[2024-01-25 19:42:50,742] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:42:50,744] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:42:50,744] [INFO] DQC Reference Directory: /var/lib/cwl/stgecb278f2-ee84-474f-a1bb-f0e5906b0f08/dqc_reference
[2024-01-25 19:42:51,832] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:42:51,832] [INFO] Task started: Prodigal
[2024-01-25 19:42:51,833] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d6cd5db-87c1-455a-b513-49e1f52b3a0f/GCF_003051085.1_ASM305108v1_genomic.fna.gz | prodigal -d GCF_003051085.1_ASM305108v1_genomic.fna/cds.fna -a GCF_003051085.1_ASM305108v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:42:59,680] [INFO] Task succeeded: Prodigal
[2024-01-25 19:42:59,680] [INFO] Task started: HMMsearch
[2024-01-25 19:42:59,680] [INFO] Running command: hmmsearch --tblout GCF_003051085.1_ASM305108v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgecb278f2-ee84-474f-a1bb-f0e5906b0f08/dqc_reference/reference_markers.hmm GCF_003051085.1_ASM305108v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:42:59,901] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:42:59,902] [INFO] Found 6/6 markers.
[2024-01-25 19:42:59,927] [INFO] Query marker FASTA was written to GCF_003051085.1_ASM305108v1_genomic.fna/markers.fasta
[2024-01-25 19:42:59,927] [INFO] Task started: Blastn
[2024-01-25 19:42:59,927] [INFO] Running command: blastn -query GCF_003051085.1_ASM305108v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgecb278f2-ee84-474f-a1bb-f0e5906b0f08/dqc_reference/reference_markers.fasta -out GCF_003051085.1_ASM305108v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:43:00,465] [INFO] Task succeeded: Blastn
[2024-01-25 19:43:00,467] [INFO] Selected 8 target genomes.
[2024-01-25 19:43:00,467] [INFO] Target genome list was writen to GCF_003051085.1_ASM305108v1_genomic.fna/target_genomes.txt
[2024-01-25 19:43:00,469] [INFO] Task started: fastANI
[2024-01-25 19:43:00,469] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d6cd5db-87c1-455a-b513-49e1f52b3a0f/GCF_003051085.1_ASM305108v1_genomic.fna.gz --refList GCF_003051085.1_ASM305108v1_genomic.fna/target_genomes.txt --output GCF_003051085.1_ASM305108v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:43:05,750] [INFO] Task succeeded: fastANI
[2024-01-25 19:43:05,750] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgecb278f2-ee84-474f-a1bb-f0e5906b0f08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:43:05,751] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgecb278f2-ee84-474f-a1bb-f0e5906b0f08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:43:05,757] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:43:05,758] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:43:05,758] [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
Trichococcus patagoniensis	strain=DSM 18806	GCA_003051085.1	382641	382641	type	True	100.0	1004	1006	95	conclusive
Trichococcus alkaliphilus	strain=B5	GCA_003008695.1	2052943	2052943	type	True	91.507	773	1006	95	below_threshold
Trichococcus shcherbakoviae subsp. psychrophilus	strain=SKBG	GCA_006370295.1	2585775	2094020	type	True	90.8092	796	1006	95	below_threshold
Trichococcus paludicola	strain=B7-2	GCA_003052295.1	2052942	2052942	type	True	90.6072	527	1006	95	below_threshold
Trichococcus collinsii	strain=DSM 14526	GCA_900107505.1	157076	157076	type	True	89.9576	800	1006	95	below_threshold
Trichococcus pasteurii	strain=DSM 2381	GCA_900112935.1	43064	43064	type	True	89.573	784	1006	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:43:05,759] [INFO] DFAST Taxonomy check result was written to GCF_003051085.1_ASM305108v1_genomic.fna/tc_result.tsv
[2024-01-25 19:43:05,760] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:43:05,760] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:43:05,760] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgecb278f2-ee84-474f-a1bb-f0e5906b0f08/dqc_reference/checkm_data
[2024-01-25 19:43:05,761] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:43:05,793] [INFO] Task started: CheckM
[2024-01-25 19:43:05,793] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003051085.1_ASM305108v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003051085.1_ASM305108v1_genomic.fna/checkm_input GCF_003051085.1_ASM305108v1_genomic.fna/checkm_result
[2024-01-25 19:43:32,436] [INFO] Task succeeded: CheckM
[2024-01-25 19:43:32,437] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:43:32,456] [INFO] ===== Completeness check finished =====
[2024-01-25 19:43:32,456] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:43:32,457] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003051085.1_ASM305108v1_genomic.fna/markers.fasta)
[2024-01-25 19:43:32,457] [INFO] Task started: Blastn
[2024-01-25 19:43:32,457] [INFO] Running command: blastn -query GCF_003051085.1_ASM305108v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgecb278f2-ee84-474f-a1bb-f0e5906b0f08/dqc_reference/reference_markers_gtdb.fasta -out GCF_003051085.1_ASM305108v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:43:33,220] [INFO] Task succeeded: Blastn
[2024-01-25 19:43:33,223] [INFO] Selected 6 target genomes.
[2024-01-25 19:43:33,224] [INFO] Target genome list was writen to GCF_003051085.1_ASM305108v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:43:33,235] [INFO] Task started: fastANI
[2024-01-25 19:43:33,235] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d6cd5db-87c1-455a-b513-49e1f52b3a0f/GCF_003051085.1_ASM305108v1_genomic.fna.gz --refList GCF_003051085.1_ASM305108v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003051085.1_ASM305108v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:43:37,917] [INFO] Task succeeded: fastANI
[2024-01-25 19:43:37,922] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:43:37,922] [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_003051085.1	s__Trichococcus patagoniensis	100.0	1004	1006	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Trichococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003008695.1	s__Trichococcus alkaliphilus	91.4908	774	1006	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Trichococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002155105.1	s__Trichococcus shcherbakoviae	90.647	802	1006	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Trichococcus	95.0	97.18	96.59	0.87	0.86	3	-
GCF_003052295.1	s__Trichococcus paludicola	90.6072	527	1006	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Trichococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107505.1	s__Trichococcus collinsii	89.9656	799	1006	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Trichococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900112935.1	s__Trichococcus pasteurii	89.5929	782	1006	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Trichococcus	95.0	99.99	99.99	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:43:37,923] [INFO] GTDB search result was written to GCF_003051085.1_ASM305108v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:43:37,924] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:43:37,941] [INFO] DFAST_QC result json was written to GCF_003051085.1_ASM305108v1_genomic.fna/dqc_result.json
[2024-01-25 19:43:37,942] [INFO] DFAST_QC completed!
[2024-01-25 19:43:37,942] [INFO] Total running time: 0h0m47s