[2024-01-25 19:51:20,672] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:51:20,673] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:51:20,673] [INFO] DQC Reference Directory: /var/lib/cwl/stg42b74d26-c9a8-4bfa-a6bb-2d24568d1baa/dqc_reference
[2024-01-25 19:51:21,908] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:51:21,908] [INFO] Task started: Prodigal
[2024-01-25 19:51:21,909] [INFO] Running command: gunzip -c /var/lib/cwl/stge3889e66-b7df-4c4a-b1d0-0c81bff59ff8/GCF_900475095.1_42197_E01_genomic.fna.gz | prodigal -d GCF_900475095.1_42197_E01_genomic.fna/cds.fna -a GCF_900475095.1_42197_E01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:51:25,629] [INFO] Task succeeded: Prodigal
[2024-01-25 19:51:25,629] [INFO] Task started: HMMsearch
[2024-01-25 19:51:25,629] [INFO] Running command: hmmsearch --tblout GCF_900475095.1_42197_E01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg42b74d26-c9a8-4bfa-a6bb-2d24568d1baa/dqc_reference/reference_markers.hmm GCF_900475095.1_42197_E01_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:51:25,879] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:51:25,880] [INFO] Found 6/6 markers.
[2024-01-25 19:51:25,900] [INFO] Query marker FASTA was written to GCF_900475095.1_42197_E01_genomic.fna/markers.fasta
[2024-01-25 19:51:25,900] [INFO] Task started: Blastn
[2024-01-25 19:51:25,900] [INFO] Running command: blastn -query GCF_900475095.1_42197_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stg42b74d26-c9a8-4bfa-a6bb-2d24568d1baa/dqc_reference/reference_markers.fasta -out GCF_900475095.1_42197_E01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:51:26,471] [INFO] Task succeeded: Blastn
[2024-01-25 19:51:26,474] [INFO] Selected 8 target genomes.
[2024-01-25 19:51:26,474] [INFO] Target genome list was writen to GCF_900475095.1_42197_E01_genomic.fna/target_genomes.txt
[2024-01-25 19:51:26,479] [INFO] Task started: fastANI
[2024-01-25 19:51:26,479] [INFO] Running command: fastANI --query /var/lib/cwl/stge3889e66-b7df-4c4a-b1d0-0c81bff59ff8/GCF_900475095.1_42197_E01_genomic.fna.gz --refList GCF_900475095.1_42197_E01_genomic.fna/target_genomes.txt --output GCF_900475095.1_42197_E01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:51:30,614] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:30,614] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg42b74d26-c9a8-4bfa-a6bb-2d24568d1baa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:51:30,614] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg42b74d26-c9a8-4bfa-a6bb-2d24568d1baa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:51:30,620] [INFO] Found 5 fastANI hits (5 hits with ANI > threshold)
[2024-01-25 19:51:30,620] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:51:30,620] [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
Streptococcus mutans	strain=NCTC10449	GCA_900475095.1	1309	1309	type	True	100.0	669	673	95	conclusive
Streptococcus mutans	strain=FDAARGOS 1458	GCA_019048645.1	1309	1309	type	True	99.9998	670	673	95	conclusive
Streptococcus mutans	strain=NBRC 13955	GCA_006739205.1	1309	1309	type	True	99.9988	669	673	95	conclusive
Streptococcus mutans	strain=ATCC 25175	GCA_000347875.1	1309	1309	type	True	99.9778	658	673	95	conclusive
Streptococcus mutans	strain=DSM 20523	GCA_000375505.1	1309	1309	type	True	99.9531	654	673	95	conclusive
--------------------------------------------------------------------------------
[2024-01-25 19:51:30,621] [INFO] DFAST Taxonomy check result was written to GCF_900475095.1_42197_E01_genomic.fna/tc_result.tsv
[2024-01-25 19:51:30,622] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:51:30,622] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:51:30,622] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg42b74d26-c9a8-4bfa-a6bb-2d24568d1baa/dqc_reference/checkm_data
[2024-01-25 19:51:30,623] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:51:30,646] [INFO] Task started: CheckM
[2024-01-25 19:51:30,647] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900475095.1_42197_E01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900475095.1_42197_E01_genomic.fna/checkm_input GCF_900475095.1_42197_E01_genomic.fna/checkm_result
[2024-01-25 19:51:47,759] [INFO] Task succeeded: CheckM
[2024-01-25 19:51:47,760] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:51:47,774] [INFO] ===== Completeness check finished =====
[2024-01-25 19:51:47,775] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:51:47,775] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900475095.1_42197_E01_genomic.fna/markers.fasta)
[2024-01-25 19:51:47,775] [INFO] Task started: Blastn
[2024-01-25 19:51:47,775] [INFO] Running command: blastn -query GCF_900475095.1_42197_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stg42b74d26-c9a8-4bfa-a6bb-2d24568d1baa/dqc_reference/reference_markers_gtdb.fasta -out GCF_900475095.1_42197_E01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:51:48,536] [INFO] Task succeeded: Blastn
[2024-01-25 19:51:48,538] [INFO] Selected 14 target genomes.
[2024-01-25 19:51:48,539] [INFO] Target genome list was writen to GCF_900475095.1_42197_E01_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:51:48,552] [INFO] Task started: fastANI
[2024-01-25 19:51:48,552] [INFO] Running command: fastANI --query /var/lib/cwl/stge3889e66-b7df-4c4a-b1d0-0c81bff59ff8/GCF_900475095.1_42197_E01_genomic.fna.gz --refList GCF_900475095.1_42197_E01_genomic.fna/target_genomes_gtdb.txt --output GCF_900475095.1_42197_E01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:51:54,231] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:54,243] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:51:54,243] [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_006739205.1	s__Streptococcus mutans	99.9988	670	673	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.12	98.73	0.95	0.87	261	conclusive
GCF_002355215.1	s__Streptococcus troglodytae	94.939	596	673	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000286075.1	s__Streptococcus ratti	79.9235	384	673	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.59	98.38	0.97	0.87	5	-
GCF_001431045.1	s__Streptococcus orisasini	79.5383	367	673	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000187995.2	s__Streptococcus macacae	79.2004	317	673	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001937065.1	s__Streptococcus sp001937065	79.179	333	673	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423725.1	s__Streptococcus devriesei	78.7141	308	673	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000283635.1	s__Streptococcus macedonicus	78.6601	143	673	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	96.3165	99.04	98.50	0.90	0.83	11	-
GCF_000379985.1	s__Streptococcus caballi	78.3537	161	673	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908655.1	s__Streptococcus saliviloxodontae	78.3208	127	673	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000188055.2	s__Streptococcus urinalis	78.1569	125	673	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.98	99.96	0.98	0.97	3	-
GCF_010604095.1	s__Streptococcus sp000187445	78.0471	109	673	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.94	96.18	0.90	0.80	19	-
GCF_000376985.1	s__Streptococcus henryi	77.6611	148	673	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.14	98.14	0.85	0.85	2	-
GCF_000380005.1	s__Streptococcus didelphis	77.6166	100	673	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:51:54,245] [INFO] GTDB search result was written to GCF_900475095.1_42197_E01_genomic.fna/result_gtdb.tsv
[2024-01-25 19:51:54,245] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:51:54,248] [INFO] DFAST_QC result json was written to GCF_900475095.1_42197_E01_genomic.fna/dqc_result.json
[2024-01-25 19:51:54,248] [INFO] DFAST_QC completed!
[2024-01-25 19:51:54,248] [INFO] Total running time: 0h0m34s