[2023-06-13 14:06:11,087] [INFO] DFAST_QC pipeline started.
[2023-06-13 14:06:11,091] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 14:06:11,091] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd176f20-2c0f-4ad5-bf6a-e51989025260/dqc_reference
[2023-06-13 14:06:12,424] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 14:06:12,425] [INFO] Task started: Prodigal
[2023-06-13 14:06:12,425] [INFO] Running command: gunzip -c /var/lib/cwl/stg74516831-e602-491b-9c60-ed82ddae1a57/GCA_022752615.1_ASM2275261v1_genomic.fna.gz | prodigal -d GCA_022752615.1_ASM2275261v1_genomic.fna/cds.fna -a GCA_022752615.1_ASM2275261v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 14:06:14,352] [INFO] Task succeeded: Prodigal
[2023-06-13 14:06:14,353] [INFO] Task started: HMMsearch
[2023-06-13 14:06:14,353] [INFO] Running command: hmmsearch --tblout GCA_022752615.1_ASM2275261v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd176f20-2c0f-4ad5-bf6a-e51989025260/dqc_reference/reference_markers.hmm GCA_022752615.1_ASM2275261v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 14:06:14,622] [INFO] Task succeeded: HMMsearch
[2023-06-13 14:06:14,624] [INFO] Found 6/6 markers.
[2023-06-13 14:06:14,641] [INFO] Query marker FASTA was written to GCA_022752615.1_ASM2275261v1_genomic.fna/markers.fasta
[2023-06-13 14:06:14,642] [INFO] Task started: Blastn
[2023-06-13 14:06:14,642] [INFO] Running command: blastn -query GCA_022752615.1_ASM2275261v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd176f20-2c0f-4ad5-bf6a-e51989025260/dqc_reference/reference_markers.fasta -out GCA_022752615.1_ASM2275261v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:06:15,239] [INFO] Task succeeded: Blastn
[2023-06-13 14:06:15,243] [INFO] Selected 23 target genomes.
[2023-06-13 14:06:15,243] [INFO] Target genome list was writen to GCA_022752615.1_ASM2275261v1_genomic.fna/target_genomes.txt
[2023-06-13 14:06:15,244] [INFO] Task started: fastANI
[2023-06-13 14:06:15,244] [INFO] Running command: fastANI --query /var/lib/cwl/stg74516831-e602-491b-9c60-ed82ddae1a57/GCA_022752615.1_ASM2275261v1_genomic.fna.gz --refList GCA_022752615.1_ASM2275261v1_genomic.fna/target_genomes.txt --output GCA_022752615.1_ASM2275261v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 14:06:22,413] [INFO] Task succeeded: fastANI
[2023-06-13 14:06:22,414] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd176f20-2c0f-4ad5-bf6a-e51989025260/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 14:06:22,414] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd176f20-2c0f-4ad5-bf6a-e51989025260/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 14:06:22,425] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2023-06-13 14:06:22,425] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 14:06:22,425] [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 iners	strain=DSM 13335	GCA_000160875.1	147802	147802	type	True	98.7315	330	351	95	conclusive
Lactobacillus iners	strain=DSM 13335	GCA_001435015.1	147802	147802	type	True	98.6761	324	351	95	conclusive
Lactobacillus gasseri	strain=ATCC 33323	GCA_000014425.1	1596	1596	type	True	78.2641	79	351	95	below_threshold
Lactobacillus rodentium	strain=DSM 24759	GCA_024622425.1	947835	947835	type	True	78.2219	81	351	95	below_threshold
Lactobacillus paragasseri	strain=JCM 5343	GCA_003307275.1	2107999	2107999	type	True	78.1902	83	351	95	below_threshold
Lactobacillus gasseri	strain=ATCC 33323	GCA_008868295.1	1596	1596	type	True	78.1626	80	351	95	below_threshold
Lactobacillus hominis	strain=DSM 23910	GCA_001436125.1	1203033	1203033	type	True	78.0351	80	351	95	below_threshold
Lactobacillus hominis	strain=type strain:CRBIP 24.179	GCA_000296835.1	1203033	1203033	type	True	77.8974	84	351	95	below_threshold
Lactobacillus mulieris	strain=c10Ua161M	GCA_007095465.1	2508708	2508708	type	True	77.3415	64	351	95	below_threshold
Lactobacillus jensenii	strain=DSM 20557	GCA_001436455.1	109790	109790	type	True	77.1935	64	351	95	below_threshold
Lactobacillus jensenii	strain=ATCC 25258	GCA_018094625.1	109790	109790	type	True	77.0711	69	351	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 14:06:22,427] [INFO] DFAST Taxonomy check result was written to GCA_022752615.1_ASM2275261v1_genomic.fna/tc_result.tsv
[2023-06-13 14:06:22,428] [INFO] ===== Taxonomy check completed =====
[2023-06-13 14:06:22,428] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 14:06:22,428] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd176f20-2c0f-4ad5-bf6a-e51989025260/dqc_reference/checkm_data
[2023-06-13 14:06:22,430] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 14:06:22,444] [INFO] Task started: CheckM
[2023-06-13 14:06:22,444] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022752615.1_ASM2275261v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022752615.1_ASM2275261v1_genomic.fna/checkm_input GCA_022752615.1_ASM2275261v1_genomic.fna/checkm_result
[2023-06-13 14:06:37,148] [INFO] Task succeeded: CheckM
[2023-06-13 14:06:37,150] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 14:06:37,170] [INFO] ===== Completeness check finished =====
[2023-06-13 14:06:37,170] [INFO] ===== Start GTDB Search =====
[2023-06-13 14:06:37,171] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022752615.1_ASM2275261v1_genomic.fna/markers.fasta)
[2023-06-13 14:06:37,171] [INFO] Task started: Blastn
[2023-06-13 14:06:37,171] [INFO] Running command: blastn -query GCA_022752615.1_ASM2275261v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd176f20-2c0f-4ad5-bf6a-e51989025260/dqc_reference/reference_markers_gtdb.fasta -out GCA_022752615.1_ASM2275261v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:06:37,965] [INFO] Task succeeded: Blastn
[2023-06-13 14:06:37,976] [INFO] Selected 27 target genomes.
[2023-06-13 14:06:37,976] [INFO] Target genome list was writen to GCA_022752615.1_ASM2275261v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 14:06:37,977] [INFO] Task started: fastANI
[2023-06-13 14:06:37,978] [INFO] Running command: fastANI --query /var/lib/cwl/stg74516831-e602-491b-9c60-ed82ddae1a57/GCA_022752615.1_ASM2275261v1_genomic.fna.gz --refList GCA_022752615.1_ASM2275261v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022752615.1_ASM2275261v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 14:06:46,413] [INFO] Task succeeded: fastANI
[2023-06-13 14:06:46,426] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 14:06:46,427] [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_000160875.1	s__Lactobacillus iners	98.7315	330	351	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.75	98.36	0.94	0.90	32	conclusive
GCF_017874575.1	s__Lactobacillus colini	78.4461	65	351	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014425.1	s__Lactobacillus gasseri	78.2641	79	351	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.12	96.79	0.93	0.86	41	-
GCF_003423665.1	s__Lactobacillus rodentium	78.239	82	351	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584685.1	s__Lactobacillus paragasseri	78.2203	82	351	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.70	97.96	0.91	0.84	40	-
GCF_000296835.1	s__Lactobacillus hominis	77.9076	83	351	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.73	99.20	0.96	0.89	4	-
GCA_910589675.1	s__Lactobacillus sp910589675	77.5834	75	351	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.72	97.13	0.73	0.71	7	-
GCF_007095465.1	s__Lactobacillus mulieris	77.3415	64	351	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.54	96.91	0.92	0.85	18	-
GCF_001436455.1	s__Lactobacillus jensenii	77.1935	64	351	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.86	99.75	0.93	0.88	31	-
GCF_007570935.1	s__Lactobacillus sp007570935	76.9724	66	351	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018987235.1	s__Lactobacillus crispatus	76.8445	52	351	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.75	96.25	0.84	0.70	161	-
--------------------------------------------------------------------------------
[2023-06-13 14:06:46,429] [INFO] GTDB search result was written to GCA_022752615.1_ASM2275261v1_genomic.fna/result_gtdb.tsv
[2023-06-13 14:06:46,430] [INFO] ===== GTDB Search completed =====
[2023-06-13 14:06:46,434] [INFO] DFAST_QC result json was written to GCA_022752615.1_ASM2275261v1_genomic.fna/dqc_result.json
[2023-06-13 14:06:46,434] [INFO] DFAST_QC completed!
[2023-06-13 14:06:46,434] [INFO] Total running time: 0h0m35s