[2024-01-24 13:57:41,821] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:41,822] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:41,823] [INFO] DQC Reference Directory: /var/lib/cwl/stg43dc9ab7-41db-4773-ac57-f8d7facaf783/dqc_reference
[2024-01-24 13:57:43,201] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:43,202] [INFO] Task started: Prodigal
[2024-01-24 13:57:43,202] [INFO] Running command: gunzip -c /var/lib/cwl/stg71ee913e-8dcb-4dc7-b99d-fad452d05e9d/GCF_008692995.1_ASM869299v1_genomic.fna.gz | prodigal -d GCF_008692995.1_ASM869299v1_genomic.fna/cds.fna -a GCF_008692995.1_ASM869299v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:46,188] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:46,188] [INFO] Task started: HMMsearch
[2024-01-24 13:57:46,188] [INFO] Running command: hmmsearch --tblout GCF_008692995.1_ASM869299v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43dc9ab7-41db-4773-ac57-f8d7facaf783/dqc_reference/reference_markers.hmm GCF_008692995.1_ASM869299v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:46,417] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:46,418] [INFO] Found 6/6 markers.
[2024-01-24 13:57:46,440] [INFO] Query marker FASTA was written to GCF_008692995.1_ASM869299v1_genomic.fna/markers.fasta
[2024-01-24 13:57:46,440] [INFO] Task started: Blastn
[2024-01-24 13:57:46,441] [INFO] Running command: blastn -query GCF_008692995.1_ASM869299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43dc9ab7-41db-4773-ac57-f8d7facaf783/dqc_reference/reference_markers.fasta -out GCF_008692995.1_ASM869299v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:47,043] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:47,047] [INFO] Selected 11 target genomes.
[2024-01-24 13:57:47,047] [INFO] Target genome list was writen to GCF_008692995.1_ASM869299v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:47,054] [INFO] Task started: fastANI
[2024-01-24 13:57:47,054] [INFO] Running command: fastANI --query /var/lib/cwl/stg71ee913e-8dcb-4dc7-b99d-fad452d05e9d/GCF_008692995.1_ASM869299v1_genomic.fna.gz --refList GCF_008692995.1_ASM869299v1_genomic.fna/target_genomes.txt --output GCF_008692995.1_ASM869299v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:52,127] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:52,128] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43dc9ab7-41db-4773-ac57-f8d7facaf783/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:52,128] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43dc9ab7-41db-4773-ac57-f8d7facaf783/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:52,135] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:57:52,136] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:52,136] [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
Gemella haemolysans	strain=CCUG 37985T	GCA_008692995.1	1379	1379	suspected-type	True	100.0	623	625	95	conclusive
Gemella haemolysans	strain=ATCC 10379	GCA_000173915.1	1379	1379	suspected-type	True	99.9731	619	625	95	conclusive
Gemella sanguinis	strain=ATCC 700632	GCA_000701685.1	84135	84135	type	True	81.5418	340	625	95	below_threshold
Gemella morbillorum	strain=NCTC11323	GCA_900476045.1	29391	29391	type	True	80.9847	318	625	95	below_threshold
Gemella morbillorum	strain=FDAARGOS_1501	GCA_020097435.1	29391	29391	type	True	80.9199	307	625	95	below_threshold
Gemella cuniculi	strain=DSM 15828	GCA_000425665.1	150240	150240	type	True	79.3208	268	625	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:52,137] [INFO] DFAST Taxonomy check result was written to GCF_008692995.1_ASM869299v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:52,138] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:52,138] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:52,139] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43dc9ab7-41db-4773-ac57-f8d7facaf783/dqc_reference/checkm_data
[2024-01-24 13:57:52,140] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:52,163] [INFO] Task started: CheckM
[2024-01-24 13:57:52,163] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008692995.1_ASM869299v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008692995.1_ASM869299v1_genomic.fna/checkm_input GCF_008692995.1_ASM869299v1_genomic.fna/checkm_result
[2024-01-24 13:58:10,612] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:10,613] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:10,637] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:10,638] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:10,638] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008692995.1_ASM869299v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:10,638] [INFO] Task started: Blastn
[2024-01-24 13:58:10,638] [INFO] Running command: blastn -query GCF_008692995.1_ASM869299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43dc9ab7-41db-4773-ac57-f8d7facaf783/dqc_reference/reference_markers_gtdb.fasta -out GCF_008692995.1_ASM869299v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:11,454] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:11,457] [INFO] Selected 6 target genomes.
[2024-01-24 13:58:11,457] [INFO] Target genome list was writen to GCF_008692995.1_ASM869299v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:11,462] [INFO] Task started: fastANI
[2024-01-24 13:58:11,462] [INFO] Running command: fastANI --query /var/lib/cwl/stg71ee913e-8dcb-4dc7-b99d-fad452d05e9d/GCF_008692995.1_ASM869299v1_genomic.fna.gz --refList GCF_008692995.1_ASM869299v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008692995.1_ASM869299v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:14,714] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:14,721] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:14,721] [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_000173915.1	s__Gemella haemolysans	99.9731	619	625	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella	95.0	99.96	99.96	0.99	0.99	3	conclusive
GCF_001553035.1	s__Gemella haemolysans_B	94.0413	500	625	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella	95.0	97.70	97.59	0.85	0.81	4	-
GCA_900766305.1	s__Gemella sp900766305	92.6495	500	625	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002871655.1	s__Gemella sp002871655	88.4415	506	625	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella	95.0	98.42	98.42	0.93	0.93	2	-
GCF_012273215.1	s__Gemella haemolysans_A	88.0301	514	625	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella	95.0	99.95	99.95	0.99	0.99	2	-
GCF_901873445.1	s__Gemella haemolysans_C	87.6251	457	625	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:14,722] [INFO] GTDB search result was written to GCF_008692995.1_ASM869299v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:14,723] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:14,726] [INFO] DFAST_QC result json was written to GCF_008692995.1_ASM869299v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:14,726] [INFO] DFAST_QC completed!
[2024-01-24 13:58:14,726] [INFO] Total running time: 0h0m33s