[2024-01-24 14:14:45,680] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:45,682] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:45,682] [INFO] DQC Reference Directory: /var/lib/cwl/stga852dc61-988a-4da8-abce-8d27a5f5a258/dqc_reference
[2024-01-24 14:14:46,900] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:46,901] [INFO] Task started: Prodigal
[2024-01-24 14:14:46,901] [INFO] Running command: gunzip -c /var/lib/cwl/stga40432e1-137d-4ca6-98f3-5df138cc2c95/GCF_900536025.1_PREIDCCOS865_genomic.fna.gz | prodigal -d GCF_900536025.1_PREIDCCOS865_genomic.fna/cds.fna -a GCF_900536025.1_PREIDCCOS865_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:07,751] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:07,751] [INFO] Task started: HMMsearch
[2024-01-24 14:15:07,751] [INFO] Running command: hmmsearch --tblout GCF_900536025.1_PREIDCCOS865_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga852dc61-988a-4da8-abce-8d27a5f5a258/dqc_reference/reference_markers.hmm GCF_900536025.1_PREIDCCOS865_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:08,086] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:08,088] [INFO] Found 6/6 markers.
[2024-01-24 14:15:08,144] [INFO] Query marker FASTA was written to GCF_900536025.1_PREIDCCOS865_genomic.fna/markers.fasta
[2024-01-24 14:15:08,144] [INFO] Task started: Blastn
[2024-01-24 14:15:08,144] [INFO] Running command: blastn -query GCF_900536025.1_PREIDCCOS865_genomic.fna/markers.fasta -db /var/lib/cwl/stga852dc61-988a-4da8-abce-8d27a5f5a258/dqc_reference/reference_markers.fasta -out GCF_900536025.1_PREIDCCOS865_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:09,277] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:09,280] [INFO] Selected 23 target genomes.
[2024-01-24 14:15:09,280] [INFO] Target genome list was writen to GCF_900536025.1_PREIDCCOS865_genomic.fna/target_genomes.txt
[2024-01-24 14:15:09,286] [INFO] Task started: fastANI
[2024-01-24 14:15:09,287] [INFO] Running command: fastANI --query /var/lib/cwl/stga40432e1-137d-4ca6-98f3-5df138cc2c95/GCF_900536025.1_PREIDCCOS865_genomic.fna.gz --refList GCF_900536025.1_PREIDCCOS865_genomic.fna/target_genomes.txt --output GCF_900536025.1_PREIDCCOS865_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:42,150] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:42,151] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga852dc61-988a-4da8-abce-8d27a5f5a258/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:42,151] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga852dc61-988a-4da8-abce-8d27a5f5a258/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:42,172] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:15:42,172] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:15:42,172] [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 faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	87.0587	1275	2033	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	87.0405	1341	2033	95	below_threshold
Pseudomonas muyukensis	strain=COW39	GCA_019139535.1	2842357	2842357	type	True	86.6413	1305	2033	95	below_threshold
Pseudomonas sichuanensis	strain=WCHPs060039	GCA_003231305.1	2213015	2213015	type	True	86.5979	1308	2033	95	below_threshold
Pseudomonas oryziphila	strain=1257	GCA_003940825.1	2894079	2894079	type	True	86.5798	1349	2033	95	below_threshold
Pseudomonas mosselii	strain=DSM 17497	GCA_000621225.1	78327	78327	type	True	86.419	1299	2033	95	below_threshold
Pseudomonas mosselii	strain=DSM 17497	GCA_019823065.1	78327	78327	type	True	86.3667	1317	2033	95	below_threshold
Pseudomonas entomophila	strain=L48	GCA_000026105.1	312306	312306	suspected-type	True	86.3634	1328	2033	95	below_threshold
Pseudomonas xanthosomae	strain=COR54	GCA_019139835.1	2842356	2842356	type	True	86.3063	1382	2033	95	below_threshold
Pseudomonas plecoglossicida	strain=NBRC 103162	GCA_000730665.1	70775	70775	suspected-type	True	86.2827	1237	2033	95	below_threshold
Pseudomonas plecoglossicida	strain=DSM 15088	GCA_000688275.1	70775	70775	suspected-type	True	86.2522	1249	2033	95	below_threshold
Pseudomonas fakonensis	strain=COW40	GCA_019139895.1	2842355	2842355	type	True	86.2521	1384	2033	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	86.1966	1283	2033	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_000731675.1	1495066	1495066	type	True	86.095	1393	2033	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	86.079	1323	2033	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	86.0042	1294	2033	95	below_threshold
Pseudomonas putida	strain=NCTC10936	GCA_900455645.1	303	303	suspected-type	True	85.857	1374	2033	95	below_threshold
Pseudomonas putida	strain=IPO3752	GCA_013387005.1	303	303	suspected-type	True	85.8537	1347	2033	95	below_threshold
Pseudomonas putida	strain=ATCC 12633	GCA_024508115.1	303	303	suspected-type	True	85.8516	1367	2033	95	below_threshold
Pseudomonas kermanshahensis	strain=SWRI100	GCA_014269205.2	2745482	2745482	type	True	85.8388	1389	2033	95	below_threshold
Pseudomonas putida	strain=NBRC 14164	GCA_000412675.1	303	303	suspected-type	True	85.811	1369	2033	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_013373895.1	2740516	2740516	type	True	85.2828	1256	2033	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_021602025.1	2740516	2740516	type	True	85.2691	1285	2033	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:42,176] [INFO] DFAST Taxonomy check result was written to GCF_900536025.1_PREIDCCOS865_genomic.fna/tc_result.tsv
[2024-01-24 14:15:42,177] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:42,177] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:42,177] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga852dc61-988a-4da8-abce-8d27a5f5a258/dqc_reference/checkm_data
[2024-01-24 14:15:42,178] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:42,235] [INFO] Task started: CheckM
[2024-01-24 14:15:42,236] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900536025.1_PREIDCCOS865_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900536025.1_PREIDCCOS865_genomic.fna/checkm_input GCF_900536025.1_PREIDCCOS865_genomic.fna/checkm_result
[2024-01-24 14:16:43,589] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:43,591] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:43,614] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:43,614] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:43,614] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900536025.1_PREIDCCOS865_genomic.fna/markers.fasta)
[2024-01-24 14:16:43,615] [INFO] Task started: Blastn
[2024-01-24 14:16:43,615] [INFO] Running command: blastn -query GCF_900536025.1_PREIDCCOS865_genomic.fna/markers.fasta -db /var/lib/cwl/stga852dc61-988a-4da8-abce-8d27a5f5a258/dqc_reference/reference_markers_gtdb.fasta -out GCF_900536025.1_PREIDCCOS865_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:45,723] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:45,727] [INFO] Selected 16 target genomes.
[2024-01-24 14:16:45,727] [INFO] Target genome list was writen to GCF_900536025.1_PREIDCCOS865_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:45,741] [INFO] Task started: fastANI
[2024-01-24 14:16:45,741] [INFO] Running command: fastANI --query /var/lib/cwl/stga40432e1-137d-4ca6-98f3-5df138cc2c95/GCF_900536025.1_PREIDCCOS865_genomic.fna.gz --refList GCF_900536025.1_PREIDCCOS865_genomic.fna/target_genomes_gtdb.txt --output GCF_900536025.1_PREIDCCOS865_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:17:11,182] [INFO] Task succeeded: fastANI
[2024-01-24 14:17:11,199] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:17:11,199] [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_900536025.1	s__Pseudomonas_E reidholzensis	100.0	2033	2033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017875955.1	s__Pseudomonas_E sp017875955	88.9892	1489	2033	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_014268815.2	s__Pseudomonas_E sp014268815	87.6387	1439	2033	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_015354575.1	s__Pseudomonas_E sp015354575	86.6479	1312	2033	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_002112505.1	s__Pseudomonas_E sp002112505	86.4788	1394	2033	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_002843585.1	s__Pseudomonas_E sp002843585	86.4768	1342	2033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.09	97.16	0.92	0.88	9	-
GCF_000282535.1	s__Pseudomonas_E sp000282535	86.4537	1181	2033	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_000621225.1	s__Pseudomonas_E mosselii	86.397	1301	2033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.55	97.48	0.92	0.90	14	-
GCF_000026105.1	s__Pseudomonas_E entomophila	86.3591	1328	2033	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_019139675.1	s__Pseudomonas_E sp019139675	86.3469	1297	2033	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_000730665.1	s__Pseudomonas_E plecoglossicida	86.2811	1237	2033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.81	99.74	0.97	0.95	6	-
GCF_000935045.1	s__Pseudomonas_E sp000935045	86.2744	1318	2033	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_011752525.1	s__Pseudomonas_E sp011752525	86.1717	1243	2033	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_016648105.1	s__Pseudomonas_E sp016648105	86.1492	1308	2033	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_002094795.1	s__Pseudomonas_E putida_K	85.8489	1250	2033	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	84.9825	1242	2033	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 14:17:11,201] [INFO] GTDB search result was written to GCF_900536025.1_PREIDCCOS865_genomic.fna/result_gtdb.tsv
[2024-01-24 14:17:11,201] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:17:11,205] [INFO] DFAST_QC result json was written to GCF_900536025.1_PREIDCCOS865_genomic.fna/dqc_result.json
[2024-01-24 14:17:11,206] [INFO] DFAST_QC completed!
[2024-01-24 14:17:11,206] [INFO] Total running time: 0h2m26s