[2024-01-24 13:58:41,634] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:41,636] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:41,636] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf87d762-5e97-4297-90c3-def5ca365ce5/dqc_reference
[2024-01-24 13:58:42,896] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:42,897] [INFO] Task started: Prodigal
[2024-01-24 13:58:42,898] [INFO] Running command: gunzip -c /var/lib/cwl/stgc91eb292-ff43-403e-89f1-00c1dee51501/GCF_014646715.1_ASM1464671v1_genomic.fna.gz | prodigal -d GCF_014646715.1_ASM1464671v1_genomic.fna/cds.fna -a GCF_014646715.1_ASM1464671v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:59:05,203] [INFO] Task succeeded: Prodigal
[2024-01-24 13:59:05,203] [INFO] Task started: HMMsearch
[2024-01-24 13:59:05,203] [INFO] Running command: hmmsearch --tblout GCF_014646715.1_ASM1464671v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf87d762-5e97-4297-90c3-def5ca365ce5/dqc_reference/reference_markers.hmm GCF_014646715.1_ASM1464671v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:59:05,604] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:59:05,606] [INFO] Found 6/6 markers.
[2024-01-24 13:59:05,676] [INFO] Query marker FASTA was written to GCF_014646715.1_ASM1464671v1_genomic.fna/markers.fasta
[2024-01-24 13:59:05,676] [INFO] Task started: Blastn
[2024-01-24 13:59:05,677] [INFO] Running command: blastn -query GCF_014646715.1_ASM1464671v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf87d762-5e97-4297-90c3-def5ca365ce5/dqc_reference/reference_markers.fasta -out GCF_014646715.1_ASM1464671v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:06,618] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:06,622] [INFO] Selected 14 target genomes.
[2024-01-24 13:59:06,623] [INFO] Target genome list was writen to GCF_014646715.1_ASM1464671v1_genomic.fna/target_genomes.txt
[2024-01-24 13:59:06,640] [INFO] Task started: fastANI
[2024-01-24 13:59:06,640] [INFO] Running command: fastANI --query /var/lib/cwl/stgc91eb292-ff43-403e-89f1-00c1dee51501/GCF_014646715.1_ASM1464671v1_genomic.fna.gz --refList GCF_014646715.1_ASM1464671v1_genomic.fna/target_genomes.txt --output GCF_014646715.1_ASM1464671v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:27,823] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:27,824] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf87d762-5e97-4297-90c3-def5ca365ce5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:27,824] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf87d762-5e97-4297-90c3-def5ca365ce5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:27,839] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:59:27,839] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:59:27,839] [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 brenneri	strain=JCM 13307	GCA_014646715.1	129817	129817	type	True	100.0	1973	1976	95	conclusive
Pseudomonas brenneri	strain=DSM 15294	GCA_007858285.1	129817	129817	type	True	99.9964	1972	1976	95	conclusive
Pseudomonas proteolytica	strain=CCUG 51515T	GCA_008692865.1	219574	219574	type	True	92.3295	1596	1976	95	below_threshold
Pseudomonas proteolytica	strain=DSM 15321	GCA_007858275.1	219574	219574	type	True	92.2744	1626	1976	95	below_threshold
Pseudomonas gessardii	strain=DSM 17152	GCA_001983165.1	78544	78544	type	True	91.7858	1642	1976	95	below_threshold
Pseudomonas gessardii	strain=DSM 17152	GCA_009671285.1	78544	78544	type	True	91.7752	1643	1976	95	below_threshold
Pseudomonas gessardii		GCA_900625085.1	78544	78544	type	True	91.7516	1638	1976	95	below_threshold
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	86.6239	1432	1976	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	86.5089	1471	1976	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	86.2844	1438	1976	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	86.2311	1389	1976	95	below_threshold
Pseudomonas karstica	strain=CCM 7891	GCA_009707515.1	1055468	1055468	type	True	86.0902	1281	1976	95	below_threshold
Pseudomonas fluorescens	strain=NCTC10038	GCA_900475215.1	294	294	suspected-type	True	86.0758	1400	1976	95	below_threshold
Pseudomonas kitaguniensis	strain=MAFF 212408	GCA_009296165.1	2607908	2607908	type	True	85.2973	1182	1976	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:27,841] [INFO] DFAST Taxonomy check result was written to GCF_014646715.1_ASM1464671v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:27,841] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:27,842] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:27,842] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf87d762-5e97-4297-90c3-def5ca365ce5/dqc_reference/checkm_data
[2024-01-24 13:59:27,843] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:27,898] [INFO] Task started: CheckM
[2024-01-24 13:59:27,898] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014646715.1_ASM1464671v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014646715.1_ASM1464671v1_genomic.fna/checkm_input GCF_014646715.1_ASM1464671v1_genomic.fna/checkm_result
[2024-01-24 14:00:31,520] [INFO] Task succeeded: CheckM
[2024-01-24 14:00:31,521] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:00:31,545] [INFO] ===== Completeness check finished =====
[2024-01-24 14:00:31,545] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:00:31,546] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014646715.1_ASM1464671v1_genomic.fna/markers.fasta)
[2024-01-24 14:00:31,546] [INFO] Task started: Blastn
[2024-01-24 14:00:31,547] [INFO] Running command: blastn -query GCF_014646715.1_ASM1464671v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf87d762-5e97-4297-90c3-def5ca365ce5/dqc_reference/reference_markers_gtdb.fasta -out GCF_014646715.1_ASM1464671v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:33,361] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:33,364] [INFO] Selected 9 target genomes.
[2024-01-24 14:00:33,364] [INFO] Target genome list was writen to GCF_014646715.1_ASM1464671v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:33,370] [INFO] Task started: fastANI
[2024-01-24 14:00:33,371] [INFO] Running command: fastANI --query /var/lib/cwl/stgc91eb292-ff43-403e-89f1-00c1dee51501/GCF_014646715.1_ASM1464671v1_genomic.fna.gz --refList GCF_014646715.1_ASM1464671v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014646715.1_ASM1464671v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:49,366] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:49,375] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:49,375] [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_007858285.1	s__Pseudomonas_E brenneri	99.9964	1972	1976	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.23	97.33	0.94	0.88	10	conclusive
GCF_007858275.1	s__Pseudomonas_E proteolytica	92.2838	1625	1976	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_001983165.1	s__Pseudomonas_E gessardii	91.7761	1642	1976	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.96	98.08	0.94	0.88	9	-
GCF_016925675.1	s__Pseudomonas_E sp012985665	91.7574	1610	1976	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_012985465.1	s__Pseudomonas_E sp012985465	91.634	1660	1976	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	91.2624	1659	1976	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_000730425.1	s__Pseudomonas_E fluorescens_X	91.1797	1578	1976	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.75	99.75	0.93	0.93	2	-
GCF_000346755.1	s__Pseudomonas_E sp000346755	86.7554	1405	1976	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_009707515.1	s__Pseudomonas_E sp009707515	86.0969	1280	1976	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 14:00:49,377] [INFO] GTDB search result was written to GCF_014646715.1_ASM1464671v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:49,378] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:49,387] [INFO] DFAST_QC result json was written to GCF_014646715.1_ASM1464671v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:49,387] [INFO] DFAST_QC completed!
[2024-01-24 14:00:49,387] [INFO] Total running time: 0h2m8s