[2024-01-24 13:58:40,715] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:40,717] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:40,718] [INFO] DQC Reference Directory: /var/lib/cwl/stgd5a46ba7-9972-4cc1-8407-1f62f8643ae6/dqc_reference
[2024-01-24 13:58:41,971] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:41,972] [INFO] Task started: Prodigal
[2024-01-24 13:58:41,972] [INFO] Running command: gunzip -c /var/lib/cwl/stgacc6b9eb-18b8-4fab-b2d5-ceb007ed0ac2/GCF_014646955.1_ASM1464695v1_genomic.fna.gz | prodigal -d GCF_014646955.1_ASM1464695v1_genomic.fna/cds.fna -a GCF_014646955.1_ASM1464695v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:59:02,693] [INFO] Task succeeded: Prodigal
[2024-01-24 13:59:02,693] [INFO] Task started: HMMsearch
[2024-01-24 13:59:02,694] [INFO] Running command: hmmsearch --tblout GCF_014646955.1_ASM1464695v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd5a46ba7-9972-4cc1-8407-1f62f8643ae6/dqc_reference/reference_markers.hmm GCF_014646955.1_ASM1464695v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:59:03,074] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:59:03,075] [INFO] Found 6/6 markers.
[2024-01-24 13:59:03,283] [INFO] Query marker FASTA was written to GCF_014646955.1_ASM1464695v1_genomic.fna/markers.fasta
[2024-01-24 13:59:03,284] [INFO] Task started: Blastn
[2024-01-24 13:59:03,284] [INFO] Running command: blastn -query GCF_014646955.1_ASM1464695v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd5a46ba7-9972-4cc1-8407-1f62f8643ae6/dqc_reference/reference_markers.fasta -out GCF_014646955.1_ASM1464695v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:04,195] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:04,199] [INFO] Selected 13 target genomes.
[2024-01-24 13:59:04,199] [INFO] Target genome list was writen to GCF_014646955.1_ASM1464695v1_genomic.fna/target_genomes.txt
[2024-01-24 13:59:04,208] [INFO] Task started: fastANI
[2024-01-24 13:59:04,208] [INFO] Running command: fastANI --query /var/lib/cwl/stgacc6b9eb-18b8-4fab-b2d5-ceb007ed0ac2/GCF_014646955.1_ASM1464695v1_genomic.fna.gz --refList GCF_014646955.1_ASM1464695v1_genomic.fna/target_genomes.txt --output GCF_014646955.1_ASM1464695v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:26,391] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:26,392] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd5a46ba7-9972-4cc1-8407-1f62f8643ae6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:26,393] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd5a46ba7-9972-4cc1-8407-1f62f8643ae6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:26,405] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:59:26,405] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:59:26,406] [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=JCM 14769	GCA_014646955.1	198620	198620	suspected-type	True	100.0	2008	2008	95	conclusive
Pseudomonas koreensis	strain=CCUG 51519	GCA_008801535.1	198620	198620	suspected-type	True	99.9949	2002	2008	95	conclusive
Pseudomonas koreensis	strain=DSM 16610	GCA_012986595.1	198620	198620	suspected-type	True	99.9918	2008	2008	95	conclusive
Pseudomonas monsensis	strain=PGSB 8459	GCA_014268495.2	2745509	2745509	type	True	90.1763	1714	2008	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	89.0363	1738	2008	95	below_threshold
Pseudomonas crudilactis	strain=UCMA 17988	GCA_013433315.1	2697028	2697028	type	True	88.9194	1715	2008	95	below_threshold
Pseudomonas kribbensis	strain=46-2	GCA_003352185.1	1628086	1628086	type	True	88.8828	1658	2008	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	88.7872	1612	2008	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	88.7573	1672	2008	95	below_threshold
Pseudomonas iranensis	strain=SWRI54	GCA_014268585.2	2745503	2745503	type	True	88.0981	1564	2008	95	below_threshold
Pseudomonas triticicola	strain=SWRI88	GCA_019145375.1	2842345	2842345	type	True	88.0837	1537	2008	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	83.4796	1271	2008	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	83.4618	1329	2008	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:26,407] [INFO] DFAST Taxonomy check result was written to GCF_014646955.1_ASM1464695v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:26,408] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:26,408] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:26,408] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd5a46ba7-9972-4cc1-8407-1f62f8643ae6/dqc_reference/checkm_data
[2024-01-24 13:59:26,409] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:26,464] [INFO] Task started: CheckM
[2024-01-24 13:59:26,465] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014646955.1_ASM1464695v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014646955.1_ASM1464695v1_genomic.fna/checkm_input GCF_014646955.1_ASM1464695v1_genomic.fna/checkm_result
[2024-01-24 14:00:29,296] [INFO] Task succeeded: CheckM
[2024-01-24 14:00:29,297] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:00:29,323] [INFO] ===== Completeness check finished =====
[2024-01-24 14:00:29,323] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:00:29,323] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014646955.1_ASM1464695v1_genomic.fna/markers.fasta)
[2024-01-24 14:00:29,324] [INFO] Task started: Blastn
[2024-01-24 14:00:29,324] [INFO] Running command: blastn -query GCF_014646955.1_ASM1464695v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd5a46ba7-9972-4cc1-8407-1f62f8643ae6/dqc_reference/reference_markers_gtdb.fasta -out GCF_014646955.1_ASM1464695v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:31,183] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:31,187] [INFO] Selected 14 target genomes.
[2024-01-24 14:00:31,187] [INFO] Target genome list was writen to GCF_014646955.1_ASM1464695v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:31,200] [INFO] Task started: fastANI
[2024-01-24 14:00:31,200] [INFO] Running command: fastANI --query /var/lib/cwl/stgacc6b9eb-18b8-4fab-b2d5-ceb007ed0ac2/GCF_014646955.1_ASM1464695v1_genomic.fna.gz --refList GCF_014646955.1_ASM1464695v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014646955.1_ASM1464695v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:56,454] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:56,466] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:56,466] [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	99.9918	2008	2008	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	92.908	1725	2008	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	92.3388	1672	2008	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	92.1373	1779	2008	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_000633255.1	s__Pseudomonas_E sp000633255	92.1079	1748	2008	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	92.0572	1732	2008	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	92.0373	1764	2008	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	91.9615	1740	2008	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	91.7457	1751	2008	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	91.5925	1631	2008	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	90.1878	1713	2008	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	89.3995	1713	2008	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	89.1245	1702	2008	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	88.6991	1666	2008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:56,477] [INFO] GTDB search result was written to GCF_014646955.1_ASM1464695v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:56,478] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:56,482] [INFO] DFAST_QC result json was written to GCF_014646955.1_ASM1464695v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:56,482] [INFO] DFAST_QC completed!
[2024-01-24 14:00:56,482] [INFO] Total running time: 0h2m16s