[2024-01-24 11:51:36,743] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:36,746] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:36,746] [INFO] DQC Reference Directory: /var/lib/cwl/stg38d4a94f-4414-4032-8429-f27676515e69/dqc_reference
[2024-01-24 11:51:38,033] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:38,034] [INFO] Task started: Prodigal
[2024-01-24 11:51:38,034] [INFO] Running command: gunzip -c /var/lib/cwl/stga0dde2ef-9448-4e62-ba59-caf88542b064/GCF_009932335.1_ASM993233v1_genomic.fna.gz | prodigal -d GCF_009932335.1_ASM993233v1_genomic.fna/cds.fna -a GCF_009932335.1_ASM993233v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:59,571] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:59,572] [INFO] Task started: HMMsearch
[2024-01-24 11:51:59,572] [INFO] Running command: hmmsearch --tblout GCF_009932335.1_ASM993233v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg38d4a94f-4414-4032-8429-f27676515e69/dqc_reference/reference_markers.hmm GCF_009932335.1_ASM993233v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:59,870] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:59,872] [INFO] Found 6/6 markers.
[2024-01-24 11:51:59,919] [INFO] Query marker FASTA was written to GCF_009932335.1_ASM993233v1_genomic.fna/markers.fasta
[2024-01-24 11:51:59,919] [INFO] Task started: Blastn
[2024-01-24 11:51:59,920] [INFO] Running command: blastn -query GCF_009932335.1_ASM993233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38d4a94f-4414-4032-8429-f27676515e69/dqc_reference/reference_markers.fasta -out GCF_009932335.1_ASM993233v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:00,874] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:00,878] [INFO] Selected 13 target genomes.
[2024-01-24 11:52:00,879] [INFO] Target genome list was writen to GCF_009932335.1_ASM993233v1_genomic.fna/target_genomes.txt
[2024-01-24 11:52:00,885] [INFO] Task started: fastANI
[2024-01-24 11:52:00,886] [INFO] Running command: fastANI --query /var/lib/cwl/stga0dde2ef-9448-4e62-ba59-caf88542b064/GCF_009932335.1_ASM993233v1_genomic.fna.gz --refList GCF_009932335.1_ASM993233v1_genomic.fna/target_genomes.txt --output GCF_009932335.1_ASM993233v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:23,521] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:23,522] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg38d4a94f-4414-4032-8429-f27676515e69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:23,522] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg38d4a94f-4414-4032-8429-f27676515e69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:23,539] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:52:23,539] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:52:23,539] [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 inefficax	strain=JV551A3	GCA_900277125.1	2078786	2078786	type	True	94.5619	1612	1988	95	below_threshold
Pseudomonas oryzicola	strain=RD9SR1	GCA_014269185.2	485876	485876	type	True	90.799	1485	1988	95	below_threshold
Pseudomonas anuradhapurensis	strain=RD8MR3	GCA_014269225.2	485870	485870	type	True	90.6904	1496	1988	95	below_threshold
Pseudomonas putida	strain=NCTC10936	GCA_900455645.1	303	303	suspected-type	True	90.1538	1556	1988	95	below_threshold
Pseudomonas putida	strain=IPO3752	GCA_013387005.1	303	303	suspected-type	True	90.1378	1523	1988	95	below_threshold
Pseudomonas putida	strain=ATCC 12633	GCA_024508115.1	303	303	suspected-type	True	90.1342	1550	1988	95	below_threshold
Pseudomonas monteilii	strain=DSM 14164	GCA_000621245.1	76759	76759	type	True	90.0141	1532	1988	95	below_threshold
Pseudomonas monteilii	strain=NBRC 103158	GCA_000730605.1	76759	76759	type	True	89.9928	1507	1988	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	88.4305	1331	1988	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	88.3571	1391	1988	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	87.949	1332	1988	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	87.7741	1422	1988	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	87.7722	1468	1988	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:23,540] [INFO] DFAST Taxonomy check result was written to GCF_009932335.1_ASM993233v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:23,541] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:23,541] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:23,542] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg38d4a94f-4414-4032-8429-f27676515e69/dqc_reference/checkm_data
[2024-01-24 11:52:23,544] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:23,601] [INFO] Task started: CheckM
[2024-01-24 11:52:23,602] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009932335.1_ASM993233v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009932335.1_ASM993233v1_genomic.fna/checkm_input GCF_009932335.1_ASM993233v1_genomic.fna/checkm_result
[2024-01-24 11:53:26,679] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:26,680] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:26,703] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:26,704] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:26,704] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009932335.1_ASM993233v1_genomic.fna/markers.fasta)
[2024-01-24 11:53:26,705] [INFO] Task started: Blastn
[2024-01-24 11:53:26,705] [INFO] Running command: blastn -query GCF_009932335.1_ASM993233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38d4a94f-4414-4032-8429-f27676515e69/dqc_reference/reference_markers_gtdb.fasta -out GCF_009932335.1_ASM993233v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:28,301] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:28,305] [INFO] Selected 9 target genomes.
[2024-01-24 11:53:28,305] [INFO] Target genome list was writen to GCF_009932335.1_ASM993233v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:28,312] [INFO] Task started: fastANI
[2024-01-24 11:53:28,312] [INFO] Running command: fastANI --query /var/lib/cwl/stga0dde2ef-9448-4e62-ba59-caf88542b064/GCF_009932335.1_ASM993233v1_genomic.fna.gz --refList GCF_009932335.1_ASM993233v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009932335.1_ASM993233v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:48,444] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:48,457] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:48,457] [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_009932335.1	s__Pseudomonas_E asiatica	100.0	1986	1988	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0481	97.98	96.05	0.89	0.79	58	conclusive
GCF_015680405.1	s__Pseudomonas_E pudica	95.0353	1597	1988	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0481	98.52	95.23	0.90	0.83	12	-
GCF_900277125.1	s__Pseudomonas_E inefficax	94.5619	1612	1988	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.83	97.08	0.92	0.89	5	-
GCF_001642705.1	s__Pseudomonas_E sp001642705	94.2795	1601	1988	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.26	95.01	0.89	0.85	3	-
GCF_002165135.1	s__Pseudomonas_E sp002165135	93.855	1537	1988	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_002113165.1	s__Pseudomonas_E sp002113165	93.5225	1595	1988	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	3	-
GCF_013179515.1	s__Pseudomonas_E sp013179515	89.5921	1373	1988	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.93	98.93	0.82	0.82	2	-
GCF_003671955.1	s__Pseudomonas_E hunanensis	89.5628	1547	1988	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.33	95.26	0.86	0.79	88	-
GCF_004214895.1	s__Pseudomonas_E sp004214895	83.8429	1195	1988	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 11:53:48,459] [INFO] GTDB search result was written to GCF_009932335.1_ASM993233v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:48,459] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:48,463] [INFO] DFAST_QC result json was written to GCF_009932335.1_ASM993233v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:48,463] [INFO] DFAST_QC completed!
[2024-01-24 11:53:48,463] [INFO] Total running time: 0h2m12s