[2024-01-24 11:21:07,412] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:21:07,414] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:21:07,414] [INFO] DQC Reference Directory: /var/lib/cwl/stgf50ab924-f0b5-4fec-abfc-90374ec6181d/dqc_reference
[2024-01-24 11:21:11,961] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:21:11,962] [INFO] Task started: Prodigal
[2024-01-24 11:21:11,963] [INFO] Running command: gunzip -c /var/lib/cwl/stg47a66029-8575-47f0-a370-51f2580d29c5/GCF_900459365.1_45296_H02_genomic.fna.gz | prodigal -d GCF_900459365.1_45296_H02_genomic.fna/cds.fna -a GCF_900459365.1_45296_H02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:21:16,862] [INFO] Task succeeded: Prodigal
[2024-01-24 11:21:16,863] [INFO] Task started: HMMsearch
[2024-01-24 11:21:16,863] [INFO] Running command: hmmsearch --tblout GCF_900459365.1_45296_H02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf50ab924-f0b5-4fec-abfc-90374ec6181d/dqc_reference/reference_markers.hmm GCF_900459365.1_45296_H02_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:21:17,125] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:21:17,127] [INFO] Found 6/6 markers.
[2024-01-24 11:21:17,159] [INFO] Query marker FASTA was written to GCF_900459365.1_45296_H02_genomic.fna/markers.fasta
[2024-01-24 11:21:17,160] [INFO] Task started: Blastn
[2024-01-24 11:21:17,160] [INFO] Running command: blastn -query GCF_900459365.1_45296_H02_genomic.fna/markers.fasta -db /var/lib/cwl/stgf50ab924-f0b5-4fec-abfc-90374ec6181d/dqc_reference/reference_markers.fasta -out GCF_900459365.1_45296_H02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:19,106] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:19,109] [INFO] Selected 19 target genomes.
[2024-01-24 11:21:19,110] [INFO] Target genome list was writen to GCF_900459365.1_45296_H02_genomic.fna/target_genomes.txt
[2024-01-24 11:21:19,189] [INFO] Task started: fastANI
[2024-01-24 11:21:19,189] [INFO] Running command: fastANI --query /var/lib/cwl/stg47a66029-8575-47f0-a370-51f2580d29c5/GCF_900459365.1_45296_H02_genomic.fna.gz --refList GCF_900459365.1_45296_H02_genomic.fna/target_genomes.txt --output GCF_900459365.1_45296_H02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:21:28,984] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:28,985] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf50ab924-f0b5-4fec-abfc-90374ec6181d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:21:28,986] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf50ab924-f0b5-4fec-abfc-90374ec6181d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:21:29,002] [INFO] Found 17 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:21:29,003] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:21:29,003] [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 massiliensis	strain=NCTC13765	GCA_900459365.1	313439	313439	type	True	100.0	672	676	95	conclusive
Streptococcus massiliensis	strain=4401825	GCA_000341525.1	313439	313439	type	True	99.9113	557	676	95	conclusive
Streptococcus massiliensis	strain=DSM 18628	GCA_000380065.1	313439	313439	type	True	99.8987	569	676	95	conclusive
Streptococcus pyogenes	strain=PartK-Spyogenes-RM8376	GCA_022869605.1	1314	1314	type	True	81.1003	64	676	95	below_threshold
Streptococcus constellatus subsp. constellatus	strain=CCUG 24889	GCA_023167545.1	184246	76860	type	True	80.9455	164	676	95	below_threshold
Streptococcus canis	strain=NCTC12191	GCA_900636575.1	1329	1329	type	True	80.3909	84	676	95	below_threshold
Streptococcus sanguinis	strain=NCTC7863	GCA_900475505.1	1305	1305	suspected-type	True	80.051	170	676	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	79.8276	135	676	95	below_threshold
Streptococcus cristatus	strain=ATCC 51100	GCA_011612585.1	45634	45634	type	True	79.7752	182	676	95	below_threshold
Streptococcus gordonii	strain=FDAARGOS 1454	GCA_019046945.1	1302	1302	suspected-type	True	79.6832	174	676	95	below_threshold
Streptococcus sinensis	strain=HKU4	GCA_000767835.1	176090	176090	type	True	79.6027	166	676	95	below_threshold
Streptococcus parasanguinis	strain=NCTC12854	GCA_900459355.1	1318	1318	suspected-type	True	79.5052	129	676	95	below_threshold
Streptococcus parasanguinis	strain=ATCC 15912	GCA_000164675.2	1318	1318	suspected-type	True	79.416	132	676	95	below_threshold
Streptococcus sanguinis	strain=NCTC 7863	GCA_001593525.1	1305	1305	suspected-type	True	79.0398	162	676	95	below_threshold
Streptococcus pseudopneumoniae	strain=ATCC BAA-960	GCA_000257825.1	257758	257758	type	True	78.9368	106	676	95	below_threshold
Streptococcus pseudopneumoniae	strain=CCUG 49455	GCA_002087075.1	257758	257758	type	True	78.9282	120	676	95	below_threshold
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	78.7101	110	676	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:21:29,005] [INFO] DFAST Taxonomy check result was written to GCF_900459365.1_45296_H02_genomic.fna/tc_result.tsv
[2024-01-24 11:21:29,006] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:21:29,006] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:21:29,006] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf50ab924-f0b5-4fec-abfc-90374ec6181d/dqc_reference/checkm_data
[2024-01-24 11:21:29,008] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:21:29,030] [INFO] Task started: CheckM
[2024-01-24 11:21:29,030] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900459365.1_45296_H02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900459365.1_45296_H02_genomic.fna/checkm_input GCF_900459365.1_45296_H02_genomic.fna/checkm_result
[2024-01-24 11:21:50,369] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:50,374] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:50,394] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:50,395] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:50,395] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900459365.1_45296_H02_genomic.fna/markers.fasta)
[2024-01-24 11:21:50,395] [INFO] Task started: Blastn
[2024-01-24 11:21:50,396] [INFO] Running command: blastn -query GCF_900459365.1_45296_H02_genomic.fna/markers.fasta -db /var/lib/cwl/stgf50ab924-f0b5-4fec-abfc-90374ec6181d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900459365.1_45296_H02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:51,235] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:51,239] [INFO] Selected 22 target genomes.
[2024-01-24 11:21:51,240] [INFO] Target genome list was writen to GCF_900459365.1_45296_H02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:51,296] [INFO] Task started: fastANI
[2024-01-24 11:21:51,297] [INFO] Running command: fastANI --query /var/lib/cwl/stg47a66029-8575-47f0-a370-51f2580d29c5/GCF_900459365.1_45296_H02_genomic.fna.gz --refList GCF_900459365.1_45296_H02_genomic.fna/target_genomes_gtdb.txt --output GCF_900459365.1_45296_H02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:22:00,086] [INFO] Task succeeded: fastANI
[2024-01-24 11:22:00,109] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:22:00,110] [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_000380065.1	s__Streptococcus massiliensis	99.8987	569	676	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.99	99.98	1.00	0.99	3	conclusive
GCF_017883985.1	s__Streptococcus oricebi	80.3212	228	676	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001078705.1	s__Streptococcus sanguinis_D	79.7651	167	676	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902167705.1	s__Streptococcus constellatus_A	79.7555	168	676	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000722765.2	s__Streptococcus mitis_AQ	79.5545	136	676	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.85	96.85	0.91	0.91	2	-
GCF_000287715.1	s__Streptococcus oralis_Y	79.5539	112	676	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.24	95.17	0.89	0.88	3	-
GCF_900104285.1	s__Streptococcus sp900104285	79.4824	125	676	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000385925.1	s__Streptococcus cristatus_B	79.4706	184	676	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.95	99.95	1.00	0.99	3	-
GCF_000164675.2	s__Streptococcus parasanguinis	79.4559	131	676	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.96	95.18	0.90	0.85	22	-
GCF_003627135.1	s__Streptococcus koreensis	79.3885	114	676	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.43	95.11	0.91	0.89	8	-
GCF_902460355.1	s__Streptococcus sp902460355	79.3595	177	676	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000194945.1	s__Streptococcus sanguinis	79.2556	165	676	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.01	0.93	0.89	47	-
GCF_001578775.1	s__Streptococcus cristatus_A	79.1698	170	676	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000212855.1	s__Streptococcus sanguinis_A	79.1674	170	676	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003943735.1	s__Streptococcus sanguinis_E	79.0702	172	676	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.70	95.02	0.91	0.89	6	-
GCF_000186465.1	s__Streptococcus australis	79.0296	118	676	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.56	95.15	0.93	0.86	5	-
GCA_001578795.1	s__Streptococcus gordonii_A	78.9629	165	676	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003943505.1	s__Streptococcus cristatus_E	78.7954	177	676	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009717815.1	s__Streptococcus parasanguinis_F	78.7569	122	676	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.25	95.86	95.53	0.89	0.86	10	-
GCF_004127215.1	s__Streptococcus oralis_BD	78.5814	133	676	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.79	95.74	0.90	0.90	3	-
GCF_017884005.1	s__Streptococcus panodentis	78.5281	182	676	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.49	98.49	0.90	0.90	2	-
GCA_001579015.1	s__Streptococcus oralis_K	78.4249	130	676	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:22:00,111] [INFO] GTDB search result was written to GCF_900459365.1_45296_H02_genomic.fna/result_gtdb.tsv
[2024-01-24 11:22:00,112] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:22:00,116] [INFO] DFAST_QC result json was written to GCF_900459365.1_45296_H02_genomic.fna/dqc_result.json
[2024-01-24 11:22:00,116] [INFO] DFAST_QC completed!
[2024-01-24 11:22:00,116] [INFO] Total running time: 0h0m53s