[2023-06-30 17:28:53,582] [INFO] DFAST_QC pipeline started.
[2023-06-30 17:28:53,584] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 17:28:53,585] [INFO] DQC Reference Directory: /var/lib/cwl/stgada5898f-88ab-4635-979b-4b5739660382/dqc_reference
[2023-06-30 17:28:54,769] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 17:28:54,770] [INFO] Task started: Prodigal
[2023-06-30 17:28:54,771] [INFO] Running command: gunzip -c /var/lib/cwl/stgdc2d0af1-8964-4c8d-952e-135ffa7b2bb5/GCA_019459245.1_ASM1945924v1_genomic.fna.gz | prodigal -d GCA_019459245.1_ASM1945924v1_genomic.fna/cds.fna -a GCA_019459245.1_ASM1945924v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 17:29:19,370] [INFO] Task succeeded: Prodigal
[2023-06-30 17:29:19,371] [INFO] Task started: HMMsearch
[2023-06-30 17:29:19,371] [INFO] Running command: hmmsearch --tblout GCA_019459245.1_ASM1945924v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgada5898f-88ab-4635-979b-4b5739660382/dqc_reference/reference_markers.hmm GCA_019459245.1_ASM1945924v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 17:29:19,660] [INFO] Task succeeded: HMMsearch
[2023-06-30 17:29:19,661] [INFO] Found 6/6 markers.
[2023-06-30 17:29:19,715] [INFO] Query marker FASTA was written to GCA_019459245.1_ASM1945924v1_genomic.fna/markers.fasta
[2023-06-30 17:29:19,715] [INFO] Task started: Blastn
[2023-06-30 17:29:19,715] [INFO] Running command: blastn -query GCA_019459245.1_ASM1945924v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgada5898f-88ab-4635-979b-4b5739660382/dqc_reference/reference_markers.fasta -out GCA_019459245.1_ASM1945924v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 17:29:20,637] [INFO] Task succeeded: Blastn
[2023-06-30 17:29:20,641] [INFO] Selected 16 target genomes.
[2023-06-30 17:29:20,642] [INFO] Target genome list was writen to GCA_019459245.1_ASM1945924v1_genomic.fna/target_genomes.txt
[2023-06-30 17:29:20,645] [INFO] Task started: fastANI
[2023-06-30 17:29:20,645] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc2d0af1-8964-4c8d-952e-135ffa7b2bb5/GCA_019459245.1_ASM1945924v1_genomic.fna.gz --refList GCA_019459245.1_ASM1945924v1_genomic.fna/target_genomes.txt --output GCA_019459245.1_ASM1945924v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 17:29:44,082] [INFO] Task succeeded: fastANI
[2023-06-30 17:29:44,083] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgada5898f-88ab-4635-979b-4b5739660382/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 17:29:44,083] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgada5898f-88ab-4635-979b-4b5739660382/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 17:29:44,096] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 17:29:44,096] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 17:29:44,097] [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 protegens	strain=CHA0	GCA_000397205.1	380021	380021	type	True	90.631	1896	2196	95	below_threshold
Pseudomonas protegens	strain=CHA0	GCA_900560965.1	380021	380021	type	True	90.584	1904	2196	95	below_threshold
Pseudomonas sessilinigenes	strain=CMR12a	GCA_003850565.1	658629	658629	type	True	87.2919	1733	2196	95	below_threshold
Pseudomonas sessilinigenes	strain=CMR12a	GCA_019139855.1	658629	658629	type	True	87.235	1717	2196	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=NBRC 3521	GCA_000813225.1	587851	587753	type	True	86.2004	1568	2196	95	below_threshold
Pseudomonas chlororaphis subsp. piscium	strain=DSM 21509	GCA_001269555.1	1513890	587753	type	True	86.1949	1594	2196	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=LMG 1245	GCA_001269575.1	587851	587753	type	True	86.1825	1566	2196	95	below_threshold
Pseudomonas chlororaphis subsp. piscium	strain=DSM 21509	GCA_003850345.1	1513890	587753	type	True	86.1799	1576	2196	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=DSM 6698	GCA_003851905.1	587851	587753	type	True	86.171	1598	2196	95	below_threshold
Pseudomonas chlororaphis subsp. aurantiaca	strain=DSM 19603	GCA_003851835.1	86192	587753	type	True	86.1389	1601	2196	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	83.2346	1308	2196	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	83.2092	1298	2196	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	81.9972	1028	2196	95	below_threshold
Pseudomonas bharatica	strain=CSV86	GCA_000319305.2	2692112	2692112	type	True	81.9835	1085	2196	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	81.9146	1090	2196	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	81.4233	941	2196	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 17:29:44,099] [INFO] DFAST Taxonomy check result was written to GCA_019459245.1_ASM1945924v1_genomic.fna/tc_result.tsv
[2023-06-30 17:29:44,099] [INFO] ===== Taxonomy check completed =====
[2023-06-30 17:29:44,099] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 17:29:44,100] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgada5898f-88ab-4635-979b-4b5739660382/dqc_reference/checkm_data
[2023-06-30 17:29:44,101] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 17:29:44,159] [INFO] Task started: CheckM
[2023-06-30 17:29:44,159] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019459245.1_ASM1945924v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019459245.1_ASM1945924v1_genomic.fna/checkm_input GCA_019459245.1_ASM1945924v1_genomic.fna/checkm_result
[2023-06-30 17:30:55,824] [INFO] Task succeeded: CheckM
[2023-06-30 17:30:55,825] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 17:30:55,847] [INFO] ===== Completeness check finished =====
[2023-06-30 17:30:55,847] [INFO] ===== Start GTDB Search =====
[2023-06-30 17:30:55,848] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019459245.1_ASM1945924v1_genomic.fna/markers.fasta)
[2023-06-30 17:30:55,848] [INFO] Task started: Blastn
[2023-06-30 17:30:55,848] [INFO] Running command: blastn -query GCA_019459245.1_ASM1945924v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgada5898f-88ab-4635-979b-4b5739660382/dqc_reference/reference_markers_gtdb.fasta -out GCA_019459245.1_ASM1945924v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 17:30:57,501] [INFO] Task succeeded: Blastn
[2023-06-30 17:30:57,505] [INFO] Selected 9 target genomes.
[2023-06-30 17:30:57,505] [INFO] Target genome list was writen to GCA_019459245.1_ASM1945924v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 17:30:57,510] [INFO] Task started: fastANI
[2023-06-30 17:30:57,510] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc2d0af1-8964-4c8d-952e-135ffa7b2bb5/GCA_019459245.1_ASM1945924v1_genomic.fna.gz --refList GCA_019459245.1_ASM1945924v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019459245.1_ASM1945924v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 17:31:13,691] [INFO] Task succeeded: fastANI
[2023-06-30 17:31:13,700] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 17:31:13,700] [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_003363755.1	s__Pseudomonas_E protegens_A	97.6349	2049	2196	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.07	97.56	0.94	0.93	12	conclusive
GCF_003732485.1	s__Pseudomonas_E protegens_B	94.3025	1977	2196	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_013407925.2	s__Pseudomonas_E fluorescens_AP	92.2924	1903	2196	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	98.42	0.98	0.91	6	-
GCF_001547895.1	s__Pseudomonas_E sp001547895	91.8709	1995	2196	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.12	98.88	0.95	0.94	4	-
GCF_900105185.1	s__Pseudomonas_E saponiphila	91.2647	1854	2196	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.25	98.25	0.89	0.89	5	-
GCF_000397205.1	s__Pseudomonas_E protegens	90.6461	1894	2196	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.81	97.08	0.96	0.89	76	-
GCF_009861525.1	s__Pseudomonas_E sp009861525	90.2259	1816	2196	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_000633395.1	s__Pseudomonas_E sp000633395	89.421	1919	2196	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_003850565.1	s__Pseudomonas_E sp001705835	87.2812	1734	2196	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.20	98.99	0.91	0.87	6	-
--------------------------------------------------------------------------------
[2023-06-30 17:31:13,702] [INFO] GTDB search result was written to GCA_019459245.1_ASM1945924v1_genomic.fna/result_gtdb.tsv
[2023-06-30 17:31:13,703] [INFO] ===== GTDB Search completed =====
[2023-06-30 17:31:13,706] [INFO] DFAST_QC result json was written to GCA_019459245.1_ASM1945924v1_genomic.fna/dqc_result.json
[2023-06-30 17:31:13,706] [INFO] DFAST_QC completed!
[2023-06-30 17:31:13,706] [INFO] Total running time: 0h2m20s