[2023-06-05 08:38:47,740] [INFO] DFAST_QC pipeline started.
[2023-06-05 08:38:47,742] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 08:38:47,742] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3f94456-9f19-4e48-9972-7831379d897d/dqc_reference
[2023-06-05 08:38:49,716] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 08:38:49,717] [INFO] Task started: Prodigal
[2023-06-05 08:38:49,718] [INFO] Running command: gunzip -c /var/lib/cwl/stg212e57b2-a40c-4ac5-baa4-3e3abaa696e3/GCA_934201875.1_ERR7738204_bin.150_genomic.fna.gz | prodigal -d GCA_934201875.1_ERR7738204_bin.150_genomic.fna/cds.fna -a GCA_934201875.1_ERR7738204_bin.150_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 08:38:52,746] [INFO] Task succeeded: Prodigal
[2023-06-05 08:38:52,746] [INFO] Task started: HMMsearch
[2023-06-05 08:38:52,746] [INFO] Running command: hmmsearch --tblout GCA_934201875.1_ERR7738204_bin.150_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3f94456-9f19-4e48-9972-7831379d897d/dqc_reference/reference_markers.hmm GCA_934201875.1_ERR7738204_bin.150_genomic.fna/protein.faa > /dev/null
[2023-06-05 08:38:52,976] [INFO] Task succeeded: HMMsearch
[2023-06-05 08:38:52,977] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg212e57b2-a40c-4ac5-baa4-3e3abaa696e3/GCA_934201875.1_ERR7738204_bin.150_genomic.fna.gz]
[2023-06-05 08:38:53,002] [INFO] Query marker FASTA was written to GCA_934201875.1_ERR7738204_bin.150_genomic.fna/markers.fasta
[2023-06-05 08:38:53,003] [INFO] Task started: Blastn
[2023-06-05 08:38:53,003] [INFO] Running command: blastn -query GCA_934201875.1_ERR7738204_bin.150_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3f94456-9f19-4e48-9972-7831379d897d/dqc_reference/reference_markers.fasta -out GCA_934201875.1_ERR7738204_bin.150_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 08:38:53,740] [INFO] Task succeeded: Blastn
[2023-06-05 08:38:53,743] [INFO] Selected 7 target genomes.
[2023-06-05 08:38:53,744] [INFO] Target genome list was writen to GCA_934201875.1_ERR7738204_bin.150_genomic.fna/target_genomes.txt
[2023-06-05 08:38:53,745] [INFO] Task started: fastANI
[2023-06-05 08:38:53,745] [INFO] Running command: fastANI --query /var/lib/cwl/stg212e57b2-a40c-4ac5-baa4-3e3abaa696e3/GCA_934201875.1_ERR7738204_bin.150_genomic.fna.gz --refList GCA_934201875.1_ERR7738204_bin.150_genomic.fna/target_genomes.txt --output GCA_934201875.1_ERR7738204_bin.150_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 08:38:56,569] [INFO] Task succeeded: fastANI
[2023-06-05 08:38:56,569] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3f94456-9f19-4e48-9972-7831379d897d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 08:38:56,569] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3f94456-9f19-4e48-9972-7831379d897d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 08:38:56,577] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 08:38:56,577] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 08:38:56,577] [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 dispar	strain=ATCC 17748	GCA_000160015.1	39778	39778	suspected-type	True	93.2125	375	392	95	below_threshold
Veillonella dispar	strain=NCTC11831	GCA_900637515.1	39778	39778	suspected-type	True	93.2113	376	392	95	below_threshold
Veillonella nakazawae	strain=T1-7	GCA_013393365.1	2682456	2682456	type	True	91.691	376	392	95	below_threshold
Veillonella infantium	strain=T11011-4	GCA_002959895.1	1911679	1911679	type	True	91.5752	370	392	95	below_threshold
Veillonella rogosae	strain=JCM 15642	GCA_002959775.1	423477	423477	type	True	88.1483	358	392	95	below_threshold
Veillonella parvula	strain=NCTC11810	GCA_900186885.1	29466	29466	suspected-type	True	86.7804	363	392	95	below_threshold
Veillonella parvula	strain=DSM 2008	GCA_000024945.1	29466	29466	suspected-type	True	86.7463	367	392	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 08:38:56,581] [INFO] DFAST Taxonomy check result was written to GCA_934201875.1_ERR7738204_bin.150_genomic.fna/tc_result.tsv
[2023-06-05 08:38:56,581] [INFO] ===== Taxonomy check completed =====
[2023-06-05 08:38:56,581] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 08:38:56,581] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3f94456-9f19-4e48-9972-7831379d897d/dqc_reference/checkm_data
[2023-06-05 08:38:56,582] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 08:38:56,601] [INFO] Task started: CheckM
[2023-06-05 08:38:56,601] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934201875.1_ERR7738204_bin.150_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934201875.1_ERR7738204_bin.150_genomic.fna/checkm_input GCA_934201875.1_ERR7738204_bin.150_genomic.fna/checkm_result
[2023-06-05 08:39:13,396] [INFO] Task succeeded: CheckM
[2023-06-05 08:39:13,397] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 08:39:13,417] [INFO] ===== Completeness check finished =====
[2023-06-05 08:39:13,417] [INFO] ===== Start GTDB Search =====
[2023-06-05 08:39:13,418] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934201875.1_ERR7738204_bin.150_genomic.fna/markers.fasta)
[2023-06-05 08:39:13,418] [INFO] Task started: Blastn
[2023-06-05 08:39:13,418] [INFO] Running command: blastn -query GCA_934201875.1_ERR7738204_bin.150_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3f94456-9f19-4e48-9972-7831379d897d/dqc_reference/reference_markers_gtdb.fasta -out GCA_934201875.1_ERR7738204_bin.150_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 08:39:13,845] [INFO] Task succeeded: Blastn
[2023-06-05 08:39:13,849] [INFO] Selected 11 target genomes.
[2023-06-05 08:39:13,850] [INFO] Target genome list was writen to GCA_934201875.1_ERR7738204_bin.150_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 08:39:13,853] [INFO] Task started: fastANI
[2023-06-05 08:39:13,853] [INFO] Running command: fastANI --query /var/lib/cwl/stg212e57b2-a40c-4ac5-baa4-3e3abaa696e3/GCA_934201875.1_ERR7738204_bin.150_genomic.fna.gz --refList GCA_934201875.1_ERR7738204_bin.150_genomic.fna/target_genomes_gtdb.txt --output GCA_934201875.1_ERR7738204_bin.150_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 08:39:17,565] [INFO] Task succeeded: fastANI
[2023-06-05 08:39:17,576] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 08:39:17,576] [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_900550175.1	s__Veillonella sp900550175	94.4202	285	392	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	98.03	98.03	0.91	0.91	2	-
GCA_900538355.1	s__Veillonella sp900538355	93.7721	370	392	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_002959755.1	s__Veillonella sp002959755	93.213	374	392	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_900637515.1	s__Veillonella dispar	93.2113	376	392	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	96.54	95.48	0.96	0.91	7	-
GCA_900545205.1	s__Veillonella sp900545205	93.0898	342	392	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	97.54	95.18	0.86	0.80	3	-
GCA_905209685.1	s__Veillonella sp905209685	92.9621	309	392	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_900552715.1	s__Veillonella sp900552715	92.7423	318	392	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_003463825.1	s__Veillonella sp003463825	92.5703	361	392	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	97.70	95.41	0.92	0.86	3	-
GCA_900549845.1	s__Veillonella sp900549845	92.2428	271	392	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_902834965.1	s__Veillonella sp902834965	92.0751	203	392	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_900766125.1	s__Veillonella sp900766125	91.0151	250	392	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 08:39:17,578] [INFO] GTDB search result was written to GCA_934201875.1_ERR7738204_bin.150_genomic.fna/result_gtdb.tsv
[2023-06-05 08:39:17,579] [INFO] ===== GTDB Search completed =====
[2023-06-05 08:39:17,583] [INFO] DFAST_QC result json was written to GCA_934201875.1_ERR7738204_bin.150_genomic.fna/dqc_result.json
[2023-06-05 08:39:17,583] [INFO] DFAST_QC completed!
[2023-06-05 08:39:17,583] [INFO] Total running time: 0h0m30s