[2024-01-25 17:44:20,444] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:44:20,446] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:44:20,446] [INFO] DQC Reference Directory: /var/lib/cwl/stge75bd598-7c9e-48b1-a1ec-17732e96b692/dqc_reference
[2024-01-25 17:44:21,630] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:44:21,631] [INFO] Task started: Prodigal
[2024-01-25 17:44:21,632] [INFO] Running command: gunzip -c /var/lib/cwl/stg9cb18fce-356f-4337-8a29-c7c1ba9b9efb/GCF_000421765.1_ASM42176v1_genomic.fna.gz | prodigal -d GCF_000421765.1_ASM42176v1_genomic.fna/cds.fna -a GCF_000421765.1_ASM42176v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:44:28,609] [INFO] Task succeeded: Prodigal
[2024-01-25 17:44:28,609] [INFO] Task started: HMMsearch
[2024-01-25 17:44:28,610] [INFO] Running command: hmmsearch --tblout GCF_000421765.1_ASM42176v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge75bd598-7c9e-48b1-a1ec-17732e96b692/dqc_reference/reference_markers.hmm GCF_000421765.1_ASM42176v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:44:28,831] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:44:28,832] [INFO] Found 6/6 markers.
[2024-01-25 17:44:28,858] [INFO] Query marker FASTA was written to GCF_000421765.1_ASM42176v1_genomic.fna/markers.fasta
[2024-01-25 17:44:28,858] [INFO] Task started: Blastn
[2024-01-25 17:44:28,858] [INFO] Running command: blastn -query GCF_000421765.1_ASM42176v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge75bd598-7c9e-48b1-a1ec-17732e96b692/dqc_reference/reference_markers.fasta -out GCF_000421765.1_ASM42176v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:29,525] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:29,528] [INFO] Selected 29 target genomes.
[2024-01-25 17:44:29,529] [INFO] Target genome list was writen to GCF_000421765.1_ASM42176v1_genomic.fna/target_genomes.txt
[2024-01-25 17:44:29,543] [INFO] Task started: fastANI
[2024-01-25 17:44:29,543] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cb18fce-356f-4337-8a29-c7c1ba9b9efb/GCF_000421765.1_ASM42176v1_genomic.fna.gz --refList GCF_000421765.1_ASM42176v1_genomic.fna/target_genomes.txt --output GCF_000421765.1_ASM42176v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:44:50,968] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:50,969] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge75bd598-7c9e-48b1-a1ec-17732e96b692/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:44:50,969] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge75bd598-7c9e-48b1-a1ec-17732e96b692/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:44:50,982] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:44:50,982] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:44:50,983] [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
Denitrificimonas caeni	strain=DSM 24390	GCA_000421765.1	521720	521720	type	True	100.0	991	993	95	conclusive
Thiopseudomonas alkaliphila	strain=B4199	GCA_001267175.1	1697053	1697053	type	True	78.1168	143	993	95	below_threshold
Pseudomonas pisciculturae	strain=P115	GCA_015461805.1	2730413	2730413	type	True	77.3807	61	993	95	below_threshold
Pseudomonas moorei	strain=CCUG 53114	GCA_008801475.1	395599	395599	type	True	77.2334	64	993	95	below_threshold
Pseudomonas versuta	strain=L10.10	GCA_001294575.1	1788301	1788301	type	True	77.0184	72	993	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	76.9954	54	993	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	76.9709	53	993	95	below_threshold
Pseudomonas marginalis	strain=ICMP 3553	GCA_003700725.1	298	298	suspected-type	True	76.9425	62	993	95	below_threshold
Pseudomonas anuradhapurensis	strain=RD8MR3	GCA_014269225.2	485870	485870	type	True	76.9364	53	993	95	below_threshold
Stutzerimonas chloritidismutans	strain=AW-1	GCA_000495915.1	203192	203192	type	True	76.9317	66	993	95	below_threshold
Pseudomonas psychrophila	strain=DSM 17535	GCA_001043005.1	122355	122355	type	True	76.9034	79	993	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	76.8766	54	993	95	below_threshold
Pseudomonas antarctica		GCA_900624995.1	219572	219572	type	True	76.8676	66	993	95	below_threshold
Pseudomonas psychrophila	strain=CCUG 53877	GCA_008801485.1	122355	122355	type	True	76.8264	81	993	95	below_threshold
Pseudomonas fragi	strain=NRRL B-727	GCA_900105835.1	296	296	type	True	76.8147	72	993	95	below_threshold
Pseudomonas antarctica	strain=CMS 35	GCA_010634845.1	219572	219572	type	True	76.8112	64	993	95	below_threshold
Pseudomonas knackmussii	strain=B13	GCA_000689415.1	65741	65741	type	True	76.8089	53	993	95	below_threshold
Pseudomonas fuscovaginae	strain=LMG 2158	GCA_900108595.1	50340	50340	suspected-type	True	76.8026	57	993	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	76.799	54	993	95	below_threshold
Pseudomonas paraversuta	strain=V4/DAB/S4/2a	GCA_904063065.1	2750624	2750624	type	True	76.7872	74	993	95	below_threshold
Pseudomonas xanthosomae	strain=COR54	GCA_019139835.1	2842356	2842356	type	True	76.7478	53	993	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	76.7377	54	993	95	below_threshold
Pseudomonas fragi	strain=NBRC 3458	GCA_002091615.1	296	296	type	True	76.6694	74	993	95	below_threshold
Pseudomonas nitrititolerans	strain=GL14	GCA_003696285.1	2482751	2482751	type	True	76.34	56	993	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:44:50,984] [INFO] DFAST Taxonomy check result was written to GCF_000421765.1_ASM42176v1_genomic.fna/tc_result.tsv
[2024-01-25 17:44:50,985] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:44:50,985] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:44:50,985] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge75bd598-7c9e-48b1-a1ec-17732e96b692/dqc_reference/checkm_data
[2024-01-25 17:44:50,986] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:44:51,016] [INFO] Task started: CheckM
[2024-01-25 17:44:51,016] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000421765.1_ASM42176v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000421765.1_ASM42176v1_genomic.fna/checkm_input GCF_000421765.1_ASM42176v1_genomic.fna/checkm_result
[2024-01-25 17:45:15,753] [INFO] Task succeeded: CheckM
[2024-01-25 17:45:15,754] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:45:15,768] [INFO] ===== Completeness check finished =====
[2024-01-25 17:45:15,769] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:45:15,769] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000421765.1_ASM42176v1_genomic.fna/markers.fasta)
[2024-01-25 17:45:15,769] [INFO] Task started: Blastn
[2024-01-25 17:45:15,769] [INFO] Running command: blastn -query GCF_000421765.1_ASM42176v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge75bd598-7c9e-48b1-a1ec-17732e96b692/dqc_reference/reference_markers_gtdb.fasta -out GCF_000421765.1_ASM42176v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:45:16,927] [INFO] Task succeeded: Blastn
[2024-01-25 17:45:16,930] [INFO] Selected 8 target genomes.
[2024-01-25 17:45:16,930] [INFO] Target genome list was writen to GCF_000421765.1_ASM42176v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:45:16,939] [INFO] Task started: fastANI
[2024-01-25 17:45:16,940] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cb18fce-356f-4337-8a29-c7c1ba9b9efb/GCF_000421765.1_ASM42176v1_genomic.fna.gz --refList GCF_000421765.1_ASM42176v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000421765.1_ASM42176v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:45:22,237] [INFO] Task succeeded: fastANI
[2024-01-25 17:45:22,256] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:45:22,256] [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_000421765.1	s__Pseudomonas_C caeni	100.0	991	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_C	95.0	96.77	96.34	0.93	0.85	7	conclusive
GCA_012719655.1	s__Pseudomonas_C sp012719655	89.6273	669	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012728315.1	s__Pseudomonas_C sp012728315	82.6828	550	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_905120345.1	s__Pseudomonas_C caeni_A	81.6077	599	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001513025.1	s__Pseudomonas_C sp001513025	81.59	529	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_C	95.0	99.84	99.84	0.94	0.94	2	-
GCF_008807395.1	s__Pseudomonas_C sp002342705	80.6802	577	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_C	95.0	99.04	98.98	0.93	0.92	7	-
GCA_012513235.1	s__Pseudomonas_C sp012513235	80.3559	338	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012800475.1	s__Pseudomonas_C sp012800475	80.317	329	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:45:22,258] [INFO] GTDB search result was written to GCF_000421765.1_ASM42176v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:45:22,259] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:45:22,263] [INFO] DFAST_QC result json was written to GCF_000421765.1_ASM42176v1_genomic.fna/dqc_result.json
[2024-01-25 17:45:22,263] [INFO] DFAST_QC completed!
[2024-01-25 17:45:22,263] [INFO] Total running time: 0h1m2s