[2023-06-29 11:07:05,789] [INFO] DFAST_QC pipeline started.
[2023-06-29 11:07:05,791] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 11:07:05,791] [INFO] DQC Reference Directory: /var/lib/cwl/stg794f8d4d-fd1c-4642-a499-a74789bc1737/dqc_reference
[2023-06-29 11:07:06,955] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 11:07:06,956] [INFO] Task started: Prodigal
[2023-06-29 11:07:06,956] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b47429c-4353-4d47-9ed4-0e02c1807459/GCA_912431345.1_DRR076990_bin.2_metaWRAP_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_912431345.1_DRR076990_bin.2_metaWRAP_v1.1_MAG_genomic.fna/cds.fna -a GCA_912431345.1_DRR076990_bin.2_metaWRAP_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 11:07:09,313] [INFO] Task succeeded: Prodigal
[2023-06-29 11:07:09,313] [INFO] Task started: HMMsearch
[2023-06-29 11:07:09,313] [INFO] Running command: hmmsearch --tblout GCA_912431345.1_DRR076990_bin.2_metaWRAP_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg794f8d4d-fd1c-4642-a499-a74789bc1737/dqc_reference/reference_markers.hmm GCA_912431345.1_DRR076990_bin.2_metaWRAP_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 11:07:09,455] [INFO] Task succeeded: HMMsearch
[2023-06-29 11:07:09,456] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg0b47429c-4353-4d47-9ed4-0e02c1807459/GCA_912431345.1_DRR076990_bin.2_metaWRAP_v1.1_MAG_genomic.fna.gz]
[2023-06-29 11:07:09,473] [INFO] Query marker FASTA was written to GCA_912431345.1_DRR076990_bin.2_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 11:07:09,474] [INFO] Task started: Blastn
[2023-06-29 11:07:09,474] [INFO] Running command: blastn -query GCA_912431345.1_DRR076990_bin.2_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg794f8d4d-fd1c-4642-a499-a74789bc1737/dqc_reference/reference_markers.fasta -out GCA_912431345.1_DRR076990_bin.2_metaWRAP_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 11:07:09,998] [INFO] Task succeeded: Blastn
[2023-06-29 11:07:10,002] [INFO] Selected 12 target genomes.
[2023-06-29 11:07:10,002] [INFO] Target genome list was writen to GCA_912431345.1_DRR076990_bin.2_metaWRAP_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 11:07:10,007] [INFO] Task started: fastANI
[2023-06-29 11:07:10,008] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b47429c-4353-4d47-9ed4-0e02c1807459/GCA_912431345.1_DRR076990_bin.2_metaWRAP_v1.1_MAG_genomic.fna.gz --refList GCA_912431345.1_DRR076990_bin.2_metaWRAP_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_912431345.1_DRR076990_bin.2_metaWRAP_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 11:07:13,490] [INFO] Task succeeded: fastANI
[2023-06-29 11:07:13,490] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg794f8d4d-fd1c-4642-a499-a74789bc1737/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 11:07:13,491] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg794f8d4d-fd1c-4642-a499-a74789bc1737/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 11:07:13,498] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 11:07:13,499] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 11:07:13,499] [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 atypica	strain=NCTC11830	GCA_900460235.1	39777	39777	type	True	93.4278	230	278	95	below_threshold
Veillonella atypica	strain=KON	GCA_000318355.2	39777	39777	type	True	93.3722	231	278	95	below_threshold
Veillonella atypica	strain=ATCC 17744	GCA_002959915.1	39777	39777	type	True	93.3193	234	278	95	below_threshold
Veillonella dispar	strain=NCTC11831	GCA_900637515.1	39778	39778	suspected-type	True	91.362	237	278	95	below_threshold
Veillonella dispar	strain=ATCC 17748	GCA_000160015.1	39778	39778	suspected-type	True	91.2868	239	278	95	below_threshold
Veillonella rogosae	strain=JCM 15642	GCA_002959775.1	423477	423477	type	True	88.3917	235	278	95	below_threshold
Veillonella rogosae	strain=JCM 15642	GCA_001312485.1	423477	423477	type	True	88.2144	233	278	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 11:07:13,501] [INFO] DFAST Taxonomy check result was written to GCA_912431345.1_DRR076990_bin.2_metaWRAP_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 11:07:13,501] [INFO] ===== Taxonomy check completed =====
[2023-06-29 11:07:13,502] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 11:07:13,502] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg794f8d4d-fd1c-4642-a499-a74789bc1737/dqc_reference/checkm_data
[2023-06-29 11:07:13,503] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 11:07:13,520] [INFO] Task started: CheckM
[2023-06-29 11:07:13,520] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_912431345.1_DRR076990_bin.2_metaWRAP_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_912431345.1_DRR076990_bin.2_metaWRAP_v1.1_MAG_genomic.fna/checkm_input GCA_912431345.1_DRR076990_bin.2_metaWRAP_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 11:07:28,120] [INFO] Task succeeded: CheckM
[2023-06-29 11:07:28,122] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 11:07:28,148] [INFO] ===== Completeness check finished =====
[2023-06-29 11:07:28,148] [INFO] ===== Start GTDB Search =====
[2023-06-29 11:07:28,148] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_912431345.1_DRR076990_bin.2_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 11:07:28,149] [INFO] Task started: Blastn
[2023-06-29 11:07:28,149] [INFO] Running command: blastn -query GCA_912431345.1_DRR076990_bin.2_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg794f8d4d-fd1c-4642-a499-a74789bc1737/dqc_reference/reference_markers_gtdb.fasta -out GCA_912431345.1_DRR076990_bin.2_metaWRAP_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 11:07:28,800] [INFO] Task succeeded: Blastn
[2023-06-29 11:07:28,804] [INFO] Selected 15 target genomes.
[2023-06-29 11:07:28,804] [INFO] Target genome list was writen to GCA_912431345.1_DRR076990_bin.2_metaWRAP_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 11:07:28,817] [INFO] Task started: fastANI
[2023-06-29 11:07:28,817] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b47429c-4353-4d47-9ed4-0e02c1807459/GCA_912431345.1_DRR076990_bin.2_metaWRAP_v1.1_MAG_genomic.fna.gz --refList GCA_912431345.1_DRR076990_bin.2_metaWRAP_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_912431345.1_DRR076990_bin.2_metaWRAP_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 11:07:33,479] [INFO] Task succeeded: fastANI
[2023-06-29 11:07:33,488] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 11:07:33,488] [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_002959915.1	s__Veillonella atypica	93.3998	233	278	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	97.10	95.19	0.91	0.87	34	-
GCF_013393365.1	s__Veillonella nakazawae	92.4303	244	278	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_003463825.1	s__Veillonella sp003463825	91.3317	223	278	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_905214495.1	s__Veillonella sp905214495	90.8849	201	278	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	90.1877	245	278	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	89.5792	237	278	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_900550175.1	s__Veillonella sp900550175	89.3538	210	278	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_905209685.1	s__Veillonella sp905209685	89.0088	212	278	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	95.07	95.07	0.78	0.78	2	-
GCF_002959775.1	s__Veillonella rogosae	88.3917	235	278	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	96.92	95.91	0.92	0.87	12	-
GCA_900552445.1	s__Veillonella sp900552445	86.7685	156	278	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	97.10	97.10	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-06-29 11:07:33,490] [INFO] GTDB search result was written to GCA_912431345.1_DRR076990_bin.2_metaWRAP_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 11:07:33,491] [INFO] ===== GTDB Search completed =====
[2023-06-29 11:07:33,494] [INFO] DFAST_QC result json was written to GCA_912431345.1_DRR076990_bin.2_metaWRAP_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 11:07:33,495] [INFO] DFAST_QC completed!
[2023-06-29 11:07:33,495] [INFO] Total running time: 0h0m28s