[2024-01-25 19:35:51,333] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:35:51,339] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:35:51,340] [INFO] DQC Reference Directory: /var/lib/cwl/stg180b6941-8d56-4eed-95b1-80b5ae2aaa7a/dqc_reference
[2024-01-25 19:35:52,642] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:35:52,643] [INFO] Task started: Prodigal
[2024-01-25 19:35:52,643] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a7a79b9-70da-425b-a6c1-59e39153d413/GCF_900459355.1_41906_A02_genomic.fna.gz | prodigal -d GCF_900459355.1_41906_A02_genomic.fna/cds.fna -a GCF_900459355.1_41906_A02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:35:57,423] [INFO] Task succeeded: Prodigal
[2024-01-25 19:35:57,423] [INFO] Task started: HMMsearch
[2024-01-25 19:35:57,423] [INFO] Running command: hmmsearch --tblout GCF_900459355.1_41906_A02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg180b6941-8d56-4eed-95b1-80b5ae2aaa7a/dqc_reference/reference_markers.hmm GCF_900459355.1_41906_A02_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:35:57,712] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:35:57,713] [INFO] Found 6/6 markers.
[2024-01-25 19:35:57,735] [INFO] Query marker FASTA was written to GCF_900459355.1_41906_A02_genomic.fna/markers.fasta
[2024-01-25 19:35:57,736] [INFO] Task started: Blastn
[2024-01-25 19:35:57,736] [INFO] Running command: blastn -query GCF_900459355.1_41906_A02_genomic.fna/markers.fasta -db /var/lib/cwl/stg180b6941-8d56-4eed-95b1-80b5ae2aaa7a/dqc_reference/reference_markers.fasta -out GCF_900459355.1_41906_A02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:35:58,310] [INFO] Task succeeded: Blastn
[2024-01-25 19:35:58,313] [INFO] Selected 13 target genomes.
[2024-01-25 19:35:58,314] [INFO] Target genome list was writen to GCF_900459355.1_41906_A02_genomic.fna/target_genomes.txt
[2024-01-25 19:35:58,320] [INFO] Task started: fastANI
[2024-01-25 19:35:58,320] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a7a79b9-70da-425b-a6c1-59e39153d413/GCF_900459355.1_41906_A02_genomic.fna.gz --refList GCF_900459355.1_41906_A02_genomic.fna/target_genomes.txt --output GCF_900459355.1_41906_A02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:36:04,514] [INFO] Task succeeded: fastANI
[2024-01-25 19:36:04,515] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg180b6941-8d56-4eed-95b1-80b5ae2aaa7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:36:04,515] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg180b6941-8d56-4eed-95b1-80b5ae2aaa7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:36:04,524] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:36:04,524] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:36:04,524] [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 parasanguinis	strain=NCTC12854	GCA_900459355.1	1318	1318	suspected-type	True	100.0	719	722	95	conclusive
Streptococcus parasanguinis	strain=ATCC 15912	GCA_000164675.2	1318	1318	suspected-type	True	99.9936	716	722	95	conclusive
Streptococcus australis	strain=ATCC 700641	GCA_000222745.2	113107	113107	type	True	85.8868	423	722	95	below_threshold
Streptococcus australis	strain=NCTC13166	GCA_900476055.1	113107	113107	type	True	85.527	450	722	95	below_threshold
Streptococcus australis	strain=ATCC 700641	GCA_000186465.1	113107	113107	type	True	85.4852	429	722	95	below_threshold
Streptococcus koreensis	strain=JS71	GCA_003627135.1	2382163	2382163	type	True	85.206	400	722	95	below_threshold
Streptococcus xiaochunlingii	strain=E24	GCA_006385805.1	2589788	2589788	type	True	85.0559	393	722	95	below_threshold
Streptococcus ilei	strain=I-G2	GCA_000479335.1	1156431	1156431	type	True	84.9312	395	722	95	below_threshold
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	80.6624	201	722	95	below_threshold
Streptococcus vulneris	strain=DM3B3	GCA_019218685.1	2853160	2853160	type	True	80.5026	200	722	95	below_threshold
Streptococcus constellatus subsp. constellatus	strain=CCUG 24889	GCA_023167545.1	184246	76860	type	True	79.9104	139	722	95	below_threshold
Streptococcus ruminantium	strain=GUT187T	GCA_003609975.1	1917441	1917441	type	True	79.625	88	722	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	79.0987	125	722	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:36:04,526] [INFO] DFAST Taxonomy check result was written to GCF_900459355.1_41906_A02_genomic.fna/tc_result.tsv
[2024-01-25 19:36:04,527] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:36:04,527] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:36:04,527] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg180b6941-8d56-4eed-95b1-80b5ae2aaa7a/dqc_reference/checkm_data
[2024-01-25 19:36:04,528] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:36:04,552] [INFO] Task started: CheckM
[2024-01-25 19:36:04,552] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900459355.1_41906_A02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900459355.1_41906_A02_genomic.fna/checkm_input GCF_900459355.1_41906_A02_genomic.fna/checkm_result
[2024-01-25 19:36:24,678] [INFO] Task succeeded: CheckM
[2024-01-25 19:36:24,679] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:36:24,693] [INFO] ===== Completeness check finished =====
[2024-01-25 19:36:24,693] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:36:24,694] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900459355.1_41906_A02_genomic.fna/markers.fasta)
[2024-01-25 19:36:24,694] [INFO] Task started: Blastn
[2024-01-25 19:36:24,694] [INFO] Running command: blastn -query GCF_900459355.1_41906_A02_genomic.fna/markers.fasta -db /var/lib/cwl/stg180b6941-8d56-4eed-95b1-80b5ae2aaa7a/dqc_reference/reference_markers_gtdb.fasta -out GCF_900459355.1_41906_A02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:36:25,532] [INFO] Task succeeded: Blastn
[2024-01-25 19:36:25,535] [INFO] Selected 10 target genomes.
[2024-01-25 19:36:25,535] [INFO] Target genome list was writen to GCF_900459355.1_41906_A02_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:36:25,542] [INFO] Task started: fastANI
[2024-01-25 19:36:25,542] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a7a79b9-70da-425b-a6c1-59e39153d413/GCF_900459355.1_41906_A02_genomic.fna.gz --refList GCF_900459355.1_41906_A02_genomic.fna/target_genomes_gtdb.txt --output GCF_900459355.1_41906_A02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:36:37,132] [INFO] Task succeeded: fastANI
[2024-01-25 19:36:37,139] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:36:37,139] [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_000164675.2	s__Streptococcus parasanguinis	99.9936	715	722	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.96	95.18	0.90	0.85	22	conclusive
GCF_001813295.1	s__Streptococcus sp001813295	94.5729	599	722	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.2593	95.62	95.52	0.88	0.87	6	-
GCF_001073155.1	s__Streptococcus parasanguinis_D	94.386	567	722	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.84	96.67	0.91	0.89	4	-
GCF_016648925.1	s__Streptococcus sp900766505	94.0154	562	722	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.2991	95.66	95.35	0.89	0.83	30	-
GCF_000448565.1	s__Streptococcus sp000448565	93.9745	603	722	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.2003	N/A	N/A	N/A	N/A	1	-
GCF_000963275.1	s__Streptococcus parasanguinis_B	93.9571	590	722	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.2991	95.64	95.37	0.88	0.85	11	-
GCA_018366675.1	s__Streptococcus parasanguinis_E	93.9455	499	722	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.293	95.61	95.45	0.89	0.84	13	-
GCF_009717815.1	s__Streptococcus parasanguinis_F	93.9028	574	722	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.25	95.86	95.53	0.89	0.86	10	-
GCA_018365265.1	s__Streptococcus parasanguinis_G	93.8023	549	722	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0331	95.56	95.56	0.87	0.87	2	-
GCF_001074805.1	s__Streptococcus parasanguinis_A	93.0623	549	722	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 19:36:37,141] [INFO] GTDB search result was written to GCF_900459355.1_41906_A02_genomic.fna/result_gtdb.tsv
[2024-01-25 19:36:37,144] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:36:37,147] [INFO] DFAST_QC result json was written to GCF_900459355.1_41906_A02_genomic.fna/dqc_result.json
[2024-01-25 19:36:37,147] [INFO] DFAST_QC completed!
[2024-01-25 19:36:37,147] [INFO] Total running time: 0h0m46s