[2023-06-28 13:50:55,244] [INFO] DFAST_QC pipeline started.
[2023-06-28 13:50:55,249] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 13:50:55,249] [INFO] DQC Reference Directory: /var/lib/cwl/stge3f1e4dc-b02f-496e-86bc-3dd23b3d323e/dqc_reference
[2023-06-28 13:50:56,582] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 13:50:56,583] [INFO] Task started: Prodigal
[2023-06-28 13:50:56,583] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c5f0ab2-644f-42a4-93e7-9ad36a8072d8/GCA_017992425.1_ASM1799242v1_genomic.fna.gz | prodigal -d GCA_017992425.1_ASM1799242v1_genomic.fna/cds.fna -a GCA_017992425.1_ASM1799242v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 13:51:00,130] [INFO] Task succeeded: Prodigal
[2023-06-28 13:51:00,131] [INFO] Task started: HMMsearch
[2023-06-28 13:51:00,131] [INFO] Running command: hmmsearch --tblout GCA_017992425.1_ASM1799242v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge3f1e4dc-b02f-496e-86bc-3dd23b3d323e/dqc_reference/reference_markers.hmm GCA_017992425.1_ASM1799242v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 13:51:00,333] [INFO] Task succeeded: HMMsearch
[2023-06-28 13:51:00,334] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3c5f0ab2-644f-42a4-93e7-9ad36a8072d8/GCA_017992425.1_ASM1799242v1_genomic.fna.gz]
[2023-06-28 13:51:00,353] [INFO] Query marker FASTA was written to GCA_017992425.1_ASM1799242v1_genomic.fna/markers.fasta
[2023-06-28 13:51:00,353] [INFO] Task started: Blastn
[2023-06-28 13:51:00,353] [INFO] Running command: blastn -query GCA_017992425.1_ASM1799242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3f1e4dc-b02f-496e-86bc-3dd23b3d323e/dqc_reference/reference_markers.fasta -out GCA_017992425.1_ASM1799242v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:51:00,872] [INFO] Task succeeded: Blastn
[2023-06-28 13:51:00,875] [INFO] Selected 16 target genomes.
[2023-06-28 13:51:00,875] [INFO] Target genome list was writen to GCA_017992425.1_ASM1799242v1_genomic.fna/target_genomes.txt
[2023-06-28 13:51:00,882] [INFO] Task started: fastANI
[2023-06-28 13:51:00,882] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c5f0ab2-644f-42a4-93e7-9ad36a8072d8/GCA_017992425.1_ASM1799242v1_genomic.fna.gz --refList GCA_017992425.1_ASM1799242v1_genomic.fna/target_genomes.txt --output GCA_017992425.1_ASM1799242v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 13:51:06,434] [INFO] Task succeeded: fastANI
[2023-06-28 13:51:06,434] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge3f1e4dc-b02f-496e-86bc-3dd23b3d323e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 13:51:06,435] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge3f1e4dc-b02f-496e-86bc-3dd23b3d323e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 13:51:06,444] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 13:51:06,444] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 13:51:06,444] [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
Veillonella nakazawae	strain=T1-7	GCA_013393365.1	2682456	2682456	type	True	80.2579	221	570	95	below_threshold
Veillonella infantium	strain=T11011-4	GCA_002959895.1	1911679	1911679	type	True	80.1572	227	570	95	below_threshold
Veillonella dispar	strain=NCTC11831	GCA_900637515.1	39778	39778	suspected-type	True	80.1471	228	570	95	below_threshold
Veillonella dispar	strain=ATCC 17748	GCA_000160015.1	39778	39778	suspected-type	True	80.0291	233	570	95	below_threshold
Veillonella rogosae	strain=JCM 15642	GCA_002959775.1	423477	423477	type	True	80.0183	220	570	95	below_threshold
Veillonella rogosae	strain=JCM 15642	GCA_001312485.1	423477	423477	type	True	79.867	214	570	95	below_threshold
Veillonella tobetsuensis	strain=ATCC BAA-2400	GCA_001078375.1	1110546	1110546	type	True	79.6949	211	570	95	below_threshold
Veillonella atypica	strain=NCTC11830	GCA_900460235.1	39777	39777	type	True	79.5879	219	570	95	below_threshold
Veillonella atypica	strain=ATCC 17744	GCA_002959915.1	39777	39777	type	True	79.5687	213	570	95	below_threshold
Veillonella atypica	strain=KON	GCA_000318355.2	39777	39777	type	True	79.4113	218	570	95	below_threshold
Veillonella parvula	strain=DSM 2008	GCA_000024945.1	29466	29466	suspected-type	True	79.3966	217	570	95	below_threshold
Veillonella parvula	strain=NCTC11810	GCA_900186885.1	29466	29466	suspected-type	True	79.3906	214	570	95	below_threshold
Veillonella caviae	strain=DSM 20738	GCA_003992125.1	248316	248316	type	True	79.3257	206	570	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 13:51:06,446] [INFO] DFAST Taxonomy check result was written to GCA_017992425.1_ASM1799242v1_genomic.fna/tc_result.tsv
[2023-06-28 13:51:06,446] [INFO] ===== Taxonomy check completed =====
[2023-06-28 13:51:06,446] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 13:51:06,446] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge3f1e4dc-b02f-496e-86bc-3dd23b3d323e/dqc_reference/checkm_data
[2023-06-28 13:51:06,447] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 13:51:06,471] [INFO] Task started: CheckM
[2023-06-28 13:51:06,471] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017992425.1_ASM1799242v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017992425.1_ASM1799242v1_genomic.fna/checkm_input GCA_017992425.1_ASM1799242v1_genomic.fna/checkm_result
[2023-06-28 13:51:22,639] [INFO] Task succeeded: CheckM
[2023-06-28 13:51:22,640] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 13:51:22,651] [INFO] ===== Completeness check finished =====
[2023-06-28 13:51:22,651] [INFO] ===== Start GTDB Search =====
[2023-06-28 13:51:22,651] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017992425.1_ASM1799242v1_genomic.fna/markers.fasta)
[2023-06-28 13:51:22,651] [INFO] Task started: Blastn
[2023-06-28 13:51:22,651] [INFO] Running command: blastn -query GCA_017992425.1_ASM1799242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3f1e4dc-b02f-496e-86bc-3dd23b3d323e/dqc_reference/reference_markers_gtdb.fasta -out GCA_017992425.1_ASM1799242v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:51:23,297] [INFO] Task succeeded: Blastn
[2023-06-28 13:51:23,299] [INFO] Selected 14 target genomes.
[2023-06-28 13:51:23,299] [INFO] Target genome list was writen to GCA_017992425.1_ASM1799242v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 13:51:23,315] [INFO] Task started: fastANI
[2023-06-28 13:51:23,315] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c5f0ab2-644f-42a4-93e7-9ad36a8072d8/GCA_017992425.1_ASM1799242v1_genomic.fna.gz --refList GCA_017992425.1_ASM1799242v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017992425.1_ASM1799242v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 13:51:28,505] [INFO] Task succeeded: fastANI
[2023-06-28 13:51:28,514] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 13:51:28,514] [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
GCA_009929605.1	s__Veillonella sp009929605	99.4524	466	570	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	99.43	99.31	0.85	0.82	7	conclusive
GCF_013393365.1	s__Veillonella nakazawae	80.2579	221	570	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	96.23	95.05	0.93	0.87	33	-
GCF_002959895.1	s__Veillonella infantium	80.1572	227	570	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	95.95	95.95	0.93	0.93	2	-
GCF_002959755.1	s__Veillonella sp002959755	80.1531	222	570	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900538355.1	s__Veillonella sp900538355	80.0179	228	570	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902810435.1	s__Veillonella parvula_A	79.7657	206	570	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.7953	96.42	95.83	0.92	0.86	54	-
GCF_001078375.1	s__Veillonella tobetsuensis	79.6949	211	570	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	97.55	97.11	0.92	0.91	7	-
GCF_002959915.1	s__Veillonella atypica	79.5609	212	570	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	97.10	95.19	0.91	0.87	34	-
GCA_900550175.1	s__Veillonella sp900550175	79.5138	173	570	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	98.03	98.03	0.91	0.91	2	-
GCF_000024945.1	s__Veillonella parvula	79.4049	218	570	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.7953	98.96	96.87	0.98	0.94	4	-
GCF_003992125.1	s__Veillonella caviae	79.3257	206	570	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	98.44	98.44	0.87	0.87	2	-
GCA_905209685.1	s__Veillonella sp905209685	78.6503	181	570	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	95.07	95.07	0.78	0.78	2	-
GCA_900757715.1	s__Veillonella sp900757715	78.4043	174	570	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.4547	97.81	97.81	0.74	0.74	2	-
GCA_900556785.1	s__Veillonella sp900556785	77.8322	139	570	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 13:51:28,518] [INFO] GTDB search result was written to GCA_017992425.1_ASM1799242v1_genomic.fna/result_gtdb.tsv
[2023-06-28 13:51:28,519] [INFO] ===== GTDB Search completed =====
[2023-06-28 13:51:28,526] [INFO] DFAST_QC result json was written to GCA_017992425.1_ASM1799242v1_genomic.fna/dqc_result.json
[2023-06-28 13:51:28,526] [INFO] DFAST_QC completed!
[2023-06-28 13:51:28,526] [INFO] Total running time: 0h0m33s