[2024-01-24 15:27:20,830] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:20,833] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:20,833] [INFO] DQC Reference Directory: /var/lib/cwl/stg2252ecf8-8948-44a3-a95d-8bc661c3a9e6/dqc_reference
[2024-01-24 15:27:23,293] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:23,295] [INFO] Task started: Prodigal
[2024-01-24 15:27:23,295] [INFO] Running command: gunzip -c /var/lib/cwl/stgb90a9d26-9383-4f8f-ab57-4b452a40a6d4/GCF_014863605.1_ASM1486360v1_genomic.fna.gz | prodigal -d GCF_014863605.1_ASM1486360v1_genomic.fna/cds.fna -a GCF_014863605.1_ASM1486360v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:47,046] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:47,046] [INFO] Task started: HMMsearch
[2024-01-24 15:27:47,046] [INFO] Running command: hmmsearch --tblout GCF_014863605.1_ASM1486360v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2252ecf8-8948-44a3-a95d-8bc661c3a9e6/dqc_reference/reference_markers.hmm GCF_014863605.1_ASM1486360v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:47,413] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:47,414] [INFO] Found 6/6 markers.
[2024-01-24 15:27:47,469] [INFO] Query marker FASTA was written to GCF_014863605.1_ASM1486360v1_genomic.fna/markers.fasta
[2024-01-24 15:27:47,470] [INFO] Task started: Blastn
[2024-01-24 15:27:47,470] [INFO] Running command: blastn -query GCF_014863605.1_ASM1486360v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2252ecf8-8948-44a3-a95d-8bc661c3a9e6/dqc_reference/reference_markers.fasta -out GCF_014863605.1_ASM1486360v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:48,522] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:48,525] [INFO] Selected 13 target genomes.
[2024-01-24 15:27:48,526] [INFO] Target genome list was writen to GCF_014863605.1_ASM1486360v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:48,533] [INFO] Task started: fastANI
[2024-01-24 15:27:48,534] [INFO] Running command: fastANI --query /var/lib/cwl/stgb90a9d26-9383-4f8f-ab57-4b452a40a6d4/GCF_014863605.1_ASM1486360v1_genomic.fna.gz --refList GCF_014863605.1_ASM1486360v1_genomic.fna/target_genomes.txt --output GCF_014863605.1_ASM1486360v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:28:10,233] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:10,233] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2252ecf8-8948-44a3-a95d-8bc661c3a9e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:28:10,234] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2252ecf8-8948-44a3-a95d-8bc661c3a9e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:28:10,246] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:28:10,246] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:28:10,246] [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 allokribbensis	strain=IzPS23	GCA_014863605.1	2774460	2774460	type	True	100.0	2184	2188	95	conclusive
Pseudomonas kribbensis	strain=46-2	GCA_003352185.1	1628086	1628086	type	True	93.4125	1900	2188	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	91.7248	1773	2188	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	91.5474	1705	2188	95	below_threshold
Pseudomonas koreensis	strain=CCUG 51519	GCA_008801535.1	198620	198620	suspected-type	True	88.9112	1697	2188	95	below_threshold
Pseudomonas koreensis	strain=DSM 16610	GCA_012986595.1	198620	198620	suspected-type	True	88.8752	1702	2188	95	below_threshold
Pseudomonas koreensis	strain=JCM 14769	GCA_014646955.1	198620	198620	suspected-type	True	88.8665	1706	2188	95	below_threshold
Pseudomonas monsensis	strain=PGSB 8459	GCA_014268495.2	2745509	2745509	type	True	88.4501	1681	2188	95	below_threshold
Pseudomonas zeae	strain=OE 48.2	GCA_014268485.2	2745510	2745510	type	True	88.3261	1693	2188	95	below_threshold
Pseudomonas neuropathica	strain=P155	GCA_015461835.1	2730425	2730425	type	True	88.1011	1698	2188	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	88.051	1721	2188	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	83.6485	1303	2188	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	82.326	859	2188	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:28:10,249] [INFO] DFAST Taxonomy check result was written to GCF_014863605.1_ASM1486360v1_genomic.fna/tc_result.tsv
[2024-01-24 15:28:10,250] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:28:10,250] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:28:10,250] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2252ecf8-8948-44a3-a95d-8bc661c3a9e6/dqc_reference/checkm_data
[2024-01-24 15:28:10,252] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:28:10,319] [INFO] Task started: CheckM
[2024-01-24 15:28:10,319] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014863605.1_ASM1486360v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014863605.1_ASM1486360v1_genomic.fna/checkm_input GCF_014863605.1_ASM1486360v1_genomic.fna/checkm_result
[2024-01-24 15:29:27,341] [INFO] Task succeeded: CheckM
[2024-01-24 15:29:27,343] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:29:27,371] [INFO] ===== Completeness check finished =====
[2024-01-24 15:29:27,372] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:29:27,373] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014863605.1_ASM1486360v1_genomic.fna/markers.fasta)
[2024-01-24 15:29:27,374] [INFO] Task started: Blastn
[2024-01-24 15:29:27,374] [INFO] Running command: blastn -query GCF_014863605.1_ASM1486360v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2252ecf8-8948-44a3-a95d-8bc661c3a9e6/dqc_reference/reference_markers_gtdb.fasta -out GCF_014863605.1_ASM1486360v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:29:29,266] [INFO] Task succeeded: Blastn
[2024-01-24 15:29:29,269] [INFO] Selected 12 target genomes.
[2024-01-24 15:29:29,270] [INFO] Target genome list was writen to GCF_014863605.1_ASM1486360v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:29:29,284] [INFO] Task started: fastANI
[2024-01-24 15:29:29,284] [INFO] Running command: fastANI --query /var/lib/cwl/stgb90a9d26-9383-4f8f-ab57-4b452a40a6d4/GCF_014863605.1_ASM1486360v1_genomic.fna.gz --refList GCF_014863605.1_ASM1486360v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014863605.1_ASM1486360v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:29:51,049] [INFO] Task succeeded: fastANI
[2024-01-24 15:29:51,062] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:29:51,062] [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_014863605.1	s__Pseudomonas_E allokribbensis	100.0	2185	2188	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.79	97.76	0.93	0.92	10	conclusive
GCF_002112385.1	s__Pseudomonas_E sp002112385	93.5702	1868	2188	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	7	-
GCF_003352185.1	s__Pseudomonas_E kribbensis	93.4126	1900	2188	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.22	95.68	0.92	0.89	10	-
GCF_012974785.1	s__Pseudomonas_E fluorescens_BT	92.6588	1854	2188	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.87	98.87	0.96	0.96	2	-
GCF_004006335.1	s__Pseudomonas_E sp002112885	92.2976	1847	2188	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_003352875.1	s__Pseudomonas_E fluorescens_BF	91.9887	1830	2188	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_002113125.1	s__Pseudomonas_E sp002113125	91.7787	1768	2188	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_002113045.1	s__Pseudomonas_E sp002113045	91.4865	1732	2188	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.93	98.93	0.93	0.93	2	-
GCF_004683905.1	s__Pseudomonas_E putida_A	88.8456	1707	2188	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_003061005.1	s__Pseudomonas_E sp003061005	88.7977	1605	2188	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	88.7822	1722	2188	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_002878485.1	s__Pseudomonas_E sp002878485	88.729	1666	2188	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:29:51,064] [INFO] GTDB search result was written to GCF_014863605.1_ASM1486360v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:29:51,064] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:29:51,068] [INFO] DFAST_QC result json was written to GCF_014863605.1_ASM1486360v1_genomic.fna/dqc_result.json
[2024-01-24 15:29:51,068] [INFO] DFAST_QC completed!
[2024-01-24 15:29:51,069] [INFO] Total running time: 0h2m30s