[2024-01-25 17:48:50,694] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:48:50,695] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:48:50,695] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d2c5a49-1637-43fa-a99a-8234e57123a8/dqc_reference
[2024-01-25 17:48:51,840] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:48:51,840] [INFO] Task started: Prodigal
[2024-01-25 17:48:51,841] [INFO] Running command: gunzip -c /var/lib/cwl/stgca0c0bbc-756d-4a89-b292-0bf2334a5325/GCF_900476045.1_50279_D01_genomic.fna.gz | prodigal -d GCF_900476045.1_50279_D01_genomic.fna/cds.fna -a GCF_900476045.1_50279_D01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:48:54,358] [INFO] Task succeeded: Prodigal
[2024-01-25 17:48:54,358] [INFO] Task started: HMMsearch
[2024-01-25 17:48:54,359] [INFO] Running command: hmmsearch --tblout GCF_900476045.1_50279_D01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d2c5a49-1637-43fa-a99a-8234e57123a8/dqc_reference/reference_markers.hmm GCF_900476045.1_50279_D01_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:48:54,556] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:48:54,557] [INFO] Found 6/6 markers.
[2024-01-25 17:48:54,573] [INFO] Query marker FASTA was written to GCF_900476045.1_50279_D01_genomic.fna/markers.fasta
[2024-01-25 17:48:54,573] [INFO] Task started: Blastn
[2024-01-25 17:48:54,573] [INFO] Running command: blastn -query GCF_900476045.1_50279_D01_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d2c5a49-1637-43fa-a99a-8234e57123a8/dqc_reference/reference_markers.fasta -out GCF_900476045.1_50279_D01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:48:55,104] [INFO] Task succeeded: Blastn
[2024-01-25 17:48:55,106] [INFO] Selected 11 target genomes.
[2024-01-25 17:48:55,107] [INFO] Target genome list was writen to GCF_900476045.1_50279_D01_genomic.fna/target_genomes.txt
[2024-01-25 17:48:55,127] [INFO] Task started: fastANI
[2024-01-25 17:48:55,127] [INFO] Running command: fastANI --query /var/lib/cwl/stgca0c0bbc-756d-4a89-b292-0bf2334a5325/GCF_900476045.1_50279_D01_genomic.fna.gz --refList GCF_900476045.1_50279_D01_genomic.fna/target_genomes.txt --output GCF_900476045.1_50279_D01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:49:00,320] [INFO] Task succeeded: fastANI
[2024-01-25 17:49:00,321] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d2c5a49-1637-43fa-a99a-8234e57123a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:49:00,321] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d2c5a49-1637-43fa-a99a-8234e57123a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:49:00,327] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:49:00,328] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:49:00,328] [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 morbillorum	strain=NCTC11323	GCA_900476045.1	29391	29391	type	True	100.0	584	586	95	conclusive
Gemella morbillorum	strain=FDAARGOS_1501	GCA_020097435.1	29391	29391	type	True	99.9999	585	586	95	conclusive
Gemella sanguinis	strain=ATCC 700632	GCA_000701685.1	84135	84135	type	True	81.7504	326	586	95	below_threshold
Gemella haemolysans	strain=ATCC 10379	GCA_000173915.1	1379	1379	suspected-type	True	81.3751	310	586	95	below_threshold
Gemella haemolysans	strain=CCUG 37985T	GCA_008692995.1	1379	1379	suspected-type	True	81.1061	301	586	95	below_threshold
Gemella cuniculi	strain=DSM 15828	GCA_000425665.1	150240	150240	type	True	80.1793	303	586	95	below_threshold
Gemella massiliensis	strain=Marseille-P3249	GCA_900120125.1	1909670	1909670	type	True	79.2138	228	586	95	below_threshold
Gemella bergeri	strain=ATCC 700627	GCA_000469465.1	84136	84136	type	True	79.0843	209	586	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:49:00,329] [INFO] DFAST Taxonomy check result was written to GCF_900476045.1_50279_D01_genomic.fna/tc_result.tsv
[2024-01-25 17:49:00,329] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:49:00,330] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:49:00,330] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d2c5a49-1637-43fa-a99a-8234e57123a8/dqc_reference/checkm_data
[2024-01-25 17:49:00,331] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:49:00,351] [INFO] Task started: CheckM
[2024-01-25 17:49:00,352] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900476045.1_50279_D01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900476045.1_50279_D01_genomic.fna/checkm_input GCF_900476045.1_50279_D01_genomic.fna/checkm_result
[2024-01-25 17:49:14,414] [INFO] Task succeeded: CheckM
[2024-01-25 17:49:14,415] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:49:14,428] [INFO] ===== Completeness check finished =====
[2024-01-25 17:49:14,428] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:49:14,428] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900476045.1_50279_D01_genomic.fna/markers.fasta)
[2024-01-25 17:49:14,428] [INFO] Task started: Blastn
[2024-01-25 17:49:14,428] [INFO] Running command: blastn -query GCF_900476045.1_50279_D01_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d2c5a49-1637-43fa-a99a-8234e57123a8/dqc_reference/reference_markers_gtdb.fasta -out GCF_900476045.1_50279_D01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:49:15,194] [INFO] Task succeeded: Blastn
[2024-01-25 17:49:15,197] [INFO] Selected 13 target genomes.
[2024-01-25 17:49:15,197] [INFO] Target genome list was writen to GCF_900476045.1_50279_D01_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:49:15,219] [INFO] Task started: fastANI
[2024-01-25 17:49:15,219] [INFO] Running command: fastANI --query /var/lib/cwl/stgca0c0bbc-756d-4a89-b292-0bf2334a5325/GCF_900476045.1_50279_D01_genomic.fna.gz --refList GCF_900476045.1_50279_D01_genomic.fna/target_genomes_gtdb.txt --output GCF_900476045.1_50279_D01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:49:20,361] [INFO] Task succeeded: fastANI
[2024-01-25 17:49:20,369] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:49:20,369] [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_900476045.1	s__Gemella morbillorum	100.0	585	586	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella	95.0	97.59	96.86	0.90	0.88	6	conclusive
GCF_012273215.1	s__Gemella haemolysans_A	82.1621	348	586	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella	95.0	99.95	99.95	0.99	0.99	2	-
GCF_000701685.1	s__Gemella sanguinis	81.7504	326	586	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella	95.0	97.27	96.22	0.93	0.90	6	-
GCF_901873445.1	s__Gemella haemolysans_C	81.5529	320	586	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000173915.1	s__Gemella haemolysans	81.3535	311	586	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella	95.0	99.96	99.96	0.99	0.99	3	-
GCF_001553035.1	s__Gemella haemolysans_B	81.0644	301	586	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	80.8939	291	586	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900555985.1	s__Gemella sp900555985	80.2937	205	586	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425665.1	s__Gemella cuniculi	80.1793	303	586	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900120125.1	s__Gemella massiliensis	79.1932	229	586	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella	95.0	99.63	99.63	0.95	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-25 17:49:20,370] [INFO] GTDB search result was written to GCF_900476045.1_50279_D01_genomic.fna/result_gtdb.tsv
[2024-01-25 17:49:20,370] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:49:20,373] [INFO] DFAST_QC result json was written to GCF_900476045.1_50279_D01_genomic.fna/dqc_result.json
[2024-01-25 17:49:20,373] [INFO] DFAST_QC completed!
[2024-01-25 17:49:20,373] [INFO] Total running time: 0h0m30s