[2024-01-25 19:43:50,647] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:43:50,648] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:43:50,648] [INFO] DQC Reference Directory: /var/lib/cwl/stg2dc29ef1-110a-4f19-aa50-4855c4e6f599/dqc_reference
[2024-01-25 19:43:51,805] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:43:51,806] [INFO] Task started: Prodigal
[2024-01-25 19:43:51,806] [INFO] Running command: gunzip -c /var/lib/cwl/stg937f9aa1-3d29-4a37-8918-7c682d53624a/GCF_001042905.1_G8692_genomic.fna.gz | prodigal -d GCF_001042905.1_G8692_genomic.fna/cds.fna -a GCF_001042905.1_G8692_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:44:10,460] [INFO] Task succeeded: Prodigal
[2024-01-25 19:44:10,460] [INFO] Task started: HMMsearch
[2024-01-25 19:44:10,461] [INFO] Running command: hmmsearch --tblout GCF_001042905.1_G8692_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2dc29ef1-110a-4f19-aa50-4855c4e6f599/dqc_reference/reference_markers.hmm GCF_001042905.1_G8692_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:44:10,755] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:44:10,756] [INFO] Found 6/6 markers.
[2024-01-25 19:44:10,804] [INFO] Query marker FASTA was written to GCF_001042905.1_G8692_genomic.fna/markers.fasta
[2024-01-25 19:44:10,805] [INFO] Task started: Blastn
[2024-01-25 19:44:10,805] [INFO] Running command: blastn -query GCF_001042905.1_G8692_genomic.fna/markers.fasta -db /var/lib/cwl/stg2dc29ef1-110a-4f19-aa50-4855c4e6f599/dqc_reference/reference_markers.fasta -out GCF_001042905.1_G8692_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:44:11,703] [INFO] Task succeeded: Blastn
[2024-01-25 19:44:11,706] [INFO] Selected 12 target genomes.
[2024-01-25 19:44:11,707] [INFO] Target genome list was writen to GCF_001042905.1_G8692_genomic.fna/target_genomes.txt
[2024-01-25 19:44:11,712] [INFO] Task started: fastANI
[2024-01-25 19:44:11,712] [INFO] Running command: fastANI --query /var/lib/cwl/stg937f9aa1-3d29-4a37-8918-7c682d53624a/GCF_001042905.1_G8692_genomic.fna.gz --refList GCF_001042905.1_G8692_genomic.fna/target_genomes.txt --output GCF_001042905.1_G8692_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:44:35,242] [INFO] Task succeeded: fastANI
[2024-01-25 19:44:35,243] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2dc29ef1-110a-4f19-aa50-4855c4e6f599/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:44:35,243] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2dc29ef1-110a-4f19-aa50-4855c4e6f599/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:44:35,252] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:44:35,252] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:44:35,252] [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 lini	strain=DSM 16768	GCA_001042905.1	163011	163011	type	True	100.0	2155	2155	95	conclusive
Pseudomonas lini	strain=CCUG 51522	GCA_008801525.1	163011	163011	type	True	99.9976	2149	2155	95	conclusive
Pseudomonas farris	strain=SWRI79	GCA_019145235.1	2841207	2841207	type	True	94.8514	1835	2155	95	below_threshold
Pseudomonas mandelii	strain=DSM 17967	GCA_007858265.1	75612	75612	suspected-type	True	88.2737	1614	2155	95	below_threshold
Pseudomonas mandelii	strain=NBRC 103147	GCA_002091695.1	75612	75612	suspected-type	True	88.2328	1588	2155	95	below_threshold
Pseudomonas laurylsulfatiphila	strain=AP3_16	GCA_002934665.1	2011015	2011015	type	True	86.7787	1444	2155	95	below_threshold
Pseudomonas izuensis	strain=IzPS43_3003	GCA_009861505.1	2684212	2684212	type	True	86.6233	1443	2155	95	below_threshold
Pseudomonas laurylsulfativorans	strain=AP3_22	GCA_002906155.1	1943631	1943631	type	True	86.5552	1432	2155	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	86.0603	1467	2155	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	86.004	1433	2155	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	85.4327	1506	2155	95	below_threshold
Pseudomonas rhizophila	strain=S211	GCA_003033885.1	2045200	2045200	type	True	84.135	1384	2155	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:44:35,253] [INFO] DFAST Taxonomy check result was written to GCF_001042905.1_G8692_genomic.fna/tc_result.tsv
[2024-01-25 19:44:35,254] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:44:35,254] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:44:35,254] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2dc29ef1-110a-4f19-aa50-4855c4e6f599/dqc_reference/checkm_data
[2024-01-25 19:44:35,255] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:44:35,317] [INFO] Task started: CheckM
[2024-01-25 19:44:35,317] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001042905.1_G8692_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001042905.1_G8692_genomic.fna/checkm_input GCF_001042905.1_G8692_genomic.fna/checkm_result
[2024-01-25 19:45:27,538] [INFO] Task succeeded: CheckM
[2024-01-25 19:45:27,539] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:45:27,558] [INFO] ===== Completeness check finished =====
[2024-01-25 19:45:27,558] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:45:27,559] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001042905.1_G8692_genomic.fna/markers.fasta)
[2024-01-25 19:45:27,559] [INFO] Task started: Blastn
[2024-01-25 19:45:27,559] [INFO] Running command: blastn -query GCF_001042905.1_G8692_genomic.fna/markers.fasta -db /var/lib/cwl/stg2dc29ef1-110a-4f19-aa50-4855c4e6f599/dqc_reference/reference_markers_gtdb.fasta -out GCF_001042905.1_G8692_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:29,223] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:29,226] [INFO] Selected 7 target genomes.
[2024-01-25 19:45:29,226] [INFO] Target genome list was writen to GCF_001042905.1_G8692_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:45:29,235] [INFO] Task started: fastANI
[2024-01-25 19:45:29,235] [INFO] Running command: fastANI --query /var/lib/cwl/stg937f9aa1-3d29-4a37-8918-7c682d53624a/GCF_001042905.1_G8692_genomic.fna.gz --refList GCF_001042905.1_G8692_genomic.fna/target_genomes_gtdb.txt --output GCF_001042905.1_G8692_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:45:44,961] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:44,966] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:45:44,966] [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_001042905.1	s__Pseudomonas_E lini	100.0	2155	2155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.33	98.85	0.97	0.92	6	conclusive
GCF_001238485.1	s__Pseudomonas_E syringae_E	94.6304	1772	2155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.97	95.90	0.85	0.84	15	-
GCF_003732275.1	s__Pseudomonas_E frederiksbergensis_H	94.395	1804	2155	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_000282375.1	s__Pseudomonas_E sp000282375	94.0396	1727	2155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.36	96.36	0.86	0.86	2	-
GCF_000282495.1	s__Pseudomonas_E sp000282495	93.8502	1757	2155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.86	95.96	0.87	0.86	6	-
GCF_000512695.2	s__Pseudomonas_E sp000512695	93.7543	1600	2155	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_900187445.1	s__Pseudomonas_E sp900187445	93.4917	1670	2155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:45:44,968] [INFO] GTDB search result was written to GCF_001042905.1_G8692_genomic.fna/result_gtdb.tsv
[2024-01-25 19:45:44,968] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:45:44,970] [INFO] DFAST_QC result json was written to GCF_001042905.1_G8692_genomic.fna/dqc_result.json
[2024-01-25 19:45:44,971] [INFO] DFAST_QC completed!
[2024-01-25 19:45:44,971] [INFO] Total running time: 0h1m54s