[2024-01-24 13:26:26,326] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:26:26,327] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:26:26,328] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f18f0a5-29ee-4fa7-a31a-e4ced8fdec8b/dqc_reference
[2024-01-24 13:26:27,494] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:26:27,495] [INFO] Task started: Prodigal
[2024-01-24 13:26:27,495] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb0c407a-6fd6-4ea3-b3a3-5e35467571f3/GCF_000730665.1_ASM73066v1_genomic.fna.gz | prodigal -d GCF_000730665.1_ASM73066v1_genomic.fna/cds.fna -a GCF_000730665.1_ASM73066v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:44,460] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:44,461] [INFO] Task started: HMMsearch
[2024-01-24 13:26:44,461] [INFO] Running command: hmmsearch --tblout GCF_000730665.1_ASM73066v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f18f0a5-29ee-4fa7-a31a-e4ced8fdec8b/dqc_reference/reference_markers.hmm GCF_000730665.1_ASM73066v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:44,779] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:44,781] [INFO] Found 6/6 markers.
[2024-01-24 13:26:44,834] [INFO] Query marker FASTA was written to GCF_000730665.1_ASM73066v1_genomic.fna/markers.fasta
[2024-01-24 13:26:44,834] [INFO] Task started: Blastn
[2024-01-24 13:26:44,835] [INFO] Running command: blastn -query GCF_000730665.1_ASM73066v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f18f0a5-29ee-4fa7-a31a-e4ced8fdec8b/dqc_reference/reference_markers.fasta -out GCF_000730665.1_ASM73066v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:45,962] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:45,966] [INFO] Selected 12 target genomes.
[2024-01-24 13:26:45,966] [INFO] Target genome list was writen to GCF_000730665.1_ASM73066v1_genomic.fna/target_genomes.txt
[2024-01-24 13:26:46,186] [INFO] Task started: fastANI
[2024-01-24 13:26:46,186] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb0c407a-6fd6-4ea3-b3a3-5e35467571f3/GCF_000730665.1_ASM73066v1_genomic.fna.gz --refList GCF_000730665.1_ASM73066v1_genomic.fna/target_genomes.txt --output GCF_000730665.1_ASM73066v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:27:02,245] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:02,245] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f18f0a5-29ee-4fa7-a31a-e4ced8fdec8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:27:02,246] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f18f0a5-29ee-4fa7-a31a-e4ced8fdec8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:27:02,256] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:27:02,256] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:27:02,256] [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 plecoglossicida	strain=NBRC 103162	GCA_000730665.1	70775	70775	suspected-type	True	100.0	1729	1733	95	conclusive
Pseudomonas plecoglossicida	strain=DSM 15088	GCA_000688275.1	70775	70775	suspected-type	True	99.993	1721	1733	95	conclusive
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	90.6206	1365	1733	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	90.6113	1437	1733	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_021602025.1	2740516	2740516	type	True	87.6906	1318	1733	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_013373895.1	2740516	2740516	type	True	87.6476	1306	1733	95	below_threshold
Pseudomonas anuradhapurensis	strain=RD8MR3	GCA_014269225.2	485870	485870	type	True	87.4421	1285	1733	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	87.4337	1209	1733	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_000731675.1	1495066	1495066	type	True	87.2999	1336	1733	95	below_threshold
Pseudomonas oryzicola	strain=RD9SR1	GCA_014269185.2	485876	485876	type	True	87.1465	1262	1733	95	below_threshold
Pseudomonas kermanshahensis	strain=SWRI100	GCA_014269205.2	2745482	2745482	type	True	87.0249	1328	1733	95	below_threshold
Pseudomonas xantholysinigenes	strain=RW9S1A	GCA_014268885.2	2745490	2745490	type	True	86.8491	1238	1733	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:27:02,258] [INFO] DFAST Taxonomy check result was written to GCF_000730665.1_ASM73066v1_genomic.fna/tc_result.tsv
[2024-01-24 13:27:02,258] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:27:02,259] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:27:02,259] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f18f0a5-29ee-4fa7-a31a-e4ced8fdec8b/dqc_reference/checkm_data
[2024-01-24 13:27:02,260] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:27:02,309] [INFO] Task started: CheckM
[2024-01-24 13:27:02,309] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000730665.1_ASM73066v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000730665.1_ASM73066v1_genomic.fna/checkm_input GCF_000730665.1_ASM73066v1_genomic.fna/checkm_result
[2024-01-24 13:27:54,743] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:54,745] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:54,768] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:54,768] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:54,769] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000730665.1_ASM73066v1_genomic.fna/markers.fasta)
[2024-01-24 13:27:54,769] [INFO] Task started: Blastn
[2024-01-24 13:27:54,769] [INFO] Running command: blastn -query GCF_000730665.1_ASM73066v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f18f0a5-29ee-4fa7-a31a-e4ced8fdec8b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000730665.1_ASM73066v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:56,812] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:56,816] [INFO] Selected 15 target genomes.
[2024-01-24 13:27:56,817] [INFO] Target genome list was writen to GCF_000730665.1_ASM73066v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:57,045] [INFO] Task started: fastANI
[2024-01-24 13:27:57,045] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb0c407a-6fd6-4ea3-b3a3-5e35467571f3/GCF_000730665.1_ASM73066v1_genomic.fna.gz --refList GCF_000730665.1_ASM73066v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000730665.1_ASM73066v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:28:18,399] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:18,416] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:28:18,417] [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_000730665.1	s__Pseudomonas_E plecoglossicida	100.0	1729	1733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.81	99.74	0.97	0.95	6	conclusive
GCF_000282535.1	s__Pseudomonas_E sp000282535	91.4888	1337	1733	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_013373935.1	s__Pseudomonas_E sp002438125	90.6256	1365	1733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.14	98.14	0.84	0.84	2	-
GCF_002112505.1	s__Pseudomonas_E sp002112505	88.6078	1396	1733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	0.99	6	-
GCF_002025705.1	s__Pseudomonas_E putida_J	88.3213	1385	1733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.29	96.26	0.90	0.90	5	-
GCF_001642705.1	s__Pseudomonas_E sp001642705	88.0403	1301	1733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.26	95.01	0.89	0.85	3	-
GCF_000935045.1	s__Pseudomonas_E sp000935045	87.8683	1324	1733	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_001320525.1	s__Pseudomonas_E sp001320525	87.6841	1283	1733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.10	98.78	0.89	0.86	10	-
GCF_016648105.1	s__Pseudomonas_E sp016648105	87.51	1233	1733	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_000019445.1	s__Pseudomonas_E putida_E	87.3941	1305	1733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.71	96.19	0.87	0.82	12	-
GCF_000731675.1	s__Pseudomonas_E capeferrum	87.2998	1336	1733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.03	98.55	0.93	0.90	7	-
GCF_014269185.2	s__Pseudomonas_E sp014269185	87.1581	1261	1733	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_002736125.1	s__Pseudomonas_E putida_M	87.0945	1350	1733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.41	97.25	0.91	0.90	8	-
GCF_014268885.2	s__Pseudomonas_E sp014268885	86.8615	1236	1733	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_004357765.1	s__Pseudomonas_E putida_U	86.2878	1215	1733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.43	99.43	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:28:18,418] [INFO] GTDB search result was written to GCF_000730665.1_ASM73066v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:28:18,419] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:28:18,424] [INFO] DFAST_QC result json was written to GCF_000730665.1_ASM73066v1_genomic.fna/dqc_result.json
[2024-01-24 13:28:18,424] [INFO] DFAST_QC completed!
[2024-01-24 13:28:18,424] [INFO] Total running time: 0h1m52s