[2023-06-19 00:04:46,745] [INFO] DFAST_QC pipeline started.
[2023-06-19 00:04:46,747] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 00:04:46,747] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c2dd788-9d57-4015-bf3e-0a49370428d3/dqc_reference
[2023-06-19 00:04:48,044] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 00:04:48,045] [INFO] Task started: Prodigal
[2023-06-19 00:04:48,045] [INFO] Running command: gunzip -c /var/lib/cwl/stg492e29df-b677-411e-b38d-296734816bd7/GCA_018607005.1_ASM1860700v1_genomic.fna.gz | prodigal -d GCA_018607005.1_ASM1860700v1_genomic.fna/cds.fna -a GCA_018607005.1_ASM1860700v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 00:04:59,913] [INFO] Task succeeded: Prodigal
[2023-06-19 00:04:59,913] [INFO] Task started: HMMsearch
[2023-06-19 00:04:59,913] [INFO] Running command: hmmsearch --tblout GCA_018607005.1_ASM1860700v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c2dd788-9d57-4015-bf3e-0a49370428d3/dqc_reference/reference_markers.hmm GCA_018607005.1_ASM1860700v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 00:05:00,168] [INFO] Task succeeded: HMMsearch
[2023-06-19 00:05:00,170] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg492e29df-b677-411e-b38d-296734816bd7/GCA_018607005.1_ASM1860700v1_genomic.fna.gz]
[2023-06-19 00:05:00,211] [INFO] Query marker FASTA was written to GCA_018607005.1_ASM1860700v1_genomic.fna/markers.fasta
[2023-06-19 00:05:00,211] [INFO] Task started: Blastn
[2023-06-19 00:05:00,211] [INFO] Running command: blastn -query GCA_018607005.1_ASM1860700v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c2dd788-9d57-4015-bf3e-0a49370428d3/dqc_reference/reference_markers.fasta -out GCA_018607005.1_ASM1860700v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 00:05:00,920] [INFO] Task succeeded: Blastn
[2023-06-19 00:05:00,924] [INFO] Selected 10 target genomes.
[2023-06-19 00:05:00,924] [INFO] Target genome list was writen to GCA_018607005.1_ASM1860700v1_genomic.fna/target_genomes.txt
[2023-06-19 00:05:00,926] [INFO] Task started: fastANI
[2023-06-19 00:05:00,926] [INFO] Running command: fastANI --query /var/lib/cwl/stg492e29df-b677-411e-b38d-296734816bd7/GCA_018607005.1_ASM1860700v1_genomic.fna.gz --refList GCA_018607005.1_ASM1860700v1_genomic.fna/target_genomes.txt --output GCA_018607005.1_ASM1860700v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 00:05:13,507] [INFO] Task succeeded: fastANI
[2023-06-19 00:05:13,507] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c2dd788-9d57-4015-bf3e-0a49370428d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 00:05:13,508] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c2dd788-9d57-4015-bf3e-0a49370428d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 00:05:13,517] [INFO] Found 10 fastANI hits (7 hits with ANI > threshold)
[2023-06-19 00:05:13,517] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-19 00:05:13,517] [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 aeruginosa	strain=DSM 50071	GCA_001042925.1	287	287	type	True	98.7331	1190	1395	95	conclusive
Pseudomonas aeruginosa	strain=DSM 50071	GCA_012987025.1	287	287	type	True	98.7331	1190	1395	95	conclusive
Pseudomonas aeruginosa	strain=NCTC10332	GCA_001457615.1	287	287	type	True	98.7314	1195	1395	95	conclusive
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	98.7222	1202	1395	95	conclusive
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	98.7187	1196	1395	95	conclusive
Pseudomonas aeruginosa	strain=DSM 50071	GCA_900167195.1	287	287	type	True	98.7123	1178	1395	95	conclusive
Pseudomonas aeruginosa	strain=CCUG 551	GCA_008801675.1	287	287	type	True	98.6917	1182	1395	95	conclusive
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	81.179	584	1395	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	80.57	618	1395	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	80.0756	541	1395	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 00:05:13,520] [INFO] DFAST Taxonomy check result was written to GCA_018607005.1_ASM1860700v1_genomic.fna/tc_result.tsv
[2023-06-19 00:05:13,520] [INFO] ===== Taxonomy check completed =====
[2023-06-19 00:05:13,520] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 00:05:13,521] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c2dd788-9d57-4015-bf3e-0a49370428d3/dqc_reference/checkm_data
[2023-06-19 00:05:13,522] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 00:05:13,567] [INFO] Task started: CheckM
[2023-06-19 00:05:13,567] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018607005.1_ASM1860700v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018607005.1_ASM1860700v1_genomic.fna/checkm_input GCA_018607005.1_ASM1860700v1_genomic.fna/checkm_result
[2023-06-19 00:05:47,548] [INFO] Task succeeded: CheckM
[2023-06-19 00:05:47,549] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 25.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 00:05:47,603] [INFO] ===== Completeness check finished =====
[2023-06-19 00:05:47,603] [INFO] ===== Start GTDB Search =====
[2023-06-19 00:05:47,603] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018607005.1_ASM1860700v1_genomic.fna/markers.fasta)
[2023-06-19 00:05:47,604] [INFO] Task started: Blastn
[2023-06-19 00:05:47,604] [INFO] Running command: blastn -query GCA_018607005.1_ASM1860700v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c2dd788-9d57-4015-bf3e-0a49370428d3/dqc_reference/reference_markers_gtdb.fasta -out GCA_018607005.1_ASM1860700v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 00:05:48,582] [INFO] Task succeeded: Blastn
[2023-06-19 00:05:48,595] [INFO] Selected 13 target genomes.
[2023-06-19 00:05:48,595] [INFO] Target genome list was writen to GCA_018607005.1_ASM1860700v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 00:05:48,609] [INFO] Task started: fastANI
[2023-06-19 00:05:48,609] [INFO] Running command: fastANI --query /var/lib/cwl/stg492e29df-b677-411e-b38d-296734816bd7/GCA_018607005.1_ASM1860700v1_genomic.fna.gz --refList GCA_018607005.1_ASM1860700v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018607005.1_ASM1860700v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 00:06:03,074] [INFO] Task succeeded: fastANI
[2023-06-19 00:06:03,090] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 00:06:03,090] [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_001457615.1	s__Pseudomonas aeruginosa	98.7314	1195	1395	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.12	97.38	0.94	0.84	5623	conclusive
GCF_000017205.1	s__Pseudomonas aeruginosa_A	93.2446	1144	1395	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.07	98.78	0.93	0.80	42	-
GCF_900187975.1	s__Pseudomonas delhiensis	83.2785	872	1395	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.078	98.79	97.59	0.94	0.89	3	-
GCF_900112375.1	s__Pseudomonas citronellolis	83.1498	876	1395	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.078	97.44	97.08	0.86	0.82	26	-
GCF_900103845.1	s__Pseudomonas jinjuensis	82.9735	745	1395	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_017589465.1	s__Pseudomonas sp017589465	82.5965	702	1395	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904061905.1	s__Pseudomonas_E carbonaria	81.8934	703	1395	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_018398425.1	s__Pseudomonas_E lalucatii	81.1554	587	1395	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	99.28	0.97	0.92	4	-
GCF_900104805.1	s__Pseudomonas_K oryzae	80.9478	553	1395	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105885.1	s__Pseudomonas_K guangdongensis	80.7285	444	1395	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	98.99	98.99	0.99	0.99	2	-
GCF_004801855.1	s__Pseudomonas_K sp004801855	80.7166	490	1395	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	98.38	98.38	0.89	0.89	2	-
GCF_003052605.1	s__Pseudomonas_E indoloxydans	80.6003	511	1395	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	96.52	N/A	N/A	N/A	N/A	1	-
GCF_016008875.1	s__Pseudomonas_E sp002439135	80.0977	548	1395	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.91	96.75	0.87	0.85	5	-
--------------------------------------------------------------------------------
[2023-06-19 00:06:03,096] [INFO] GTDB search result was written to GCA_018607005.1_ASM1860700v1_genomic.fna/result_gtdb.tsv
[2023-06-19 00:06:03,097] [INFO] ===== GTDB Search completed =====
[2023-06-19 00:06:03,109] [INFO] DFAST_QC result json was written to GCA_018607005.1_ASM1860700v1_genomic.fna/dqc_result.json
[2023-06-19 00:06:03,109] [INFO] DFAST_QC completed!
[2023-06-19 00:06:03,109] [INFO] Total running time: 0h1m16s