[2024-01-24 13:13:16,262] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:16,264] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:16,264] [INFO] DQC Reference Directory: /var/lib/cwl/stg30321a95-0d3b-4bee-84d5-eb33478a6c9c/dqc_reference
[2024-01-24 13:13:17,439] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:17,440] [INFO] Task started: Prodigal
[2024-01-24 13:13:17,440] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ea37f98-b910-437c-ae3c-cc7a1f249f59/GCF_002355475.1_ASM235547v1_genomic.fna.gz | prodigal -d GCF_002355475.1_ASM235547v1_genomic.fna/cds.fna -a GCF_002355475.1_ASM235547v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:38,856] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:38,856] [INFO] Task started: HMMsearch
[2024-01-24 13:13:38,856] [INFO] Running command: hmmsearch --tblout GCF_002355475.1_ASM235547v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg30321a95-0d3b-4bee-84d5-eb33478a6c9c/dqc_reference/reference_markers.hmm GCF_002355475.1_ASM235547v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:39,290] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:39,291] [INFO] Found 6/6 markers.
[2024-01-24 13:13:39,393] [INFO] Query marker FASTA was written to GCF_002355475.1_ASM235547v1_genomic.fna/markers.fasta
[2024-01-24 13:13:39,394] [INFO] Task started: Blastn
[2024-01-24 13:13:39,394] [INFO] Running command: blastn -query GCF_002355475.1_ASM235547v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30321a95-0d3b-4bee-84d5-eb33478a6c9c/dqc_reference/reference_markers.fasta -out GCF_002355475.1_ASM235547v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:40,536] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:40,539] [INFO] Selected 17 target genomes.
[2024-01-24 13:13:40,539] [INFO] Target genome list was writen to GCF_002355475.1_ASM235547v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:40,552] [INFO] Task started: fastANI
[2024-01-24 13:13:40,552] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ea37f98-b910-437c-ae3c-cc7a1f249f59/GCF_002355475.1_ASM235547v1_genomic.fna.gz --refList GCF_002355475.1_ASM235547v1_genomic.fna/target_genomes.txt --output GCF_002355475.1_ASM235547v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:03,775] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:03,776] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg30321a95-0d3b-4bee-84d5-eb33478a6c9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:03,776] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg30321a95-0d3b-4bee-84d5-eb33478a6c9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:03,795] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:14:03,795] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:03,796] [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 furukawaii	strain=KF707	GCA_002355475.1	1149133	1149133	type	True	100.0	2079	2080	95	conclusive
Pseudomonas furukawaii	strain=KF707	GCA_000262065.3	1149133	1149133	type	True	99.9371	1998	2080	95	conclusive
Pseudomonas otitidis	strain=DSM 17224	GCA_900111835.1	319939	319939	suspected-type	True	85.3917	1286	2080	95	below_threshold
Pseudomonas tohonis	strain=TUM18999	GCA_012767755.2	2725477	2725477	type	True	85.28	1286	2080	95	below_threshold
Pseudomonas citronellolis	strain=LMG 18378	GCA_900112375.1	53408	53408	type	True	83.2428	1225	2080	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	83.1769	1229	2080	95	below_threshold
Pseudomonas citronellolis	strain=DSM 50332	GCA_004745455.1	53408	53408	type	True	83.156	1243	2080	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	83.0906	1028	2080	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	83.0049	892	2080	95	below_threshold
Pseudomonas alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	82.9819	986	2080	95	below_threshold
Pseudomonas alcaligenes	strain=NBRC 14159	GCA_000467105.1	43263	43263	type	True	82.8788	962	2080	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	82.6214	898	2080	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	82.5587	1039	2080	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	82.3042	971	2080	95	below_threshold
Pseudomonas campi	strain=S1-A32-2	GCA_013200955.2	2731681	2731681	type	True	82.0862	901	2080	95	below_threshold
Pseudomonas ullengensis	strain=UL070	GCA_014174475.1	2759166	2759166	type	True	82.0609	946	2080	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	81.7068	760	2080	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:03,797] [INFO] DFAST Taxonomy check result was written to GCF_002355475.1_ASM235547v1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:03,798] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:03,798] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:03,798] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg30321a95-0d3b-4bee-84d5-eb33478a6c9c/dqc_reference/checkm_data
[2024-01-24 13:14:03,799] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:03,859] [INFO] Task started: CheckM
[2024-01-24 13:14:03,859] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002355475.1_ASM235547v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002355475.1_ASM235547v1_genomic.fna/checkm_input GCF_002355475.1_ASM235547v1_genomic.fna/checkm_result
[2024-01-24 13:15:11,463] [INFO] Task succeeded: CheckM
[2024-01-24 13:15:11,465] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:15:11,486] [INFO] ===== Completeness check finished =====
[2024-01-24 13:15:11,486] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:15:11,487] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002355475.1_ASM235547v1_genomic.fna/markers.fasta)
[2024-01-24 13:15:11,487] [INFO] Task started: Blastn
[2024-01-24 13:15:11,487] [INFO] Running command: blastn -query GCF_002355475.1_ASM235547v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30321a95-0d3b-4bee-84d5-eb33478a6c9c/dqc_reference/reference_markers_gtdb.fasta -out GCF_002355475.1_ASM235547v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:15:13,496] [INFO] Task succeeded: Blastn
[2024-01-24 13:15:13,499] [INFO] Selected 10 target genomes.
[2024-01-24 13:15:13,499] [INFO] Target genome list was writen to GCF_002355475.1_ASM235547v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:15:13,522] [INFO] Task started: fastANI
[2024-01-24 13:15:13,522] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ea37f98-b910-437c-ae3c-cc7a1f249f59/GCF_002355475.1_ASM235547v1_genomic.fna.gz --refList GCF_002355475.1_ASM235547v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002355475.1_ASM235547v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:29,837] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:29,846] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:29,847] [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_002355475.1	s__Pseudomonas_F furukawaii	100.0	2080	2080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	99.26	98.53	0.90	0.84	3	conclusive
GCF_000412695.1	s__Pseudomonas_F resinovorans_A	87.2375	1505	2080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008807375.1	s__Pseudomonas_F lalkuanensis	86.8739	1442	2080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000949385.2	s__Pseudomonas_F sp000949385	86.7065	1425	2080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014700075.1	s__Pseudomonas_F sp014700075	86.5238	1421	2080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013393345.1	s__Pseudomonas_F resinovorans_C	86.0918	1431	2080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	95.04	95.04	0.90	0.90	2	-
GCF_003626975.1	s__Pseudomonas_F sp003626975	85.5729	1436	2080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	99.49	99.49	0.93	0.93	2	-
GCF_900111835.1	s__Pseudomonas_F otitidis	85.3666	1288	2080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	96.35	95.43	0.89	0.84	21	-
GCF_012767755.2	s__Pseudomonas_F sp003234055	85.2877	1285	2080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	96.89	96.11	0.89	0.88	3	-
GCF_904061905.1	s__Pseudomonas_E carbonaria	83.2954	1074	2080	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 13:15:29,848] [INFO] GTDB search result was written to GCF_002355475.1_ASM235547v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:29,849] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:29,853] [INFO] DFAST_QC result json was written to GCF_002355475.1_ASM235547v1_genomic.fna/dqc_result.json
[2024-01-24 13:15:29,853] [INFO] DFAST_QC completed!
[2024-01-24 13:15:29,853] [INFO] Total running time: 0h2m14s