[2023-06-13 11:50:16,160] [INFO] DFAST_QC pipeline started.
[2023-06-13 11:50:16,162] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 11:50:16,162] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d88d4e5-c642-4d7e-b0b0-89a82e781b3a/dqc_reference
[2023-06-13 11:50:17,389] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 11:50:17,390] [INFO] Task started: Prodigal
[2023-06-13 11:50:17,391] [INFO] Running command: gunzip -c /var/lib/cwl/stgc3850969-df02-4961-9bb1-206f8e348017/GCA_022752835.1_ASM2275283v1_genomic.fna.gz | prodigal -d GCA_022752835.1_ASM2275283v1_genomic.fna/cds.fna -a GCA_022752835.1_ASM2275283v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 11:50:19,201] [INFO] Task succeeded: Prodigal
[2023-06-13 11:50:19,201] [INFO] Task started: HMMsearch
[2023-06-13 11:50:19,201] [INFO] Running command: hmmsearch --tblout GCA_022752835.1_ASM2275283v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d88d4e5-c642-4d7e-b0b0-89a82e781b3a/dqc_reference/reference_markers.hmm GCA_022752835.1_ASM2275283v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 11:50:19,423] [INFO] Task succeeded: HMMsearch
[2023-06-13 11:50:19,424] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc3850969-df02-4961-9bb1-206f8e348017/GCA_022752835.1_ASM2275283v1_genomic.fna.gz]
[2023-06-13 11:50:19,440] [INFO] Query marker FASTA was written to GCA_022752835.1_ASM2275283v1_genomic.fna/markers.fasta
[2023-06-13 11:50:19,440] [INFO] Task started: Blastn
[2023-06-13 11:50:19,441] [INFO] Running command: blastn -query GCA_022752835.1_ASM2275283v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d88d4e5-c642-4d7e-b0b0-89a82e781b3a/dqc_reference/reference_markers.fasta -out GCA_022752835.1_ASM2275283v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:50:20,045] [INFO] Task succeeded: Blastn
[2023-06-13 11:50:20,050] [INFO] Selected 13 target genomes.
[2023-06-13 11:50:20,050] [INFO] Target genome list was writen to GCA_022752835.1_ASM2275283v1_genomic.fna/target_genomes.txt
[2023-06-13 11:50:20,056] [INFO] Task started: fastANI
[2023-06-13 11:50:20,057] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3850969-df02-4961-9bb1-206f8e348017/GCA_022752835.1_ASM2275283v1_genomic.fna.gz --refList GCA_022752835.1_ASM2275283v1_genomic.fna/target_genomes.txt --output GCA_022752835.1_ASM2275283v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 11:50:23,913] [INFO] Task succeeded: fastANI
[2023-06-13 11:50:23,914] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d88d4e5-c642-4d7e-b0b0-89a82e781b3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 11:50:23,914] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d88d4e5-c642-4d7e-b0b0-89a82e781b3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 11:50:23,930] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2023-06-13 11:50:23,930] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 11:50:23,931] [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
Lactobacillus jensenii	strain=ATCC 25258	GCA_018094625.1	109790	109790	type	True	99.8962	269	270	95	conclusive
Lactobacillus jensenii	strain=DSM 20557	GCA_001436455.1	109790	109790	type	True	99.7916	264	270	95	conclusive
Lactobacillus mulieris	strain=c10Ua161M	GCA_007095465.1	2508708	2508708	type	True	88.1948	230	270	95	below_threshold
Lactobacillus psittaci	strain=DSM 15354	GCA_001435695.1	116089	116089	type	True	87.1983	168	270	95	below_threshold
Lactobacillus psittaci	strain=DSM 15354	GCA_000425905.1	116089	116089	type	True	86.9738	167	270	95	below_threshold
Lactobacillus intestinalis	strain=DSM 6629	GCA_024397795.1	151781	151781	type	True	77.6028	60	270	95	below_threshold
Lactobacillus acidophilus	strain=ATCC 4356	GCA_000786395.1	1579	1579	type	True	77.331	72	270	95	below_threshold
Lactobacillus acidophilus	strain=DSM 20079	GCA_001433895.1	1579	1579	type	True	77.3309	72	270	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 11:50:23,933] [INFO] DFAST Taxonomy check result was written to GCA_022752835.1_ASM2275283v1_genomic.fna/tc_result.tsv
[2023-06-13 11:50:23,934] [INFO] ===== Taxonomy check completed =====
[2023-06-13 11:50:23,934] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 11:50:23,934] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d88d4e5-c642-4d7e-b0b0-89a82e781b3a/dqc_reference/checkm_data
[2023-06-13 11:50:23,936] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 11:50:23,954] [INFO] Task started: CheckM
[2023-06-13 11:50:23,955] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022752835.1_ASM2275283v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022752835.1_ASM2275283v1_genomic.fna/checkm_input GCA_022752835.1_ASM2275283v1_genomic.fna/checkm_result
[2023-06-13 11:50:37,920] [INFO] Task succeeded: CheckM
[2023-06-13 11:50:37,921] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 33.33%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 11:50:37,943] [INFO] ===== Completeness check finished =====
[2023-06-13 11:50:37,943] [INFO] ===== Start GTDB Search =====
[2023-06-13 11:50:37,944] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022752835.1_ASM2275283v1_genomic.fna/markers.fasta)
[2023-06-13 11:50:37,944] [INFO] Task started: Blastn
[2023-06-13 11:50:37,944] [INFO] Running command: blastn -query GCA_022752835.1_ASM2275283v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d88d4e5-c642-4d7e-b0b0-89a82e781b3a/dqc_reference/reference_markers_gtdb.fasta -out GCA_022752835.1_ASM2275283v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:50:38,769] [INFO] Task succeeded: Blastn
[2023-06-13 11:50:38,773] [INFO] Selected 15 target genomes.
[2023-06-13 11:50:38,774] [INFO] Target genome list was writen to GCA_022752835.1_ASM2275283v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 11:50:38,778] [INFO] Task started: fastANI
[2023-06-13 11:50:38,778] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3850969-df02-4961-9bb1-206f8e348017/GCA_022752835.1_ASM2275283v1_genomic.fna.gz --refList GCA_022752835.1_ASM2275283v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022752835.1_ASM2275283v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 11:50:43,034] [INFO] Task succeeded: fastANI
[2023-06-13 11:50:43,052] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 11:50:43,053] [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_001436455.1	s__Lactobacillus jensenii	99.7916	264	270	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.86	99.75	0.93	0.88	31	conclusive
GCF_007095465.1	s__Lactobacillus mulieris	88.1948	230	270	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.54	96.91	0.92	0.85	18	-
GCF_000425905.1	s__Lactobacillus psittaci	86.9738	167	270	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.95	99.95	0.99	0.99	2	-
GCF_000160855.1	s__Lactobacillus helveticus	77.9494	54	270	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.35	96.37	0.85	0.75	146	-
GCF_000615285.1	s__Lactobacillus kitasatonis	77.7338	56	270	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.87	97.76	0.93	0.87	3	-
GCF_001434975.1	s__Lactobacillus gallinarum	77.7101	54	270	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.30	97.84	0.88	0.84	17	-
GCF_001435325.1	s__Lactobacillus intestinalis	77.6041	60	270	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.33	96.07	0.89	0.82	9	-
GCF_001436695.1	s__Lactobacillus taiwanensis	77.4506	51	270	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.80	98.01	0.90	0.86	31	-
GCF_001591845.1	s__Lactobacillus acidophilus	77.3999	71	270	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.96	99.12	0.99	0.94	59	-
GCF_001434335.1	s__Lactobacillus kalixensis	77.3782	61	270	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883635.1	s__Lactobacillus pullistercoris	77.1671	60	270	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 11:50:43,055] [INFO] GTDB search result was written to GCA_022752835.1_ASM2275283v1_genomic.fna/result_gtdb.tsv
[2023-06-13 11:50:43,056] [INFO] ===== GTDB Search completed =====
[2023-06-13 11:50:43,060] [INFO] DFAST_QC result json was written to GCA_022752835.1_ASM2275283v1_genomic.fna/dqc_result.json
[2023-06-13 11:50:43,060] [INFO] DFAST_QC completed!
[2023-06-13 11:50:43,060] [INFO] Total running time: 0h0m27s