	s__Pseudomonas_E capeferrum	86.7485	1378	2070	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.03	98.55	0.93	0.90	7	-
GCF_002736125.1	s__Pseudomonas_E putida_M	86.6718	1386	2070	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.41	97.25	0.91	0.90	8	-
GCF_000730605.1	s__Pseudomonas_E monteilii	86.4907	1401	2070	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.80	95.46	0.86	0.79	45	-
GCF_016648105.1	s__Pseudomonas_E sp016648105	86.3456	1293	2070	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002356095.1	s__Pseudomonas_E putida_H	86.138	1489	2070	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.82	98.35	0.91	0.82	20	-
GCF_003671955.1	s__Pseudomonas_E hunanensis	86.1126	1312	2070	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.33	95.26	0.86	0.79	88	-
GCF_019139535.1	s__Pseudomonas_E sp019139535	85.9862	1269	2070	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009932375.1	s__Pseudomonas_E juntendi	85.8358	1201	2070	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.06	97.13	0.84	0.79	41	-
GCF_004519305.1	s__Pseudomonas_E sp004519305	85.7772	1217	2070	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004357765.1	s__Pseudomonas_E putida_U	85.3999	1232	2070	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.43	99.43	0.90	0.90	2	-
GCF_002741075.1	s__Pseudomonas_E putida_T	85.2928	1269	2070	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.21	95.06	0.91	0.90	4	-
GCF_013523055.1	s__Pseudomonas_E capeferrum_A	83.3174	1116	2070	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002806685.1	s__Pseudomonas_E qingdaonensis	83.3129	1153	2070	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.05	98.91	0.93	0.89	13	-
--------------------------------------------------------------------------------
[2024-01-24 11:54:04,904] [INFO] GTDB search result was written to GCF_021602025.1_ASM2160202v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:54:04,905] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:54:04,909] [INFO] DFAST_QC result json was written to GCF_021602025.1_ASM2160202v1_genomic.fna/dqc_result.json
[2024-01-24 11:54:04,909] [INFO] DFAST_QC completed!
[2024-01-24 11:54:04,910] [INFO] Total running time: 0h2m14s