[2023-06-27 00:33:14,906] [INFO] DFAST_QC pipeline started.
[2023-06-27 00:33:14,910] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 00:33:14,910] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ba42346-09d6-49fd-8250-b3cf095c9efa/dqc_reference
[2023-06-27 00:33:16,279] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 00:33:16,280] [INFO] Task started: Prodigal
[2023-06-27 00:33:16,280] [INFO] Running command: gunzip -c /var/lib/cwl/stg9a92db3c-8327-48aa-965d-3b0441a21523/GCA_002340175.1_ASM234017v1_genomic.fna.gz | prodigal -d GCA_002340175.1_ASM234017v1_genomic.fna/cds.fna -a GCA_002340175.1_ASM234017v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 00:33:22,197] [INFO] Task succeeded: Prodigal
[2023-06-27 00:33:22,198] [INFO] Task started: HMMsearch
[2023-06-27 00:33:22,198] [INFO] Running command: hmmsearch --tblout GCA_002340175.1_ASM234017v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ba42346-09d6-49fd-8250-b3cf095c9efa/dqc_reference/reference_markers.hmm GCA_002340175.1_ASM234017v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 00:33:22,456] [INFO] Task succeeded: HMMsearch
[2023-06-27 00:33:22,458] [INFO] Found 6/6 markers.
[2023-06-27 00:33:22,492] [INFO] Query marker FASTA was written to GCA_002340175.1_ASM234017v1_genomic.fna/markers.fasta
[2023-06-27 00:33:22,492] [INFO] Task started: Blastn
[2023-06-27 00:33:22,492] [INFO] Running command: blastn -query GCA_002340175.1_ASM234017v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ba42346-09d6-49fd-8250-b3cf095c9efa/dqc_reference/reference_markers.fasta -out GCA_002340175.1_ASM234017v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 00:33:23,115] [INFO] Task succeeded: Blastn
[2023-06-27 00:33:23,121] [INFO] Selected 12 target genomes.
[2023-06-27 00:33:23,121] [INFO] Target genome list was writen to GCA_002340175.1_ASM234017v1_genomic.fna/target_genomes.txt
[2023-06-27 00:33:23,126] [INFO] Task started: fastANI
[2023-06-27 00:33:23,127] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a92db3c-8327-48aa-965d-3b0441a21523/GCA_002340175.1_ASM234017v1_genomic.fna.gz --refList GCA_002340175.1_ASM234017v1_genomic.fna/target_genomes.txt --output GCA_002340175.1_ASM234017v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 00:33:30,922] [INFO] Task succeeded: fastANI
[2023-06-27 00:33:30,923] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ba42346-09d6-49fd-8250-b3cf095c9efa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 00:33:30,923] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ba42346-09d6-49fd-8250-b3cf095c9efa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 00:33:30,937] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2023-06-27 00:33:30,937] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-27 00:33:30,938] [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
Psychrobacter sanguinis	strain=FDAARGOS_1598	GCA_020736705.1	861445	861445	type	True	96.6055	871	966	95	conclusive
Psychrobacter phenylpyruvicus	strain=NBRC 102152	GCA_001591185.1	29432	29432	type	True	82.3769	589	966	95	below_threshold
Psychrobacter phenylpyruvicus	strain=NCTC10526	GCA_900455955.1	29432	29432	type	True	82.3625	632	966	95	below_threshold
Psychrobacter phenylpyruvicus	strain=DSM 7000	GCA_000685805.1	29432	29432	type	True	82.3562	602	966	95	below_threshold
Psychrobacter lutiphocae	strain=DSM 21542	GCA_000382145.1	540500	540500	type	True	78.6732	286	966	95	below_threshold
Psychrobacter coccoides	strain=F1192	GCA_017498085.1	2818440	2818440	type	True	77.672	98	966	95	below_threshold
Psychrobacter faecalis	strain=DSM 14664	GCA_016107575.1	180588	180588	type	True	77.3825	148	966	95	below_threshold
Psychrobacter arcticus	strain=273-4	GCA_000012305.1	334543	334543	type	True	77.328	131	966	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 00:33:30,940] [INFO] DFAST Taxonomy check result was written to GCA_002340175.1_ASM234017v1_genomic.fna/tc_result.tsv
[2023-06-27 00:33:30,941] [INFO] ===== Taxonomy check completed =====
[2023-06-27 00:33:30,941] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 00:33:30,941] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ba42346-09d6-49fd-8250-b3cf095c9efa/dqc_reference/checkm_data
[2023-06-27 00:33:30,942] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 00:33:30,978] [INFO] Task started: CheckM
[2023-06-27 00:33:30,979] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002340175.1_ASM234017v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002340175.1_ASM234017v1_genomic.fna/checkm_input GCA_002340175.1_ASM234017v1_genomic.fna/checkm_result
[2023-06-27 00:33:54,924] [INFO] Task succeeded: CheckM
[2023-06-27 00:33:54,926] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.12%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 00:33:54,950] [INFO] ===== Completeness check finished =====
[2023-06-27 00:33:54,951] [INFO] ===== Start GTDB Search =====
[2023-06-27 00:33:54,952] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002340175.1_ASM234017v1_genomic.fna/markers.fasta)
[2023-06-27 00:33:54,952] [INFO] Task started: Blastn
[2023-06-27 00:33:54,952] [INFO] Running command: blastn -query GCA_002340175.1_ASM234017v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ba42346-09d6-49fd-8250-b3cf095c9efa/dqc_reference/reference_markers_gtdb.fasta -out GCA_002340175.1_ASM234017v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 00:33:55,725] [INFO] Task succeeded: Blastn
[2023-06-27 00:33:55,752] [INFO] Selected 8 target genomes.
[2023-06-27 00:33:55,752] [INFO] Target genome list was writen to GCA_002340175.1_ASM234017v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 00:33:55,761] [INFO] Task started: fastANI
[2023-06-27 00:33:55,761] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a92db3c-8327-48aa-965d-3b0441a21523/GCA_002340175.1_ASM234017v1_genomic.fna.gz --refList GCA_002340175.1_ASM234017v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002340175.1_ASM234017v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 00:34:00,892] [INFO] Task succeeded: fastANI
[2023-06-27 00:34:00,902] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 00:34:00,903] [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_904846495.1	s__Psychrobacter sanguinis	97.4434	876	966	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	96.88	96.57	0.90	0.89	7	conclusive
GCA_002385225.1	s__Psychrobacter sp002385225	83.0038	603	966	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900162825.1	s__Psychrobacter piechaudii	82.5646	531	966	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685805.1	s__Psychrobacter phenylpyruvicus	82.3486	602	966	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	100.00	99.99	1.00	0.99	4	-
GCF_900162815.1	s__Psychrobacter pasteurii	81.2277	554	966	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018260395.1	s__Psychrobacter sp018260395	79.6001	353	966	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002313155.2	s__Psychrobacter sp002313155	79.2522	336	966	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382145.1	s__Psychrobacter lutiphocae	78.6668	287	966	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	99.95	99.95	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2023-06-27 00:34:00,905] [INFO] GTDB search result was written to GCA_002340175.1_ASM234017v1_genomic.fna/result_gtdb.tsv
[2023-06-27 00:34:00,906] [INFO] ===== GTDB Search completed =====
[2023-06-27 00:34:00,910] [INFO] DFAST_QC result json was written to GCA_002340175.1_ASM234017v1_genomic.fna/dqc_result.json
[2023-06-27 00:34:00,910] [INFO] DFAST_QC completed!
[2023-06-27 00:34:00,910] [INFO] Total running time: 0h0m46s