[2024-01-24 11:51:23,310] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:23,316] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:23,316] [INFO] DQC Reference Directory: /var/lib/cwl/stgdef13020-fbaa-4877-a422-c4d115749e28/dqc_reference
[2024-01-24 11:51:24,621] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:24,622] [INFO] Task started: Prodigal
[2024-01-24 11:51:24,622] [INFO] Running command: gunzip -c /var/lib/cwl/stg4af1ec9a-a142-4284-88c9-37533abf642c/GCF_014268495.2_ASM1426849v2_genomic.fna.gz | prodigal -d GCF_014268495.2_ASM1426849v2_genomic.fna/cds.fna -a GCF_014268495.2_ASM1426849v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:52,752] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:52,752] [INFO] Task started: HMMsearch
[2024-01-24 11:51:52,752] [INFO] Running command: hmmsearch --tblout GCF_014268495.2_ASM1426849v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdef13020-fbaa-4877-a422-c4d115749e28/dqc_reference/reference_markers.hmm GCF_014268495.2_ASM1426849v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:53,083] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:53,084] [INFO] Found 6/6 markers.
[2024-01-24 11:51:53,142] [INFO] Query marker FASTA was written to GCF_014268495.2_ASM1426849v2_genomic.fna/markers.fasta
[2024-01-24 11:51:53,143] [INFO] Task started: Blastn
[2024-01-24 11:51:53,143] [INFO] Running command: blastn -query GCF_014268495.2_ASM1426849v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgdef13020-fbaa-4877-a422-c4d115749e28/dqc_reference/reference_markers.fasta -out GCF_014268495.2_ASM1426849v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:54,202] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:54,205] [INFO] Selected 13 target genomes.
[2024-01-24 11:51:54,205] [INFO] Target genome list was writen to GCF_014268495.2_ASM1426849v2_genomic.fna/target_genomes.txt
[2024-01-24 11:51:54,210] [INFO] Task started: fastANI
[2024-01-24 11:51:54,211] [INFO] Running command: fastANI --query /var/lib/cwl/stg4af1ec9a-a142-4284-88c9-37533abf642c/GCF_014268495.2_ASM1426849v2_genomic.fna.gz --refList GCF_014268495.2_ASM1426849v2_genomic.fna/target_genomes.txt --output GCF_014268495.2_ASM1426849v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:17,182] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:17,182] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdef13020-fbaa-4877-a422-c4d115749e28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:17,182] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdef13020-fbaa-4877-a422-c4d115749e28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:17,194] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:52:17,194] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:17,194] [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 monsensis	strain=PGSB 8459	GCA_014268495.2	2745509	2745509	type	True	100.0	2139	2140	95	conclusive
Pseudomonas koreensis	strain=JCM 14769	GCA_014646955.1	198620	198620	suspected-type	True	90.21	1712	2140	95	below_threshold
Pseudomonas koreensis	strain=DSM 16610	GCA_012986595.1	198620	198620	suspected-type	True	90.205	1723	2140	95	below_threshold
Pseudomonas koreensis	strain=CCUG 51519	GCA_008801535.1	198620	198620	suspected-type	True	90.1973	1715	2140	95	below_threshold
Pseudomonas neuropathica	strain=P155	GCA_015461835.1	2730425	2730425	type	True	89.7636	1788	2140	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	89.6597	1833	2140	95	below_threshold
Pseudomonas crudilactis	strain=UCMA 17988	GCA_013433315.1	2697028	2697028	type	True	89.4801	1774	2140	95	below_threshold
Pseudomonas allokribbensis	strain=IzPS23	GCA_014863605.1	2774460	2774460	type	True	88.5215	1691	2140	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	88.4099	1674	2140	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	88.2921	1610	2140	95	below_threshold
Pseudomonas atacamensis	strain=M7D1	GCA_004801935.1	2565368	2565368	type	True	88.1003	1605	2140	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	83.4318	1294	2140	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	81.9786	851	2140	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:17,196] [INFO] DFAST Taxonomy check result was written to GCF_014268495.2_ASM1426849v2_genomic.fna/tc_result.tsv
[2024-01-24 11:52:17,196] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:17,196] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:17,196] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdef13020-fbaa-4877-a422-c4d115749e28/dqc_reference/checkm_data
[2024-01-24 11:52:17,197] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:17,257] [INFO] Task started: CheckM
[2024-01-24 11:52:17,258] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014268495.2_ASM1426849v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014268495.2_ASM1426849v2_genomic.fna/checkm_input GCF_014268495.2_ASM1426849v2_genomic.fna/checkm_result
[2024-01-24 11:53:38,172] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:38,173] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:38,201] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:38,201] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:38,201] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014268495.2_ASM1426849v2_genomic.fna/markers.fasta)
[2024-01-24 11:53:38,202] [INFO] Task started: Blastn
[2024-01-24 11:53:38,202] [INFO] Running command: blastn -query GCF_014268495.2_ASM1426849v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgdef13020-fbaa-4877-a422-c4d115749e28/dqc_reference/reference_markers_gtdb.fasta -out GCF_014268495.2_ASM1426849v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:40,106] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:40,110] [INFO] Selected 20 target genomes.
[2024-01-24 11:53:40,111] [INFO] Target genome list was writen to GCF_014268495.2_ASM1426849v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:40,127] [INFO] Task started: fastANI
[2024-01-24 11:53:40,128] [INFO] Running command: fastANI --query /var/lib/cwl/stg4af1ec9a-a142-4284-88c9-37533abf642c/GCF_014268495.2_ASM1426849v2_genomic.fna.gz --refList GCF_014268495.2_ASM1426849v2_genomic.fna/target_genomes_gtdb.txt --output GCF_014268495.2_ASM1426849v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:54:14,365] [INFO] Task succeeded: fastANI
[2024-01-24 11:54:14,392] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:54:14,392] [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_014268495.2	s__Pseudomonas_E fluorescens_BC	100.0	2138	2140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.66	98.66	0.95	0.95	2	conclusive
GCF_003999415.1	s__Pseudomonas_E koreensis_E	90.3433	1672	2140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.57	98.57	0.92	0.92	2	-
GCF_012986595.1	s__Pseudomonas_E koreensis	90.2124	1722	2140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.85	97.85	0.96	0.91	8	-
GCF_002878485.1	s__Pseudomonas_E sp002878485	89.972	1662	2140	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_004683905.1	s__Pseudomonas_E putida_A	89.9549	1757	2140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.80	95.08	0.93	0.90	22	-
GCF_003732425.1	s__Pseudomonas_E fluorescens_BE	89.7976	1762	2140	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_003061005.1	s__Pseudomonas_E sp003061005	89.7364	1600	2140	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_000292795.1	s__Pseudomonas_E fluorescens_H	89.7295	1768	2140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.99	97.99	0.94	0.93	3	-
GCF_002287825.1	s__Pseudomonas_E koreensis_B	89.654	1737	2140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.58	96.55	0.92	0.86	13	-
GCF_000633255.1	s__Pseudomonas_E sp000633255	89.6272	1722	2140	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_005938625.1	s__Pseudomonas_E fluorescens_BD	89.5741	1724	2140	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_018138145.1	s__Pseudomonas_E koreensis_A	89.5691	1789	2140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.53	97.00	0.95	0.94	5	-
GCF_902497745.1	s__Pseudomonas_E fluorescens_BM	89.4246	1755	2140	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_018326005.1	s__Pseudomonas_E sp002901475	89.3548	1777	2140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.45	98.45	0.94	0.94	2	-
GCF_004124275.1	s__Pseudomonas_E sp004124275	89.2442	1744	2140	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_011369485.1	s__Pseudomonas_E sp011369485	88.8934	1703	2140	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_004006335.1	s__Pseudomonas_E sp002112885	88.6795	1699	2140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.01	95.48	0.92	0.90	14	-
GCF_010448615.1	s__Pseudomonas_E sp001655595	88.4788	1689	2140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.61	96.24	0.94	0.90	22	-
GCF_001594225.2	s__Pseudomonas_E glycinae	88.3524	1678	2140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.56	95.98	0.93	0.88	9	-
GCF_900105805.1	s__Pseudomonas_E moraviensis_A	87.849	1640	2140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.79	98.30	0.96	0.94	7	-
--------------------------------------------------------------------------------
[2024-01-24 11:54:14,394] [INFO] GTDB search result was written to GCF_014268495.2_ASM1426849v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:54:14,395] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:54:14,399] [INFO] DFAST_QC result json was written to GCF_014268495.2_ASM1426849v2_genomic.fna/dqc_result.json
[2024-01-24 11:54:14,399] [INFO] DFAST_QC completed!
[2024-01-24 11:54:14,399] [INFO] Total running time: 0h2m51s