[2024-01-24 13:40:00,401] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:00,403] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:00,403] [INFO] DQC Reference Directory: /var/lib/cwl/stg38b5b4f5-0e6d-497a-a8ba-ccef5c1766c9/dqc_reference
[2024-01-24 13:40:01,588] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:01,589] [INFO] Task started: Prodigal
[2024-01-24 13:40:01,589] [INFO] Running command: gunzip -c /var/lib/cwl/stg49f1a578-9940-4e42-81fb-767a885c726a/GCF_009671285.1_ASM967128v1_genomic.fna.gz | prodigal -d GCF_009671285.1_ASM967128v1_genomic.fna/cds.fna -a GCF_009671285.1_ASM967128v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:25,508] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:25,509] [INFO] Task started: HMMsearch
[2024-01-24 13:40:25,509] [INFO] Running command: hmmsearch --tblout GCF_009671285.1_ASM967128v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg38b5b4f5-0e6d-497a-a8ba-ccef5c1766c9/dqc_reference/reference_markers.hmm GCF_009671285.1_ASM967128v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:25,847] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:25,849] [INFO] Found 6/6 markers.
[2024-01-24 13:40:25,923] [INFO] Query marker FASTA was written to GCF_009671285.1_ASM967128v1_genomic.fna/markers.fasta
[2024-01-24 13:40:25,923] [INFO] Task started: Blastn
[2024-01-24 13:40:25,924] [INFO] Running command: blastn -query GCF_009671285.1_ASM967128v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38b5b4f5-0e6d-497a-a8ba-ccef5c1766c9/dqc_reference/reference_markers.fasta -out GCF_009671285.1_ASM967128v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:26,872] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:26,875] [INFO] Selected 13 target genomes.
[2024-01-24 13:40:26,876] [INFO] Target genome list was writen to GCF_009671285.1_ASM967128v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:26,887] [INFO] Task started: fastANI
[2024-01-24 13:40:26,887] [INFO] Running command: fastANI --query /var/lib/cwl/stg49f1a578-9940-4e42-81fb-767a885c726a/GCF_009671285.1_ASM967128v1_genomic.fna.gz --refList GCF_009671285.1_ASM967128v1_genomic.fna/target_genomes.txt --output GCF_009671285.1_ASM967128v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:47,509] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:47,509] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg38b5b4f5-0e6d-497a-a8ba-ccef5c1766c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:47,510] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg38b5b4f5-0e6d-497a-a8ba-ccef5c1766c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:47,521] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:40:47,521] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:47,521] [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 gessardii	strain=DSM 17152	GCA_001983165.1	78544	78544	type	True	100.0	2087	2092	95	conclusive
Pseudomonas gessardii	strain=DSM 17152	GCA_009671285.1	78544	78544	type	True	100.0	2087	2092	95	conclusive
Pseudomonas gessardii		GCA_900625085.1	78544	78544	type	True	99.9955	2079	2092	95	conclusive
Pseudomonas brenneri	strain=JCM 13307	GCA_014646715.1	129817	129817	type	True	91.8406	1630	2092	95	below_threshold
Pseudomonas brenneri	strain=DSM 15294	GCA_007858285.1	129817	129817	type	True	91.8313	1644	2092	95	below_threshold
Pseudomonas proteolytica	strain=DSM 15321	GCA_007858275.1	219574	219574	type	True	91.6456	1580	2092	95	below_threshold
Pseudomonas proteolytica	strain=CCUG 51515T	GCA_008692865.1	219574	219574	type	True	91.64	1583	2092	95	below_threshold
Pseudomonas yamanorum	strain=LMG 27247	GCA_900105735.1	515393	515393	suspected-type	True	86.7167	1455	2092	95	below_threshold
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	86.6537	1441	2092	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	86.4958	1435	2092	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	86.4555	1382	2092	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	86.2645	1371	2092	95	below_threshold
Pseudomonas karstica	strain=CCM 7891	GCA_009707515.1	1055468	1055468	type	True	85.7673	1279	2092	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:47,524] [INFO] DFAST Taxonomy check result was written to GCF_009671285.1_ASM967128v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:47,525] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:47,525] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:47,525] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg38b5b4f5-0e6d-497a-a8ba-ccef5c1766c9/dqc_reference/checkm_data
[2024-01-24 13:40:47,526] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:47,591] [INFO] Task started: CheckM
[2024-01-24 13:40:47,591] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009671285.1_ASM967128v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009671285.1_ASM967128v1_genomic.fna/checkm_input GCF_009671285.1_ASM967128v1_genomic.fna/checkm_result
[2024-01-24 13:41:58,326] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:58,331] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:58,355] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:58,355] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:58,356] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009671285.1_ASM967128v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:58,356] [INFO] Task started: Blastn
[2024-01-24 13:41:58,356] [INFO] Running command: blastn -query GCF_009671285.1_ASM967128v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38b5b4f5-0e6d-497a-a8ba-ccef5c1766c9/dqc_reference/reference_markers_gtdb.fasta -out GCF_009671285.1_ASM967128v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:00,216] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:00,221] [INFO] Selected 11 target genomes.
[2024-01-24 13:42:00,221] [INFO] Target genome list was writen to GCF_009671285.1_ASM967128v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:00,263] [INFO] Task started: fastANI
[2024-01-24 13:42:00,264] [INFO] Running command: fastANI --query /var/lib/cwl/stg49f1a578-9940-4e42-81fb-767a885c726a/GCF_009671285.1_ASM967128v1_genomic.fna.gz --refList GCF_009671285.1_ASM967128v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009671285.1_ASM967128v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:18,573] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:18,586] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:18,587] [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_001983165.1	s__Pseudomonas_E gessardii	100.0	2087	2092	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.96	98.08	0.94	0.88	9	conclusive
GCF_012985465.1	s__Pseudomonas_E sp012985465	92.8649	1665	2092	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.03	98.94	0.91	0.90	5	-
GCF_003626995.1	s__Pseudomonas_E fluorescens_BA	92.8136	1636	2092	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.95	98.57	0.93	0.88	19	-
GCF_007858285.1	s__Pseudomonas_E brenneri	91.8313	1644	2092	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.23	97.33	0.94	0.88	10	-
GCF_016925675.1	s__Pseudomonas_E sp012985665	91.7821	1597	2092	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.30	97.44	0.92	0.88	4	-
GCF_007858275.1	s__Pseudomonas_E proteolytica	91.6242	1582	2092	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.69	98.38	0.90	0.86	19	-
GCF_002874965.1	s__Pseudomonas_E sp002874965	87.1229	1429	2092	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.77	98.46	0.92	0.88	48	-
GCF_013386825.1	s__Pseudomonas_E sp013386825	86.9349	1383	2092	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002204795.1	s__Pseudomonas_E sp002204795	86.9027	1377	2092	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_900105325.1	s__Pseudomonas_E marginalis	86.6335	1450	2092	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.53	96.47	0.90	0.85	19	-
GCF_001050345.1	s__Pseudomonas_E fildesensis	86.3958	1414	2092	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 13:42:18,588] [INFO] GTDB search result was written to GCF_009671285.1_ASM967128v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:18,589] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:18,592] [INFO] DFAST_QC result json was written to GCF_009671285.1_ASM967128v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:18,592] [INFO] DFAST_QC completed!
[2024-01-24 13:42:18,593] [INFO] Total running time: 0h2m18s