[2024-01-24 13:37:11,336] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:11,337] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:11,338] [INFO] DQC Reference Directory: /var/lib/cwl/stg518f1fa4-7001-4b3a-95f1-68e0360d44e5/dqc_reference
[2024-01-24 13:37:12,734] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:12,735] [INFO] Task started: Prodigal
[2024-01-24 13:37:12,735] [INFO] Running command: gunzip -c /var/lib/cwl/stgfbf7966d-2a22-47d1-8c0a-58bbac290faa/GCF_000423725.1_ASM42372v1_genomic.fna.gz | prodigal -d GCF_000423725.1_ASM42372v1_genomic.fna/cds.fna -a GCF_000423725.1_ASM42372v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:17,865] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:17,865] [INFO] Task started: HMMsearch
[2024-01-24 13:37:17,865] [INFO] Running command: hmmsearch --tblout GCF_000423725.1_ASM42372v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg518f1fa4-7001-4b3a-95f1-68e0360d44e5/dqc_reference/reference_markers.hmm GCF_000423725.1_ASM42372v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:18,101] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:18,103] [INFO] Found 6/6 markers.
[2024-01-24 13:37:18,126] [INFO] Query marker FASTA was written to GCF_000423725.1_ASM42372v1_genomic.fna/markers.fasta
[2024-01-24 13:37:18,127] [INFO] Task started: Blastn
[2024-01-24 13:37:18,127] [INFO] Running command: blastn -query GCF_000423725.1_ASM42372v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg518f1fa4-7001-4b3a-95f1-68e0360d44e5/dqc_reference/reference_markers.fasta -out GCF_000423725.1_ASM42372v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:18,771] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:18,775] [INFO] Selected 22 target genomes.
[2024-01-24 13:37:18,776] [INFO] Target genome list was writen to GCF_000423725.1_ASM42372v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:18,842] [INFO] Task started: fastANI
[2024-01-24 13:37:18,842] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbf7966d-2a22-47d1-8c0a-58bbac290faa/GCF_000423725.1_ASM42372v1_genomic.fna.gz --refList GCF_000423725.1_ASM42372v1_genomic.fna/target_genomes.txt --output GCF_000423725.1_ASM42372v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:28,179] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:28,180] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg518f1fa4-7001-4b3a-95f1-68e0360d44e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:28,180] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg518f1fa4-7001-4b3a-95f1-68e0360d44e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:28,195] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:28,195] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:28,195] [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 devriesei	strain=DSM 19639	GCA_000423725.1	231233	231233	type	True	100.0	699	700	95	conclusive
Streptococcus ratti	strain=DSM 20564	GCA_000347915.1	1341	1341	suspected-type	True	85.5591	473	700	95	below_threshold
Streptococcus ratti	strain=FA-1	GCA_000286075.1	1341	1341	suspected-type	True	85.5466	526	700	95	below_threshold
Streptococcus criceti	strain=HS-6	GCA_000187975.3	1333	1333	type	True	79.9251	167	700	95	below_threshold
Streptococcus criceti	strain=NCTC12277	GCA_900459215.1	1333	1333	type	True	79.8014	167	700	95	below_threshold
Streptococcus mutans	strain=DSM 20523	GCA_000375505.1	1309	1309	type	True	78.8259	294	700	95	below_threshold
Streptococcus mutans	strain=NCTC10449	GCA_900475095.1	1309	1309	type	True	78.8123	303	700	95	below_threshold
Streptococcus hyointestinalis	strain=NCTC12224	GCA_900459405.1	1337	1337	type	True	78.3525	86	700	95	below_threshold
Streptococcus ovis	strain=DSM 16829	GCA_000380125.1	82806	82806	type	True	78.2904	80	700	95	below_threshold
Streptococcus rubneri	strain=DSM 26920	GCA_004785935.1	1234680	1234680	type	True	78.0019	64	700	95	below_threshold
Streptococcus hillyeri	strain=28462	GCA_003686955.1	2282420	2282420	type	True	78.0	94	700	95	below_threshold
Streptococcus anginosus	strain=ATCC 33397	GCA_002088025.1	1328	1328	type	True	77.9898	82	700	95	below_threshold
Streptococcus hyovaginalis	strain=DSM 12219	GCA_000420785.1	149015	149015	type	True	77.8196	79	700	95	below_threshold
Streptococcus anginosus	strain=NCTC10713	GCA_900636475.1	1328	1328	type	True	77.7948	84	700	95	below_threshold
Streptococcus anginosus subsp. whileyi	strain=CCUG 39159	GCA_000257765.1	1272910	1328	type	True	77.7833	78	700	95	below_threshold
Streptococcus henryi	strain=DSM 19005	GCA_000376985.1	439219	439219	type	True	77.7702	113	700	95	below_threshold
Streptococcus parauberis	strain=NCFD 2020	GCA_000187935.2	1348	1348	type	True	77.7316	77	700	95	below_threshold
Streptococcus constellatus subsp. constellatus	strain=CCUG 24889	GCA_023167545.1	184246	76860	type	True	77.6771	85	700	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:28,207] [INFO] DFAST Taxonomy check result was written to GCF_000423725.1_ASM42372v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:28,208] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:28,209] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:28,209] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg518f1fa4-7001-4b3a-95f1-68e0360d44e5/dqc_reference/checkm_data
[2024-01-24 13:37:28,210] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:28,266] [INFO] Task started: CheckM
[2024-01-24 13:37:28,267] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000423725.1_ASM42372v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000423725.1_ASM42372v1_genomic.fna/checkm_input GCF_000423725.1_ASM42372v1_genomic.fna/checkm_result
[2024-01-24 13:37:50,784] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:50,785] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:50,802] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:50,802] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:50,803] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000423725.1_ASM42372v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:50,803] [INFO] Task started: Blastn
[2024-01-24 13:37:50,803] [INFO] Running command: blastn -query GCF_000423725.1_ASM42372v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg518f1fa4-7001-4b3a-95f1-68e0360d44e5/dqc_reference/reference_markers_gtdb.fasta -out GCF_000423725.1_ASM42372v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:51,538] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:51,542] [INFO] Selected 13 target genomes.
[2024-01-24 13:37:51,542] [INFO] Target genome list was writen to GCF_000423725.1_ASM42372v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:51,584] [INFO] Task started: fastANI
[2024-01-24 13:37:51,584] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbf7966d-2a22-47d1-8c0a-58bbac290faa/GCF_000423725.1_ASM42372v1_genomic.fna.gz --refList GCF_000423725.1_ASM42372v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000423725.1_ASM42372v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:57,274] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:57,286] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:37:57,286] [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_000423725.1	s__Streptococcus devriesei	100.0	699	700	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001937065.1	s__Streptococcus sp001937065	87.4193	574	700	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	85.5467	526	700	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	85.1207	527	700	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006739205.1	s__Streptococcus mutans	78.8127	297	700	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.12	98.73	0.95	0.87	261	-
GCF_002355215.1	s__Streptococcus troglodytae	78.7862	304	700	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900459405.1	s__Streptococcus hyointestinalis	78.3525	86	700	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380125.1	s__Streptococcus ovis	78.3247	81	700	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425025.1	s__Streptococcus castoreus	78.3095	80	700	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003686955.1	s__Streptococcus sp003686955	78.0178	93	700	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000376985.1	s__Streptococcus henryi	77.7702	113	700	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.14	98.14	0.85	0.85	2	-
GCF_902729355.1	s__Streptococcus sp902729355	77.6054	91	700	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.77	98.74	0.88	0.87	5	-
GCF_017884005.1	s__Streptococcus panodentis	76.858	102	700	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.49	98.49	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:37:57,288] [INFO] GTDB search result was written to GCF_000423725.1_ASM42372v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:57,289] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:57,295] [INFO] DFAST_QC result json was written to GCF_000423725.1_ASM42372v1_genomic.fna/dqc_result.json
[2024-01-24 13:37:57,296] [INFO] DFAST_QC completed!
[2024-01-24 13:37:57,296] [INFO] Total running time: 0h0m46s