[2023-06-27 17:17:43,243] [INFO] DFAST_QC pipeline started.
[2023-06-27 17:17:43,247] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 17:17:43,247] [INFO] DQC Reference Directory: /var/lib/cwl/stg4225eb16-c680-4339-971d-fbd632a6dc73/dqc_reference
[2023-06-27 17:17:45,516] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 17:17:45,517] [INFO] Task started: Prodigal
[2023-06-27 17:17:45,518] [INFO] Running command: gunzip -c /var/lib/cwl/stgabbf8bae-7a61-4192-b45b-f93e8c1a75c8/GCA_026398835.1_ASM2639883v1_genomic.fna.gz | prodigal -d GCA_026398835.1_ASM2639883v1_genomic.fna/cds.fna -a GCA_026398835.1_ASM2639883v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 17:17:54,933] [INFO] Task succeeded: Prodigal
[2023-06-27 17:17:54,934] [INFO] Task started: HMMsearch
[2023-06-27 17:17:54,934] [INFO] Running command: hmmsearch --tblout GCA_026398835.1_ASM2639883v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4225eb16-c680-4339-971d-fbd632a6dc73/dqc_reference/reference_markers.hmm GCA_026398835.1_ASM2639883v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 17:17:55,205] [INFO] Task succeeded: HMMsearch
[2023-06-27 17:17:55,207] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgabbf8bae-7a61-4192-b45b-f93e8c1a75c8/GCA_026398835.1_ASM2639883v1_genomic.fna.gz]
[2023-06-27 17:17:55,247] [INFO] Query marker FASTA was written to GCA_026398835.1_ASM2639883v1_genomic.fna/markers.fasta
[2023-06-27 17:17:55,247] [INFO] Task started: Blastn
[2023-06-27 17:17:55,248] [INFO] Running command: blastn -query GCA_026398835.1_ASM2639883v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4225eb16-c680-4339-971d-fbd632a6dc73/dqc_reference/reference_markers.fasta -out GCA_026398835.1_ASM2639883v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 17:17:56,019] [INFO] Task succeeded: Blastn
[2023-06-27 17:17:56,025] [INFO] Selected 26 target genomes.
[2023-06-27 17:17:56,026] [INFO] Target genome list was writen to GCA_026398835.1_ASM2639883v1_genomic.fna/target_genomes.txt
[2023-06-27 17:17:56,031] [INFO] Task started: fastANI
[2023-06-27 17:17:56,031] [INFO] Running command: fastANI --query /var/lib/cwl/stgabbf8bae-7a61-4192-b45b-f93e8c1a75c8/GCA_026398835.1_ASM2639883v1_genomic.fna.gz --refList GCA_026398835.1_ASM2639883v1_genomic.fna/target_genomes.txt --output GCA_026398835.1_ASM2639883v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 17:18:21,037] [INFO] Task succeeded: fastANI
[2023-06-27 17:18:21,038] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4225eb16-c680-4339-971d-fbd632a6dc73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 17:18:21,039] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4225eb16-c680-4339-971d-fbd632a6dc73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 17:18:21,061] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 17:18:21,061] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 17:18:21,061] [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=CCUG 51522	GCA_008801525.1	163011	163011	type	True	85.592	675	825	95	below_threshold
Pseudomonas lini	strain=DSM 16768	GCA_001042905.1	163011	163011	type	True	85.5771	675	825	95	below_threshold
Pseudomonas farris	strain=SWRI79	GCA_019145235.1	2841207	2841207	type	True	85.5027	676	825	95	below_threshold
Pseudomonas chlororaphis subsp. piscium	strain=DSM 21509	GCA_001269555.1	1513890	587753	type	True	85.302	662	825	95	below_threshold
Pseudomonas chlororaphis subsp. piscium	strain=DSM 21509	GCA_003850345.1	1513890	587753	type	True	85.2676	665	825	95	below_threshold
Pseudomonas mandelii	strain=DSM 17967	GCA_007858265.1	75612	75612	suspected-type	True	85.1875	685	825	95	below_threshold
Pseudomonas mandelii	strain=NBRC 103147	GCA_002091695.1	75612	75612	suspected-type	True	85.0878	681	825	95	below_threshold
Pseudomonas kielensis	strain=MBT-1	GCA_014236655.1	2762577	2762577	type	True	84.8403	640	825	95	below_threshold
Pseudomonas jessenii	strain=DSM 17150	GCA_002236115.1	77298	77298	suspected-type	True	84.6818	668	825	95	below_threshold
Pseudomonas azerbaijanoriens	strain=SWRI123	GCA_019139795.1	2842350	2842350	type	True	84.5514	664	825	95	below_threshold
Pseudomonas reinekei	strain=MT1	GCA_001945365.1	395598	395598	type	True	84.5383	631	825	95	below_threshold
Pseudomonas mohnii	strain=DSM 18327	GCA_900105115.1	395600	395600	type	True	84.4734	673	825	95	below_threshold
Pseudomonas reinekei	strain=CCUG 53116	GCA_008801455.1	395598	395598	type	True	84.4637	636	825	95	below_threshold
Pseudomonas extremorientalis	strain=CCUG 51517	GCA_008801565.1	169669	169669	type	True	83.4884	604	825	95	below_threshold
Pseudomonas extremorientalis		GCA_900625005.1	169669	169669	type	True	83.4479	608	825	95	below_threshold
Pseudomonas extremorientalis	strain=LMG 19695	GCA_001870465.1	169669	169669	type	True	83.4304	604	825	95	below_threshold
Pseudomonas deceptionensis	strain=LMG 25555	GCA_900106095.1	882211	882211	type	True	82.4439	522	825	95	below_threshold
Pseudomonas deceptionensis	strain=DSM 26521	GCA_001042895.1	882211	882211	type	True	82.3678	525	825	95	below_threshold
Pseudomonas taetrolens	strain=DSM 21104	GCA_001042915.1	47884	47884	type	True	82.1271	474	825	95	below_threshold
Pseudomonas helleri	strain=DSM 29165	GCA_001043025.1	1608996	1608996	type	True	82.0509	484	825	95	below_threshold
Pseudomonas taetrolens	strain=NCTC10697	GCA_900475285.1	47884	47884	type	True	82.0416	479	825	95	below_threshold
Pseudomonas bharatica	strain=CSV86	GCA_000319305.2	2692112	2692112	type	True	81.017	488	825	95	below_threshold
Pseudomonas amygdali	strain=DSM 105780	GCA_022828345.1	47877	47877	pathovar	True	80.8963	457	825	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	80.8119	480	825	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	80.7797	497	825	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	80.7031	452	825	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 17:18:21,065] [INFO] DFAST Taxonomy check result was written to GCA_026398835.1_ASM2639883v1_genomic.fna/tc_result.tsv
[2023-06-27 17:18:21,066] [INFO] ===== Taxonomy check completed =====
[2023-06-27 17:18:21,066] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 17:18:21,066] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4225eb16-c680-4339-971d-fbd632a6dc73/dqc_reference/checkm_data
[2023-06-27 17:18:21,067] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 17:18:21,110] [INFO] Task started: CheckM
[2023-06-27 17:18:21,111] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026398835.1_ASM2639883v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026398835.1_ASM2639883v1_genomic.fna/checkm_input GCA_026398835.1_ASM2639883v1_genomic.fna/checkm_result
[2023-06-27 17:18:53,815] [INFO] Task succeeded: CheckM
[2023-06-27 17:18:53,817] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.11%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-27 17:18:53,840] [INFO] ===== Completeness check finished =====
[2023-06-27 17:18:53,840] [INFO] ===== Start GTDB Search =====
[2023-06-27 17:18:53,841] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026398835.1_ASM2639883v1_genomic.fna/markers.fasta)
[2023-06-27 17:18:53,841] [INFO] Task started: Blastn
[2023-06-27 17:18:53,841] [INFO] Running command: blastn -query GCA_026398835.1_ASM2639883v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4225eb16-c680-4339-971d-fbd632a6dc73/dqc_reference/reference_markers_gtdb.fasta -out GCA_026398835.1_ASM2639883v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 17:18:55,031] [INFO] Task succeeded: Blastn
[2023-06-27 17:18:55,036] [INFO] Selected 16 target genomes.
[2023-06-27 17:18:55,037] [INFO] Target genome list was writen to GCA_026398835.1_ASM2639883v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 17:18:55,148] [INFO] Task started: fastANI
[2023-06-27 17:18:55,148] [INFO] Running command: fastANI --query /var/lib/cwl/stgabbf8bae-7a61-4192-b45b-f93e8c1a75c8/GCA_026398835.1_ASM2639883v1_genomic.fna.gz --refList GCA_026398835.1_ASM2639883v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026398835.1_ASM2639883v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 17:19:12,989] [INFO] Task succeeded: fastANI
[2023-06-27 17:19:13,005] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 17:19:13,006] [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_902497875.1	s__Pseudomonas_E fluorescens_BR	88.3362	722	825	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_902497895.1	s__Pseudomonas_E fluorescens_BP	88.2473	706	825	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_003732225.1	s__Pseudomonas_E brassicacearum_E	86.234	696	825	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_001874645.1	s__Pseudomonas_E frederiksbergensis_B	86.055	660	825	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_001297125.1	s__Pseudomonas_E sp001297125	85.6869	682	825	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_000282195.1	s__Pseudomonas_E sp000282195	85.6596	682	825	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_001308855.1	s__Pseudomonas_E sp001308855	85.4071	685	825	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.04	96.24	0.91	0.89	3	-
GCF_003732705.1	s__Pseudomonas_E frederiksbergensis_F	85.2713	690	825	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.43	98.43	0.94	0.94	2	-
GCF_003850345.1	s__Pseudomonas_E chlororaphis_F	85.2676	665	825	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.16	95.02	0.90	0.86	82	-
GCF_002091715.1	s__Pseudomonas_E migulae	85.2442	656	825	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.54	99.09	0.95	0.90	3	-
GCF_003945765.1	s__Pseudomonas_E chlororaphis	85.1407	672	825	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.91	95.71	0.92	0.83	34	-
GCF_900187505.1	s__Pseudomonas_E sp900187505	85.0628	622	825	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.12	96.03	0.87	0.86	4	-
GCF_001921865.1	s__Pseudomonas_E chlororaphis_D	84.816	665	825	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_003731765.1	s__Pseudomonas_E chlororaphis_G	84.6514	636	825	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_001870465.1	s__Pseudomonas_E extremorientalis	83.4304	604	825	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.37	98.13	0.91	0.89	29	-
GCF_900106095.1	s__Pseudomonas_E deceptionensis	82.4544	521	825	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-27 17:19:13,008] [INFO] GTDB search result was written to GCA_026398835.1_ASM2639883v1_genomic.fna/result_gtdb.tsv
[2023-06-27 17:19:13,008] [INFO] ===== GTDB Search completed =====
[2023-06-27 17:19:13,013] [INFO] DFAST_QC result json was written to GCA_026398835.1_ASM2639883v1_genomic.fna/dqc_result.json
[2023-06-27 17:19:13,014] [INFO] DFAST_QC completed!
[2023-06-27 17:19:13,014] [INFO] Total running time: 0h1m30s