[2024-01-24 13:57:42,932] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:42,934] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:42,934] [INFO] DQC Reference Directory: /var/lib/cwl/stga48bc1f5-1c56-4d34-a9c7-22cea34e89d3/dqc_reference
[2024-01-24 13:57:44,187] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:44,188] [INFO] Task started: Prodigal
[2024-01-24 13:57:44,188] [INFO] Running command: gunzip -c /var/lib/cwl/stgf718764a-72f5-4f0d-a35b-bd719b240126/GCF_000237065.1_ASM23706v1_genomic.fna.gz | prodigal -d GCF_000237065.1_ASM23706v1_genomic.fna/cds.fna -a GCF_000237065.1_ASM23706v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:08,403] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:08,404] [INFO] Task started: HMMsearch
[2024-01-24 13:58:08,404] [INFO] Running command: hmmsearch --tblout GCF_000237065.1_ASM23706v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga48bc1f5-1c56-4d34-a9c7-22cea34e89d3/dqc_reference/reference_markers.hmm GCF_000237065.1_ASM23706v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:08,788] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:08,790] [INFO] Found 6/6 markers.
[2024-01-24 13:58:08,844] [INFO] Query marker FASTA was written to GCF_000237065.1_ASM23706v1_genomic.fna/markers.fasta
[2024-01-24 13:58:08,844] [INFO] Task started: Blastn
[2024-01-24 13:58:08,844] [INFO] Running command: blastn -query GCF_000237065.1_ASM23706v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga48bc1f5-1c56-4d34-a9c7-22cea34e89d3/dqc_reference/reference_markers.fasta -out GCF_000237065.1_ASM23706v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:09,864] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:09,869] [INFO] Selected 14 target genomes.
[2024-01-24 13:58:09,869] [INFO] Target genome list was writen to GCF_000237065.1_ASM23706v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:09,881] [INFO] Task started: fastANI
[2024-01-24 13:58:09,881] [INFO] Running command: fastANI --query /var/lib/cwl/stgf718764a-72f5-4f0d-a35b-bd719b240126/GCF_000237065.1_ASM23706v1_genomic.fna.gz --refList GCF_000237065.1_ASM23706v1_genomic.fna/target_genomes.txt --output GCF_000237065.1_ASM23706v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:37,545] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:37,545] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga48bc1f5-1c56-4d34-a9c7-22cea34e89d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:37,546] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga48bc1f5-1c56-4d34-a9c7-22cea34e89d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:37,562] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:58:37,563] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:58:37,563] [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 kilonensis	strain=DSM 13647	GCA_001269885.1	132476	132476	type	True	95.9503	1841	2281	95	inconclusive
Pseudomonas brassicacearum subsp. brassicacearum	strain=CCUG 51508	GCA_008801605.1	86264	930166	type	True	95.1694	1926	2281	95	inconclusive
Pseudomonas brassicacearum	strain=JCM 11938	GCA_012034345.1	930166	930166	suspected-type	True	95.1493	1928	2281	95	inconclusive
Pseudomonas thivervalensis	strain=DSM 13194	GCA_001269655.1	86265	86265	type	True	92.4588	1844	2281	95	below_threshold
Pseudomonas bijieensis	strain=L22-9	GCA_013347965.1	2681983	2681983	type	True	92.1287	1876	2281	95	below_threshold
Pseudomonas zanjanensis	strain=SWRI12	GCA_014268745.2	2745496	2745496	type	True	91.8802	1766	2281	95	below_threshold
Pseudomonas viciae	strain=11K1	GCA_004786035.1	2505979	2505979	type	True	90.0691	1797	2281	95	below_threshold
Pseudomonas rhizophila	strain=S211	GCA_003033885.1	2045200	2045200	type	True	88.6913	1676	2281	95	below_threshold
Pseudomonas marvdashtae	strain=SWRI102	GCA_014268655.2	2745500	2745500	type	True	88.3252	1582	2281	95	below_threshold
Pseudomonas tehranensis	strain=SWRI196	GCA_014268615.1	2745502	2745502	type	True	88.146	1448	2281	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	84.5926	1344	2281	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	83.7307	1347	2281	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	83.414	1251	2281	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	83.3544	1218	2281	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:37,565] [INFO] DFAST Taxonomy check result was written to GCF_000237065.1_ASM23706v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:37,565] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:37,565] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:37,565] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga48bc1f5-1c56-4d34-a9c7-22cea34e89d3/dqc_reference/checkm_data
[2024-01-24 13:58:37,567] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:37,630] [INFO] Task started: CheckM
[2024-01-24 13:58:37,631] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000237065.1_ASM23706v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000237065.1_ASM23706v1_genomic.fna/checkm_input GCF_000237065.1_ASM23706v1_genomic.fna/checkm_result
[2024-01-24 13:59:50,059] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:50,061] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:50,093] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:50,093] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:50,094] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000237065.1_ASM23706v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:50,094] [INFO] Task started: Blastn
[2024-01-24 13:59:50,095] [INFO] Running command: blastn -query GCF_000237065.1_ASM23706v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga48bc1f5-1c56-4d34-a9c7-22cea34e89d3/dqc_reference/reference_markers_gtdb.fasta -out GCF_000237065.1_ASM23706v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:51,842] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:51,846] [INFO] Selected 8 target genomes.
[2024-01-24 13:59:51,846] [INFO] Target genome list was writen to GCF_000237065.1_ASM23706v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:51,854] [INFO] Task started: fastANI
[2024-01-24 13:59:51,854] [INFO] Running command: fastANI --query /var/lib/cwl/stgf718764a-72f5-4f0d-a35b-bd719b240126/GCF_000237065.1_ASM23706v1_genomic.fna.gz --refList GCF_000237065.1_ASM23706v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000237065.1_ASM23706v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:12,773] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:12,787] [INFO] Found 8 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 14:00:12,788] [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_001269885.1	s__Pseudomonas_E kilonensis	95.9257	1843	2281	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.12	95.91	0.90	0.87	15	inconclusive
GCF_008801605.1	s__Pseudomonas_E brassicacearum	95.1724	1925	2281	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.43	96.48	0.95	0.86	21	inconclusive
GCF_009601685.2	s__Pseudomonas_E kilonensis_B	93.7872	1879	2281	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.30	99.26	0.94	0.93	4	-
GCF_001623525.1	s__Pseudomonas_E fluorescens_Q	93.6539	1882	2281	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.03	97.11	0.90	0.89	14	-
GCF_018325905.1	s__Pseudomonas_E sp018325905	93.648	1882	2281	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_900581005.1	s__Pseudomonas_E sp900581005	92.5776	1815	2281	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_001269655.1	s__Pseudomonas_E thivervalensis	92.4504	1845	2281	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.35	98.81	0.96	0.93	6	-
GCF_001307275.1	s__Pseudomonas_E fluorescens_AA	92.2311	1879	2281	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.99	95.90	0.90	0.85	18	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:12,789] [INFO] GTDB search result was written to GCF_000237065.1_ASM23706v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:12,790] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:12,793] [INFO] DFAST_QC result json was written to GCF_000237065.1_ASM23706v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:12,793] [INFO] DFAST_QC completed!
[2024-01-24 14:00:12,793] [INFO] Total running time: 0h2m30s