[2024-01-24 15:02:18,548] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:18,555] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:18,555] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf941d8b-3d1f-4281-9f91-d37b5e037505/dqc_reference
[2024-01-24 15:02:20,832] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:20,836] [INFO] Task started: Prodigal
[2024-01-24 15:02:20,836] [INFO] Running command: gunzip -c /var/lib/cwl/stgab18f49a-0cec-422f-9264-bfec91b61b4a/GCF_900113645.1_IMG-taxon_2619618836_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900113645.1_IMG-taxon_2619618836_annotated_assembly_genomic.fna/cds.fna -a GCF_900113645.1_IMG-taxon_2619618836_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:29,130] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:29,131] [INFO] Task started: HMMsearch
[2024-01-24 15:02:29,131] [INFO] Running command: hmmsearch --tblout GCF_900113645.1_IMG-taxon_2619618836_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf941d8b-3d1f-4281-9f91-d37b5e037505/dqc_reference/reference_markers.hmm GCF_900113645.1_IMG-taxon_2619618836_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:29,418] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:29,419] [INFO] Found 6/6 markers.
[2024-01-24 15:02:29,460] [INFO] Query marker FASTA was written to GCF_900113645.1_IMG-taxon_2619618836_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 15:02:29,460] [INFO] Task started: Blastn
[2024-01-24 15:02:29,460] [INFO] Running command: blastn -query GCF_900113645.1_IMG-taxon_2619618836_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf941d8b-3d1f-4281-9f91-d37b5e037505/dqc_reference/reference_markers.fasta -out GCF_900113645.1_IMG-taxon_2619618836_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:30,106] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:30,110] [INFO] Selected 11 target genomes.
[2024-01-24 15:02:30,111] [INFO] Target genome list was writen to GCF_900113645.1_IMG-taxon_2619618836_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 15:02:30,155] [INFO] Task started: fastANI
[2024-01-24 15:02:30,156] [INFO] Running command: fastANI --query /var/lib/cwl/stgab18f49a-0cec-422f-9264-bfec91b61b4a/GCF_900113645.1_IMG-taxon_2619618836_annotated_assembly_genomic.fna.gz --refList GCF_900113645.1_IMG-taxon_2619618836_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900113645.1_IMG-taxon_2619618836_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:39,068] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:39,068] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf941d8b-3d1f-4281-9f91-d37b5e037505/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:39,068] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf941d8b-3d1f-4281-9f91-d37b5e037505/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:39,076] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:02:39,076] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:39,076] [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 flocculiformis	strain=DSM 2094	GCA_900113645.1	82803	82803	type	True	100.0	927	935	95	conclusive
Trichococcus pasteurii	strain=DSM 2381	GCA_900112935.1	43064	43064	type	True	90.7234	758	935	95	below_threshold
Trichococcus shcherbakoviae subsp. psychrophilus	strain=SKBG	GCA_006370295.1	2585775	2094020	type	True	89.9119	709	935	95	below_threshold
Trichococcus alkaliphilus	strain=B5	GCA_003008695.1	2052943	2052943	type	True	89.204	710	935	95	below_threshold
Trichococcus paludicola	strain=B7-2	GCA_003052295.1	2052942	2052942	type	True	88.6771	483	935	95	below_threshold
Trichococcus patagoniensis	strain=DSM 18806	GCA_003051085.1	382641	382641	type	True	88.3623	701	935	95	below_threshold
Trichococcus collinsii	strain=DSM 14526	GCA_900107505.1	157076	157076	type	True	88.1316	743	935	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:39,078] [INFO] DFAST Taxonomy check result was written to GCF_900113645.1_IMG-taxon_2619618836_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 15:02:39,078] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:39,079] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:39,079] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf941d8b-3d1f-4281-9f91-d37b5e037505/dqc_reference/checkm_data
[2024-01-24 15:02:39,080] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:39,112] [INFO] Task started: CheckM
[2024-01-24 15:02:39,113] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900113645.1_IMG-taxon_2619618836_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900113645.1_IMG-taxon_2619618836_annotated_assembly_genomic.fna/checkm_input GCF_900113645.1_IMG-taxon_2619618836_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 15:03:09,529] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:09,531] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:09,550] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:09,550] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:09,550] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900113645.1_IMG-taxon_2619618836_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 15:03:09,551] [INFO] Task started: Blastn
[2024-01-24 15:03:09,551] [INFO] Running command: blastn -query GCF_900113645.1_IMG-taxon_2619618836_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf941d8b-3d1f-4281-9f91-d37b5e037505/dqc_reference/reference_markers_gtdb.fasta -out GCF_900113645.1_IMG-taxon_2619618836_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:10,472] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:10,476] [INFO] Selected 7 target genomes.
[2024-01-24 15:03:10,477] [INFO] Target genome list was writen to GCF_900113645.1_IMG-taxon_2619618836_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:10,483] [INFO] Task started: fastANI
[2024-01-24 15:03:10,484] [INFO] Running command: fastANI --query /var/lib/cwl/stgab18f49a-0cec-422f-9264-bfec91b61b4a/GCF_900113645.1_IMG-taxon_2619618836_annotated_assembly_genomic.fna.gz --refList GCF_900113645.1_IMG-taxon_2619618836_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900113645.1_IMG-taxon_2619618836_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:16,544] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:16,558] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:16,558] [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_900113645.1	s__Trichococcus flocculiformis	100.0	927	935	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Trichococcus	95.0	98.05	95.30	0.92	0.79	15	conclusive
GCF_900112935.1	s__Trichococcus pasteurii	90.7095	759	935	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Trichococcus	95.0	99.99	99.99	1.00	1.00	3	-
GCA_002155105.1	s__Trichococcus shcherbakoviae	89.6986	736	935	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Trichococcus	95.0	97.18	96.59	0.87	0.86	3	-
GCF_003008695.1	s__Trichococcus alkaliphilus	89.1868	711	935	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Trichococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003052295.1	s__Trichococcus paludicola	88.6687	483	935	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Trichococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003051085.1	s__Trichococcus patagoniensis	88.4153	697	935	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	88.1352	743	935	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Trichococcus	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:03:16,570] [INFO] GTDB search result was written to GCF_900113645.1_IMG-taxon_2619618836_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:16,571] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:16,573] [INFO] DFAST_QC result json was written to GCF_900113645.1_IMG-taxon_2619618836_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 15:03:16,573] [INFO] DFAST_QC completed!
[2024-01-24 15:03:16,574] [INFO] Total running time: 0h0m58s