[2024-01-24 12:23:50,900] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:50,902] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:50,902] [INFO] DQC Reference Directory: /var/lib/cwl/stg564507dc-8042-4842-b610-8696b1de4000/dqc_reference
[2024-01-24 12:23:52,185] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:52,186] [INFO] Task started: Prodigal
[2024-01-24 12:23:52,187] [INFO] Running command: gunzip -c /var/lib/cwl/stgad8c7018-cc74-4822-9888-13df9b43cf88/GCF_014268755.2_ASM1426875v2_genomic.fna.gz | prodigal -d GCF_014268755.2_ASM1426875v2_genomic.fna/cds.fna -a GCF_014268755.2_ASM1426875v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:24:16,566] [INFO] Task succeeded: Prodigal
[2024-01-24 12:24:16,566] [INFO] Task started: HMMsearch
[2024-01-24 12:24:16,566] [INFO] Running command: hmmsearch --tblout GCF_014268755.2_ASM1426875v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg564507dc-8042-4842-b610-8696b1de4000/dqc_reference/reference_markers.hmm GCF_014268755.2_ASM1426875v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:24:16,898] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:24:16,900] [INFO] Found 6/6 markers.
[2024-01-24 12:24:16,955] [INFO] Query marker FASTA was written to GCF_014268755.2_ASM1426875v2_genomic.fna/markers.fasta
[2024-01-24 12:24:16,955] [INFO] Task started: Blastn
[2024-01-24 12:24:16,956] [INFO] Running command: blastn -query GCF_014268755.2_ASM1426875v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg564507dc-8042-4842-b610-8696b1de4000/dqc_reference/reference_markers.fasta -out GCF_014268755.2_ASM1426875v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:18,002] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:18,006] [INFO] Selected 18 target genomes.
[2024-01-24 12:24:18,006] [INFO] Target genome list was writen to GCF_014268755.2_ASM1426875v2_genomic.fna/target_genomes.txt
[2024-01-24 12:24:18,012] [INFO] Task started: fastANI
[2024-01-24 12:24:18,012] [INFO] Running command: fastANI --query /var/lib/cwl/stgad8c7018-cc74-4822-9888-13df9b43cf88/GCF_014268755.2_ASM1426875v2_genomic.fna.gz --refList GCF_014268755.2_ASM1426875v2_genomic.fna/target_genomes.txt --output GCF_014268755.2_ASM1426875v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:24:42,504] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:42,504] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg564507dc-8042-4842-b610-8696b1de4000/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:24:42,505] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg564507dc-8042-4842-b610-8696b1de4000/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:24:42,525] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:24:42,525] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:24:42,525] [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 fuscovaginae	strain=LMG 2158	GCA_900108595.1	50340	50340	suspected-type	True	88.8667	1680	2342	95	below_threshold
Pseudomonas batumici	strain=UCM B-321	GCA_000820515.1	226910	226910	type	True	85.9388	1377	2342	95	below_threshold
Pseudomonas agarici	strain=LMG 2112	GCA_900109755.1	46677	46677	type	True	84.998	1189	2342	95	below_threshold
Pseudomonas agarici	strain=IPO3740	GCA_013385305.1	46677	46677	type	True	84.9657	1192	2342	95	below_threshold
Pseudomonas agarici	strain=NCPPB 2289	GCA_000280785.1	46677	46677	type	True	84.9038	1201	2342	95	below_threshold
Pseudomonas ekonensis	strain=COR58	GCA_019145435.1	2842353	2842353	type	True	84.6091	1343	2342	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=NBRC 3521	GCA_000813225.1	587851	587753	type	True	84.4882	1403	2342	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=DSM 6698	GCA_003851905.1	587851	587753	type	True	84.467	1444	2342	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=LMG 1245	GCA_001269575.1	587851	587753	type	True	84.4372	1421	2342	95	below_threshold
Pseudomonas chlororaphis subsp. aurantiaca	strain=DSM 19603	GCA_003851835.1	86192	587753	type	True	84.3796	1456	2342	95	below_threshold
Pseudomonas protegens	strain=CHA0	GCA_000397205.1	380021	380021	type	True	83.9425	1434	2342	95	below_threshold
Pseudomonas protegens	strain=CHA0	GCA_900560965.1	380021	380021	type	True	83.9362	1437	2342	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	82.8737	1105	2342	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	82.865	1057	2342	95	below_threshold
Pseudomonas bharatica	strain=CSV86	GCA_000319305.2	2692112	2692112	type	True	82.7176	1176	2342	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	82.0342	1015	2342	95	below_threshold
Pseudomonas baltica	strain=MBT-2	GCA_014235765.1	2762576	2762576	type	True	81.7408	858	2342	95	below_threshold
Pseudomonas cavernicola	strain=K1S02-6	GCA_003596405.1	2320866	2320866	type	True	80.4624	806	2342	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:24:42,527] [INFO] DFAST Taxonomy check result was written to GCF_014268755.2_ASM1426875v2_genomic.fna/tc_result.tsv
[2024-01-24 12:24:42,527] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:24:42,527] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:24:42,528] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg564507dc-8042-4842-b610-8696b1de4000/dqc_reference/checkm_data
[2024-01-24 12:24:42,529] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:24:42,590] [INFO] Task started: CheckM
[2024-01-24 12:24:42,590] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014268755.2_ASM1426875v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014268755.2_ASM1426875v2_genomic.fna/checkm_input GCF_014268755.2_ASM1426875v2_genomic.fna/checkm_result
[2024-01-24 12:26:02,428] [INFO] Task succeeded: CheckM
[2024-01-24 12:26:02,430] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:26:02,457] [INFO] ===== Completeness check finished =====
[2024-01-24 12:26:02,457] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:26:02,458] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014268755.2_ASM1426875v2_genomic.fna/markers.fasta)
[2024-01-24 12:26:02,458] [INFO] Task started: Blastn
[2024-01-24 12:26:02,458] [INFO] Running command: blastn -query GCF_014268755.2_ASM1426875v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg564507dc-8042-4842-b610-8696b1de4000/dqc_reference/reference_markers_gtdb.fasta -out GCF_014268755.2_ASM1426875v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:26:04,377] [INFO] Task succeeded: Blastn
[2024-01-24 12:26:04,382] [INFO] Selected 8 target genomes.
[2024-01-24 12:26:04,382] [INFO] Target genome list was writen to GCF_014268755.2_ASM1426875v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:26:04,389] [INFO] Task started: fastANI
[2024-01-24 12:26:04,389] [INFO] Running command: fastANI --query /var/lib/cwl/stgad8c7018-cc74-4822-9888-13df9b43cf88/GCF_014268755.2_ASM1426875v2_genomic.fna.gz --refList GCF_014268755.2_ASM1426875v2_genomic.fna/target_genomes_gtdb.txt --output GCF_014268755.2_ASM1426875v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:26:19,462] [INFO] Task succeeded: fastANI
[2024-01-24 12:26:19,473] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:26:19,473] [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_014268755.2	s__Pseudomonas_E sp014268755	100.0	2341	2342	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_000364705.1	s__Pseudomonas_E fuscovaginae_A	92.1654	1734	2342	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_001293465.1	s__Pseudomonas_E fuscovaginae_B	90.8732	1896	2342	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.24	99.24	0.95	0.95	2	-
GCF_900105475.1	s__Pseudomonas_E asplenii	88.7638	1695	2342	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.96	97.58	0.90	0.87	7	-
GCF_013386115.1	s__Pseudomonas_E gingeri_B	87.4893	1699	2342	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.74	98.43	0.94	0.92	9	-
GCF_013385635.1	s__Pseudomonas_E gingeri_A	87.2744	1676	2342	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.63	99.24	0.97	0.93	14	-
GCF_000820515.1	s__Pseudomonas_E batumici	85.9328	1381	2342	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_000931465.1	s__Pseudomonas_E sp000931465	84.55	1384	2342	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.57	98.57	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:26:19,475] [INFO] GTDB search result was written to GCF_014268755.2_ASM1426875v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:26:19,476] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:26:19,479] [INFO] DFAST_QC result json was written to GCF_014268755.2_ASM1426875v2_genomic.fna/dqc_result.json
[2024-01-24 12:26:19,479] [INFO] DFAST_QC completed!
[2024-01-24 12:26:19,479] [INFO] Total running time: 0h2m29s