[2024-01-24 13:19:11,996] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:11,998] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:11,999] [INFO] DQC Reference Directory: /var/lib/cwl/stgf23df26c-17c2-4430-b55a-7b85a6f2dd62/dqc_reference
[2024-01-24 13:19:13,309] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:13,310] [INFO] Task started: Prodigal
[2024-01-24 13:19:13,311] [INFO] Running command: gunzip -c /var/lib/cwl/stgd13d979c-25fc-4fd3-9756-73ea432a8c4a/GCF_021603585.1_ASM2160358v1_genomic.fna.gz | prodigal -d GCF_021603585.1_ASM2160358v1_genomic.fna/cds.fna -a GCF_021603585.1_ASM2160358v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:35,175] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:35,175] [INFO] Task started: HMMsearch
[2024-01-24 13:19:35,175] [INFO] Running command: hmmsearch --tblout GCF_021603585.1_ASM2160358v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf23df26c-17c2-4430-b55a-7b85a6f2dd62/dqc_reference/reference_markers.hmm GCF_021603585.1_ASM2160358v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:35,613] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:35,615] [INFO] Found 6/6 markers.
[2024-01-24 13:19:35,676] [INFO] Query marker FASTA was written to GCF_021603585.1_ASM2160358v1_genomic.fna/markers.fasta
[2024-01-24 13:19:35,677] [INFO] Task started: Blastn
[2024-01-24 13:19:35,677] [INFO] Running command: blastn -query GCF_021603585.1_ASM2160358v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf23df26c-17c2-4430-b55a-7b85a6f2dd62/dqc_reference/reference_markers.fasta -out GCF_021603585.1_ASM2160358v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:36,715] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:36,720] [INFO] Selected 14 target genomes.
[2024-01-24 13:19:36,721] [INFO] Target genome list was writen to GCF_021603585.1_ASM2160358v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:36,737] [INFO] Task started: fastANI
[2024-01-24 13:19:36,737] [INFO] Running command: fastANI --query /var/lib/cwl/stgd13d979c-25fc-4fd3-9756-73ea432a8c4a/GCF_021603585.1_ASM2160358v1_genomic.fna.gz --refList GCF_021603585.1_ASM2160358v1_genomic.fna/target_genomes.txt --output GCF_021603585.1_ASM2160358v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:59,767] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:59,767] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf23df26c-17c2-4430-b55a-7b85a6f2dd62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:59,768] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf23df26c-17c2-4430-b55a-7b85a6f2dd62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:59,779] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:59,780] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:59,780] [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 sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	100.0	2065	2068	95	conclusive
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	94.2875	1788	2068	95	below_threshold
Pseudomonas allokribbensis	strain=IzPS23	GCA_014863605.1	2774460	2774460	type	True	91.5349	1710	2068	95	below_threshold
Pseudomonas kribbensis	strain=46-2	GCA_003352185.1	1628086	1628086	type	True	91.3764	1696	2068	95	below_threshold
Pseudomonas bananamidigenes	strain=BW11P2	GCA_001679645.1	2843610	2843610	type	True	90.2777	1622	2068	95	below_threshold
Pseudomonas koreensis	strain=DSM 16610	GCA_012986595.1	198620	198620	suspected-type	True	88.7774	1633	2068	95	below_threshold
Pseudomonas koreensis	strain=JCM 14769	GCA_014646955.1	198620	198620	suspected-type	True	88.7646	1642	2068	95	below_threshold
Pseudomonas monsensis	strain=PGSB 8459	GCA_014268495.2	2745509	2745509	type	True	88.3766	1628	2068	95	below_threshold
Pseudomonas neuropathica	strain=P155	GCA_015461835.1	2730425	2730425	type	True	88.0347	1644	2068	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	87.9007	1671	2068	95	below_threshold
Pseudomonas hamedanensis	strain=SWRI65	GCA_014268595.2	2745504	2745504	type	True	87.3576	1521	2068	95	below_threshold
Pseudomonas moorei	strain=CCUG 53114	GCA_008801475.1	395599	395599	type	True	85.7974	1370	2068	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	83.6197	1286	2068	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	83.6002	1220	2068	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:59,782] [INFO] DFAST Taxonomy check result was written to GCF_021603585.1_ASM2160358v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:59,782] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:59,783] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:59,783] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf23df26c-17c2-4430-b55a-7b85a6f2dd62/dqc_reference/checkm_data
[2024-01-24 13:19:59,785] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:59,847] [INFO] Task started: CheckM
[2024-01-24 13:19:59,847] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021603585.1_ASM2160358v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021603585.1_ASM2160358v1_genomic.fna/checkm_input GCF_021603585.1_ASM2160358v1_genomic.fna/checkm_result
[2024-01-24 13:21:02,881] [INFO] Task succeeded: CheckM
[2024-01-24 13:21:02,883] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:21:02,907] [INFO] ===== Completeness check finished =====
[2024-01-24 13:21:02,907] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:21:02,908] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021603585.1_ASM2160358v1_genomic.fna/markers.fasta)
[2024-01-24 13:21:02,908] [INFO] Task started: Blastn
[2024-01-24 13:21:02,908] [INFO] Running command: blastn -query GCF_021603585.1_ASM2160358v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf23df26c-17c2-4430-b55a-7b85a6f2dd62/dqc_reference/reference_markers_gtdb.fasta -out GCF_021603585.1_ASM2160358v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:04,827] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:04,831] [INFO] Selected 9 target genomes.
[2024-01-24 13:21:04,831] [INFO] Target genome list was writen to GCF_021603585.1_ASM2160358v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:21:04,848] [INFO] Task started: fastANI
[2024-01-24 13:21:04,848] [INFO] Running command: fastANI --query /var/lib/cwl/stgd13d979c-25fc-4fd3-9756-73ea432a8c4a/GCF_021603585.1_ASM2160358v1_genomic.fna.gz --refList GCF_021603585.1_ASM2160358v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021603585.1_ASM2160358v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:21:20,154] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:20,162] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:21:20,162] [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_010448615.1	s__Pseudomonas_E sp001655595	94.2478	1783	2068	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.61	96.24	0.94	0.90	22	-
GCF_004006335.1	s__Pseudomonas_E sp002112885	94.0157	1769	2068	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.01	95.48	0.92	0.90	14	-
GCF_001594225.2	s__Pseudomonas_E glycinae	94.0081	1750	2068	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.56	95.98	0.93	0.88	9	-
GCF_003352875.1	s__Pseudomonas_E fluorescens_BF	93.6973	1752	2068	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_014863585.1	s__Pseudomonas_E gozinkensis	93.6477	1781	2068	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_002113125.1	s__Pseudomonas_E sp002113125	93.4217	1721	2068	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002113045.1	s__Pseudomonas_E sp002113045	93.2073	1721	2068	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.93	98.93	0.93	0.93	2	-
GCF_003352185.1	s__Pseudomonas_E kribbensis	91.3808	1695	2068	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.22	95.68	0.92	0.89	10	-
GCF_002112385.1	s__Pseudomonas_E sp002112385	91.3499	1713	2068	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	7	-
--------------------------------------------------------------------------------
[2024-01-24 13:21:20,164] [INFO] GTDB search result was written to GCF_021603585.1_ASM2160358v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:21:20,165] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:21:20,168] [INFO] DFAST_QC result json was written to GCF_021603585.1_ASM2160358v1_genomic.fna/dqc_result.json
[2024-01-24 13:21:20,168] [INFO] DFAST_QC completed!
[2024-01-24 13:21:20,168] [INFO] Total running time: 0h2m8s