[2024-01-24 12:05:50,436] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:05:50,443] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:05:50,443] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc540339-3d78-471b-80f3-d6e48bee810b/dqc_reference
[2024-01-24 12:05:52,741] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:05:52,741] [INFO] Task started: Prodigal
[2024-01-24 12:05:52,742] [INFO] Running command: gunzip -c /var/lib/cwl/stg17651264-ff83-4cf4-85dc-f1b113fae586/GCF_014235765.1_ASM1423576v1_genomic.fna.gz | prodigal -d GCF_014235765.1_ASM1423576v1_genomic.fna/cds.fna -a GCF_014235765.1_ASM1423576v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:07,277] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:07,277] [INFO] Task started: HMMsearch
[2024-01-24 12:06:07,277] [INFO] Running command: hmmsearch --tblout GCF_014235765.1_ASM1423576v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc540339-3d78-471b-80f3-d6e48bee810b/dqc_reference/reference_markers.hmm GCF_014235765.1_ASM1423576v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:07,526] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:07,527] [INFO] Found 6/6 markers.
[2024-01-24 12:06:07,566] [INFO] Query marker FASTA was written to GCF_014235765.1_ASM1423576v1_genomic.fna/markers.fasta
[2024-01-24 12:06:07,567] [INFO] Task started: Blastn
[2024-01-24 12:06:07,567] [INFO] Running command: blastn -query GCF_014235765.1_ASM1423576v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc540339-3d78-471b-80f3-d6e48bee810b/dqc_reference/reference_markers.fasta -out GCF_014235765.1_ASM1423576v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:08,565] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:08,568] [INFO] Selected 18 target genomes.
[2024-01-24 12:06:08,568] [INFO] Target genome list was writen to GCF_014235765.1_ASM1423576v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:08,610] [INFO] Task started: fastANI
[2024-01-24 12:06:08,610] [INFO] Running command: fastANI --query /var/lib/cwl/stg17651264-ff83-4cf4-85dc-f1b113fae586/GCF_014235765.1_ASM1423576v1_genomic.fna.gz --refList GCF_014235765.1_ASM1423576v1_genomic.fna/target_genomes.txt --output GCF_014235765.1_ASM1423576v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:29,827] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:29,827] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc540339-3d78-471b-80f3-d6e48bee810b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:29,828] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc540339-3d78-471b-80f3-d6e48bee810b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:29,842] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:29,842] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:29,843] [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 baltica	strain=MBT-2	GCA_014235765.1	2762576	2762576	type	True	100.0	1512	1516	95	conclusive
Pseudomonas rhizosphaerae	strain=DSM 16299	GCA_000761155.1	216142	216142	type	True	89.178	1350	1516	95	below_threshold
Pseudomonas coleopterorum	strain=LMG 28558	GCA_900105555.1	1605838	1605838	type	True	88.9659	1310	1516	95	below_threshold
Pseudomonas ekonensis	strain=COR58	GCA_019145435.1	2842353	2842353	type	True	82.3519	873	1516	95	below_threshold
Pseudomonas eucalypticola	strain=NP-1	GCA_013374995.1	2599595	2599595	type	True	82.2051	869	1516	95	below_threshold
Pseudomonas japonica	strain=NBRC 103040	GCA_000730585.1	256466	256466	type	True	82.1675	821	1516	95	below_threshold
Pseudomonas muyukensis	strain=COW39	GCA_019139535.1	2842357	2842357	type	True	82.0483	820	1516	95	below_threshold
Pseudomonas japonica	strain=DSM 22348	GCA_900188455.1	256466	256466	type	True	82.0118	830	1516	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	81.8986	816	1516	95	below_threshold
Pseudomonas batumici	strain=UCM B-321	GCA_000820515.1	226910	226910	type	True	81.826	773	1516	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	81.818	862	1516	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	81.344	801	1516	95	below_threshold
Pseudomonas fuscovaginae	strain=LMG 2158	GCA_900108595.1	50340	50340	suspected-type	True	81.3438	814	1516	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	81.3106	767	1516	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	81.3047	795	1516	95	below_threshold
Pseudomonas defluvii	strain=WCHP16	GCA_001695625.1	1876757	1876757	type	True	80.8147	624	1516	95	below_threshold
Pseudomonas bohemica	strain=IA19	GCA_002934685.1	2044872	2044872	type	True	80.2947	765	1516	95	below_threshold
Pseudomonas arcuscaelestis	strain=P66	GCA_016881005.1	2710591	2710591	type	True	80.2907	700	1516	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:29,844] [INFO] DFAST Taxonomy check result was written to GCF_014235765.1_ASM1423576v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:29,845] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:29,845] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:29,846] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc540339-3d78-471b-80f3-d6e48bee810b/dqc_reference/checkm_data
[2024-01-24 12:06:29,847] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:29,891] [INFO] Task started: CheckM
[2024-01-24 12:06:29,891] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014235765.1_ASM1423576v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014235765.1_ASM1423576v1_genomic.fna/checkm_input GCF_014235765.1_ASM1423576v1_genomic.fna/checkm_result
[2024-01-24 12:07:15,225] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:15,227] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:15,244] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:15,244] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:15,245] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014235765.1_ASM1423576v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:15,245] [INFO] Task started: Blastn
[2024-01-24 12:07:15,245] [INFO] Running command: blastn -query GCF_014235765.1_ASM1423576v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc540339-3d78-471b-80f3-d6e48bee810b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014235765.1_ASM1423576v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:17,198] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:17,201] [INFO] Selected 6 target genomes.
[2024-01-24 12:07:17,201] [INFO] Target genome list was writen to GCF_014235765.1_ASM1423576v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:17,206] [INFO] Task started: fastANI
[2024-01-24 12:07:17,207] [INFO] Running command: fastANI --query /var/lib/cwl/stg17651264-ff83-4cf4-85dc-f1b113fae586/GCF_014235765.1_ASM1423576v1_genomic.fna.gz --refList GCF_014235765.1_ASM1423576v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014235765.1_ASM1423576v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:24,794] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:24,801] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:24,801] [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_014235765.1	s__Pseudomonas_E baltica	100.0	1512	1516	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.29	98.19	0.94	0.93	6	conclusive
GCA_900596015.1	s__Pseudomonas_E sp900596015	94.8237	1399	1516	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.88	96.15	0.95	0.92	8	-
GCF_000761155.1	s__Pseudomonas_E rhizosphaerae	89.178	1350	1516	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.13	98.13	0.92	0.92	2	-
GCF_900105555.1	s__Pseudomonas_E coleopterorum	88.9659	1310	1516	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.66	96.53	0.90	0.88	9	-
GCA_002379585.1	s__Pseudomonas_E sp002379585	84.0118	1012	1516	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_011355085.1	s__Pseudomonas_E sp011355085	81.5924	763	1516	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:24,803] [INFO] GTDB search result was written to GCF_014235765.1_ASM1423576v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:24,804] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:24,818] [INFO] DFAST_QC result json was written to GCF_014235765.1_ASM1423576v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:24,818] [INFO] DFAST_QC completed!
[2024-01-24 12:07:24,818] [INFO] Total running time: 0h1m34s