[2024-01-24 14:55:08,257] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:08,259] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:08,259] [INFO] DQC Reference Directory: /var/lib/cwl/stg001048e6-a851-4b33-b3da-7c0c4b80aa6a/dqc_reference
[2024-01-24 14:55:09,927] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:09,928] [INFO] Task started: Prodigal
[2024-01-24 14:55:09,928] [INFO] Running command: gunzip -c /var/lib/cwl/stgf04b6727-d99d-406a-9b37-abcdf4f0b005/GCF_002866065.1_ASM286606v1_genomic.fna.gz | prodigal -d GCF_002866065.1_ASM286606v1_genomic.fna/cds.fna -a GCF_002866065.1_ASM286606v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:19,228] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:19,228] [INFO] Task started: HMMsearch
[2024-01-24 14:55:19,228] [INFO] Running command: hmmsearch --tblout GCF_002866065.1_ASM286606v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg001048e6-a851-4b33-b3da-7c0c4b80aa6a/dqc_reference/reference_markers.hmm GCF_002866065.1_ASM286606v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:19,505] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:19,507] [INFO] Found 6/6 markers.
[2024-01-24 14:55:19,533] [INFO] Query marker FASTA was written to GCF_002866065.1_ASM286606v1_genomic.fna/markers.fasta
[2024-01-24 14:55:19,534] [INFO] Task started: Blastn
[2024-01-24 14:55:19,534] [INFO] Running command: blastn -query GCF_002866065.1_ASM286606v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg001048e6-a851-4b33-b3da-7c0c4b80aa6a/dqc_reference/reference_markers.fasta -out GCF_002866065.1_ASM286606v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:20,464] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:20,468] [INFO] Selected 23 target genomes.
[2024-01-24 14:55:20,468] [INFO] Target genome list was writen to GCF_002866065.1_ASM286606v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:20,490] [INFO] Task started: fastANI
[2024-01-24 14:55:20,490] [INFO] Running command: fastANI --query /var/lib/cwl/stgf04b6727-d99d-406a-9b37-abcdf4f0b005/GCF_002866065.1_ASM286606v1_genomic.fna.gz --refList GCF_002866065.1_ASM286606v1_genomic.fna/target_genomes.txt --output GCF_002866065.1_ASM286606v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:39,417] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:39,418] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg001048e6-a851-4b33-b3da-7c0c4b80aa6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:39,418] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg001048e6-a851-4b33-b3da-7c0c4b80aa6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:39,441] [INFO] Found 23 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:55:39,442] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:39,442] [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
Thiopseudomonas denitrificans	strain=X2	GCA_002866065.1	1501432	1501432	type	True	100.0	943	943	95	conclusive
Thiopseudomonas denitrificans	strain=DSM 28679	GCA_004363035.1	1501432	1501432	type	True	99.9676	925	943	95	conclusive
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	78.8363	307	943	95	below_threshold
Pseudomonas flexibilis	strain=ATCC 29606	GCA_900155995.1	706570	706570	type	True	78.7451	313	943	95	below_threshold
Pseudomonas flexibilis	strain=ATCC 29606	GCA_000802425.1	706570	706570	type	True	78.7329	314	943	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	78.7035	316	943	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	78.665	303	943	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	78.636	313	943	95	below_threshold
Pseudomonas linyingensis	strain=LMG 25967	GCA_900109175.1	915471	915471	type	True	78.6249	319	943	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	78.6054	301	943	95	below_threshold
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	78.514	325	943	95	below_threshold
Pseudomonas carbonaria	strain=CIP 111764	GCA_904061905.1	2762745	2762745	type	True	78.499	313	943	95	below_threshold
Pseudomonas argentinensis	strain=CCUG 50743	GCA_008801645.1	289370	289370	type	True	78.2111	288	943	95	below_threshold
Stutzerimonas azotifigens	strain=DSM 17556	GCA_000425625.1	291995	291995	type	True	78.2093	305	943	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	78.2048	281	943	95	below_threshold
Pseudomonas campi	strain=S1-A32-2	GCA_013200955.2	2731681	2731681	type	True	78.161	303	943	95	below_threshold
Pseudomonas saudiphocaensis	strain=20_BN	GCA_000756775.2	1499686	1499686	type	True	78.1394	255	943	95	below_threshold
Pseudomonas argentinensis	strain=LMG 22563	GCA_900113905.1	289370	289370	type	True	78.1384	287	943	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	78.1352	263	943	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	77.9417	297	943	95	below_threshold
Pseudomonas punonensis	strain=CECT 8089	GCA_900142655.1	1220495	1220495	type	True	77.9128	244	943	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	77.8623	238	943	95	below_threshold
Pseudomonas kairouanensis	strain=KC12	GCA_004682055.1	2293832	2293832	type	True	77.5792	228	943	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:39,444] [INFO] DFAST Taxonomy check result was written to GCF_002866065.1_ASM286606v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:39,444] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:39,444] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:39,445] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg001048e6-a851-4b33-b3da-7c0c4b80aa6a/dqc_reference/checkm_data
[2024-01-24 14:55:39,446] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:39,478] [INFO] Task started: CheckM
[2024-01-24 14:55:39,478] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002866065.1_ASM286606v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002866065.1_ASM286606v1_genomic.fna/checkm_input GCF_002866065.1_ASM286606v1_genomic.fna/checkm_result
[2024-01-24 14:56:12,327] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:12,329] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:12,350] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:12,350] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:12,351] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002866065.1_ASM286606v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:12,351] [INFO] Task started: Blastn
[2024-01-24 14:56:12,352] [INFO] Running command: blastn -query GCF_002866065.1_ASM286606v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg001048e6-a851-4b33-b3da-7c0c4b80aa6a/dqc_reference/reference_markers_gtdb.fasta -out GCF_002866065.1_ASM286606v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:13,862] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:13,865] [INFO] Selected 20 target genomes.
[2024-01-24 14:56:13,865] [INFO] Target genome list was writen to GCF_002866065.1_ASM286606v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:13,882] [INFO] Task started: fastANI
[2024-01-24 14:56:13,882] [INFO] Running command: fastANI --query /var/lib/cwl/stgf04b6727-d99d-406a-9b37-abcdf4f0b005/GCF_002866065.1_ASM286606v1_genomic.fna.gz --refList GCF_002866065.1_ASM286606v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002866065.1_ASM286606v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:29,233] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:29,251] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:29,251] [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_002866065.1	s__Thiopseudomonas denitrificans	100.0	943	943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Thiopseudomonas	95.0	99.98	99.98	0.99	0.99	2	conclusive
GCA_012728415.1	s__Thiopseudomonas sp012728415	81.9462	578	943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Thiopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018384595.1	s__Thiopseudomonas sp018384595	80.9173	481	943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Thiopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019097855.1	s__Pseudomonas_K sp019097855	78.6788	303	943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109175.1	s__Pseudomonas_K linyingensis	78.6381	317	943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009799925.1	s__Pseudomonas_E sp009799925	78.5737	337	943	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_005508865.1	s__Pseudomonas_E sp005508865	78.5289	311	943	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_904061905.1	s__Pseudomonas_E carbonaria	78.5111	311	943	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_002304225.1	s__Pseudomonas_E sp002304225	78.49	275	943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.09	95.09	0.93	0.93	2	-
GCF_001839655.1	s__Pseudomonas_E argentinensis_B	78.4568	285	943	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_001592875.1	s__Pseudomonas_E sp001592875	78.4455	288	943	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_015070855.1	s__Pseudomonas_A lopnurensis	78.3596	324	943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.76	98.41	0.83	0.83	4	-
GCF_014490745.1	s__Pseudomonas_E alcaligenes_C	78.2808	329	943	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_013522825.1	s__Pseudomonas_A stutzeri_AK	78.2547	301	943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425625.1	s__Pseudomonas_N azotifigens	78.2214	304	943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000364625.1	s__Pseudomonas_E thermotolerans	78.1756	285	943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.25	99.24	0.93	0.93	3	-
GCF_900113905.1	s__Pseudomonas_E argentinensis	78.1255	288	943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000282535.1	s__Pseudomonas_E sp000282535	78.1148	247	943	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_902506535.1	s__Pseudomonas_E sp902506535	78.0072	256	943	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_001547895.1	s__Pseudomonas_E sp001547895	77.7811	269	943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.12	98.88	0.95	0.94	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:29,253] [INFO] GTDB search result was written to GCF_002866065.1_ASM286606v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:29,254] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:29,258] [INFO] DFAST_QC result json was written to GCF_002866065.1_ASM286606v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:29,258] [INFO] DFAST_QC completed!
[2024-01-24 14:56:29,258] [INFO] Total running time: 0h1m21s