[2024-01-24 13:57:42,073] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:42,075] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:42,075] [INFO] DQC Reference Directory: /var/lib/cwl/stga3add49c-c7c3-4cb3-92d0-2a722b2123c9/dqc_reference
[2024-01-24 13:57:43,393] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:43,393] [INFO] Task started: Prodigal
[2024-01-24 13:57:43,394] [INFO] Running command: gunzip -c /var/lib/cwl/stgddd63ef2-6cd4-41e0-99b3-c85514e1dba6/GCF_012986595.1_ASM1298659v1_genomic.fna.gz | prodigal -d GCF_012986595.1_ASM1298659v1_genomic.fna/cds.fna -a GCF_012986595.1_ASM1298659v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:04,249] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:04,249] [INFO] Task started: HMMsearch
[2024-01-24 13:58:04,250] [INFO] Running command: hmmsearch --tblout GCF_012986595.1_ASM1298659v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3add49c-c7c3-4cb3-92d0-2a722b2123c9/dqc_reference/reference_markers.hmm GCF_012986595.1_ASM1298659v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:04,596] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:04,598] [INFO] Found 6/6 markers.
[2024-01-24 13:58:04,646] [INFO] Query marker FASTA was written to GCF_012986595.1_ASM1298659v1_genomic.fna/markers.fasta
[2024-01-24 13:58:04,646] [INFO] Task started: Blastn
[2024-01-24 13:58:04,647] [INFO] Running command: blastn -query GCF_012986595.1_ASM1298659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3add49c-c7c3-4cb3-92d0-2a722b2123c9/dqc_reference/reference_markers.fasta -out GCF_012986595.1_ASM1298659v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:05,769] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:05,774] [INFO] Selected 16 target genomes.
[2024-01-24 13:58:05,774] [INFO] Target genome list was writen to GCF_012986595.1_ASM1298659v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:05,788] [INFO] Task started: fastANI
[2024-01-24 13:58:05,788] [INFO] Running command: fastANI --query /var/lib/cwl/stgddd63ef2-6cd4-41e0-99b3-c85514e1dba6/GCF_012986595.1_ASM1298659v1_genomic.fna.gz --refList GCF_012986595.1_ASM1298659v1_genomic.fna/target_genomes.txt --output GCF_012986595.1_ASM1298659v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:36,609] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:36,609] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3add49c-c7c3-4cb3-92d0-2a722b2123c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:36,610] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3add49c-c7c3-4cb3-92d0-2a722b2123c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:36,622] [INFO] Found 16 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:58:36,622] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:36,623] [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 koreensis	strain=DSM 16610	GCA_012986595.1	198620	198620	suspected-type	True	100.0	2017	2018	95	conclusive
Pseudomonas koreensis	strain=CCUG 51519	GCA_008801535.1	198620	198620	suspected-type	True	99.9928	2014	2018	95	conclusive
Pseudomonas koreensis	strain=JCM 14769	GCA_014646955.1	198620	198620	suspected-type	True	99.988	2006	2018	95	conclusive
Pseudomonas monsensis	strain=PGSB 8459	GCA_014268495.2	2745509	2745509	type	True	90.2018	1707	2018	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	89.0128	1736	2018	95	below_threshold
Pseudomonas baetica	strain=LMG 25716	GCA_002813455.1	674054	674054	type	True	88.9568	1686	2018	95	below_threshold
Pseudomonas baetica	strain=a390	GCA_003031005.1	674054	674054	type	True	88.9045	1660	2018	95	below_threshold
Pseudomonas crudilactis	strain=UCMA 17988	GCA_013433315.1	2697028	2697028	type	True	88.8984	1730	2018	95	below_threshold
Pseudomonas kribbensis	strain=46-2	GCA_003352185.1	1628086	1628086	type	True	88.8907	1663	2018	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	88.8117	1695	2018	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	88.7868	1612	2018	95	below_threshold
Pseudomonas iranensis	strain=SWRI54	GCA_014268585.2	2745503	2745503	type	True	88.0808	1579	2018	95	below_threshold
Pseudomonas triticicola	strain=SWRI88	GCA_019145375.1	2842345	2842345	type	True	88.0434	1531	2018	95	below_threshold
Pseudomonas hamedanensis	strain=SWRI65	GCA_014268595.2	2745504	2745504	type	True	87.8551	1565	2018	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	83.601	1307	2018	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	83.5566	1269	2018	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:36,624] [INFO] DFAST Taxonomy check result was written to GCF_012986595.1_ASM1298659v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:36,625] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:36,625] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:36,625] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3add49c-c7c3-4cb3-92d0-2a722b2123c9/dqc_reference/checkm_data
[2024-01-24 13:58:36,626] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:36,686] [INFO] Task started: CheckM
[2024-01-24 13:58:36,686] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012986595.1_ASM1298659v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012986595.1_ASM1298659v1_genomic.fna/checkm_input GCF_012986595.1_ASM1298659v1_genomic.fna/checkm_result
[2024-01-24 13:59:37,270] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:37,271] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:37,296] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:37,296] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:37,297] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012986595.1_ASM1298659v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:37,297] [INFO] Task started: Blastn
[2024-01-24 13:59:37,297] [INFO] Running command: blastn -query GCF_012986595.1_ASM1298659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3add49c-c7c3-4cb3-92d0-2a722b2123c9/dqc_reference/reference_markers_gtdb.fasta -out GCF_012986595.1_ASM1298659v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:39,140] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:39,144] [INFO] Selected 15 target genomes.
[2024-01-24 13:59:39,144] [INFO] Target genome list was writen to GCF_012986595.1_ASM1298659v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:39,167] [INFO] Task started: fastANI
[2024-01-24 13:59:39,168] [INFO] Running command: fastANI --query /var/lib/cwl/stgddd63ef2-6cd4-41e0-99b3-c85514e1dba6/GCF_012986595.1_ASM1298659v1_genomic.fna.gz --refList GCF_012986595.1_ASM1298659v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012986595.1_ASM1298659v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:06,064] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:06,079] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:06,080] [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_012986595.1	s__Pseudomonas_E koreensis	100.0	2017	2018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.85	97.85	0.96	0.91	8	conclusive
GCF_003999415.1	s__Pseudomonas_E koreensis_E	92.911	1730	2018	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_002878485.1	s__Pseudomonas_E sp002878485	92.3676	1694	2018	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_000633255.1	s__Pseudomonas_E sp000633255	92.1273	1736	2018	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_000631985.1	s__Pseudomonas_E sp000631985	92.0978	1740	2018	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	92.0564	1794	2018	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_000292795.1	s__Pseudomonas_E fluorescens_H	92.0272	1791	2018	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_000282275.2	s__Pseudomonas_E sp000282275	91.9785	1743	2018	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_002287825.1	s__Pseudomonas_E koreensis_B	91.7629	1758	2018	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_003061005.1	s__Pseudomonas_E sp003061005	91.6044	1623	2018	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_014268495.2	s__Pseudomonas_E fluorescens_BC	90.2018	1707	2018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.66	98.66	0.95	0.95	2	-
GCF_018326005.1	s__Pseudomonas_E sp002901475	89.4258	1735	2018	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_016651305.1	s__Pseudomonas_E sp016651305	89.177	1716	2018	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_014472415.1	s__Pseudomonas_E sp014472415	88.9411	1619	2018	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_002813455.1	s__Pseudomonas_E baetica	88.9397	1688	2018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.98	95.55	0.93	0.86	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:06,082] [INFO] GTDB search result was written to GCF_012986595.1_ASM1298659v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:06,082] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:06,089] [INFO] DFAST_QC result json was written to GCF_012986595.1_ASM1298659v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:06,089] [INFO] DFAST_QC completed!
[2024-01-24 14:00:06,089] [INFO] Total running time: 0h2m24s