[2024-01-24 15:26:39,851] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:39,853] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:39,853] [INFO] DQC Reference Directory: /var/lib/cwl/stg9702e844-6e14-4756-8577-627012b5e221/dqc_reference
[2024-01-24 15:26:41,091] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:41,092] [INFO] Task started: Prodigal
[2024-01-24 15:26:41,093] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d488bfd-ad9f-4be9-84f9-a84680a5406a/GCF_014268455.2_ASM1426845v2_genomic.fna.gz | prodigal -d GCF_014268455.2_ASM1426845v2_genomic.fna/cds.fna -a GCF_014268455.2_ASM1426845v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:01,989] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:01,989] [INFO] Task started: HMMsearch
[2024-01-24 15:27:01,989] [INFO] Running command: hmmsearch --tblout GCF_014268455.2_ASM1426845v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9702e844-6e14-4756-8577-627012b5e221/dqc_reference/reference_markers.hmm GCF_014268455.2_ASM1426845v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:02,321] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:02,322] [INFO] Found 6/6 markers.
[2024-01-24 15:27:02,369] [INFO] Query marker FASTA was written to GCF_014268455.2_ASM1426845v2_genomic.fna/markers.fasta
[2024-01-24 15:27:02,370] [INFO] Task started: Blastn
[2024-01-24 15:27:02,370] [INFO] Running command: blastn -query GCF_014268455.2_ASM1426845v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg9702e844-6e14-4756-8577-627012b5e221/dqc_reference/reference_markers.fasta -out GCF_014268455.2_ASM1426845v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:03,280] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:03,284] [INFO] Selected 14 target genomes.
[2024-01-24 15:27:03,284] [INFO] Target genome list was writen to GCF_014268455.2_ASM1426845v2_genomic.fna/target_genomes.txt
[2024-01-24 15:27:03,290] [INFO] Task started: fastANI
[2024-01-24 15:27:03,290] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d488bfd-ad9f-4be9-84f9-a84680a5406a/GCF_014268455.2_ASM1426845v2_genomic.fna.gz --refList GCF_014268455.2_ASM1426845v2_genomic.fna/target_genomes.txt --output GCF_014268455.2_ASM1426845v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:25,408] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:25,409] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9702e844-6e14-4756-8577-627012b5e221/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:25,409] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9702e844-6e14-4756-8577-627012b5e221/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:25,422] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:27:25,422] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:27:25,422] [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		GCA_900625085.1	78544	78544	type	True	92.8201	1625	2018	95	below_threshold
Pseudomonas gessardii	strain=DSM 17152	GCA_009671285.1	78544	78544	type	True	92.8182	1630	2018	95	below_threshold
Pseudomonas gessardii	strain=DSM 17152	GCA_001983165.1	78544	78544	type	True	92.8161	1631	2018	95	below_threshold
Pseudomonas proteolytica	strain=CCUG 51515T	GCA_008692865.1	219574	219574	type	True	91.9418	1632	2018	95	below_threshold
Pseudomonas proteolytica	strain=DSM 15321	GCA_007858275.1	219574	219574	type	True	91.9198	1639	2018	95	below_threshold
Pseudomonas brenneri	strain=JCM 13307	GCA_014646715.1	129817	129817	type	True	91.3474	1652	2018	95	below_threshold
Pseudomonas brenneri	strain=DSM 15294	GCA_007858285.1	129817	129817	type	True	91.3192	1651	2018	95	below_threshold
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	86.746	1446	2018	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	86.5956	1437	2018	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	86.5375	1462	2018	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	86.3738	1454	2018	95	below_threshold
Pseudomonas fluorescens	strain=NCTC10038	GCA_900475215.1	294	294	suspected-type	True	86.1531	1420	2018	95	below_threshold
Pseudomonas karstica	strain=CCM 7891	GCA_009707515.1	1055468	1055468	type	True	85.8556	1308	2018	95	below_threshold
Serpens gallinarum	strain=Sa2CUA2	GCA_014836765.1	2763075	2763075	type	True	78.5624	503	2018	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:25,428] [INFO] DFAST Taxonomy check result was written to GCF_014268455.2_ASM1426845v2_genomic.fna/tc_result.tsv
[2024-01-24 15:27:25,429] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:25,429] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:25,429] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9702e844-6e14-4756-8577-627012b5e221/dqc_reference/checkm_data
[2024-01-24 15:27:25,431] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:25,490] [INFO] Task started: CheckM
[2024-01-24 15:27:25,491] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014268455.2_ASM1426845v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014268455.2_ASM1426845v2_genomic.fna/checkm_input GCF_014268455.2_ASM1426845v2_genomic.fna/checkm_result
[2024-01-24 15:28:27,453] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:27,454] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:27,476] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:27,477] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:27,477] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014268455.2_ASM1426845v2_genomic.fna/markers.fasta)
[2024-01-24 15:28:27,478] [INFO] Task started: Blastn
[2024-01-24 15:28:27,478] [INFO] Running command: blastn -query GCF_014268455.2_ASM1426845v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg9702e844-6e14-4756-8577-627012b5e221/dqc_reference/reference_markers_gtdb.fasta -out GCF_014268455.2_ASM1426845v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:28,804] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:28,808] [INFO] Selected 13 target genomes.
[2024-01-24 15:28:28,808] [INFO] Target genome list was writen to GCF_014268455.2_ASM1426845v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:28,820] [INFO] Task started: fastANI
[2024-01-24 15:28:28,820] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d488bfd-ad9f-4be9-84f9-a84680a5406a/GCF_014268455.2_ASM1426845v2_genomic.fna.gz --refList GCF_014268455.2_ASM1426845v2_genomic.fna/target_genomes_gtdb.txt --output GCF_014268455.2_ASM1426845v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:47,034] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:47,055] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:47,055] [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_003626995.1	s__Pseudomonas_E fluorescens_BA	99.1881	1894	2018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.95	98.57	0.93	0.88	19	conclusive
GCF_012985465.1	s__Pseudomonas_E sp012985465	93.3555	1682	2018	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_001983165.1	s__Pseudomonas_E gessardii	92.8197	1629	2018	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_007858275.1	s__Pseudomonas_E proteolytica	91.9236	1639	2018	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_016925675.1	s__Pseudomonas_E sp012985665	91.9078	1688	2018	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_000730425.1	s__Pseudomonas_E fluorescens_X	91.42	1573	2018	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_007858285.1	s__Pseudomonas_E brenneri	91.3091	1652	2018	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_900105325.1	s__Pseudomonas_E marginalis	86.8338	1463	2018	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_004310295.1	s__Pseudomonas_E sp004310295	83.5833	1159	2018	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_004331835.1	s__Pseudomonas_A sp004331835	78.6205	456	2018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.93	97.83	0.93	0.91	3	-
GCA_001513025.1	s__Pseudomonas_C sp001513025	76.3436	61	2018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_C	95.0	99.84	99.84	0.94	0.94	2	-
GCA_003963115.1	s__Aquabacterium sp003963115	75.7225	108	2018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:47,057] [INFO] GTDB search result was written to GCF_014268455.2_ASM1426845v2_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:47,057] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:47,061] [INFO] DFAST_QC result json was written to GCF_014268455.2_ASM1426845v2_genomic.fna/dqc_result.json
[2024-01-24 15:28:47,062] [INFO] DFAST_QC completed!
[2024-01-24 15:28:47,062] [INFO] Total running time: 0h2m7s