[2023-06-13 18:12:32,611] [INFO] DFAST_QC pipeline started.
[2023-06-13 18:12:32,619] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 18:12:32,619] [INFO] DQC Reference Directory: /var/lib/cwl/stgfde14a3c-f322-4667-b18d-f1f890213fe5/dqc_reference
[2023-06-13 18:12:34,406] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 18:12:34,407] [INFO] Task started: Prodigal
[2023-06-13 18:12:34,407] [INFO] Running command: gunzip -c /var/lib/cwl/stg57e488bb-a1c9-4a35-8c24-0e0ebb0a757c/GCA_022752635.1_ASM2275263v1_genomic.fna.gz | prodigal -d GCA_022752635.1_ASM2275263v1_genomic.fna/cds.fna -a GCA_022752635.1_ASM2275263v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 18:12:36,153] [INFO] Task succeeded: Prodigal
[2023-06-13 18:12:36,153] [INFO] Task started: HMMsearch
[2023-06-13 18:12:36,154] [INFO] Running command: hmmsearch --tblout GCA_022752635.1_ASM2275263v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfde14a3c-f322-4667-b18d-f1f890213fe5/dqc_reference/reference_markers.hmm GCA_022752635.1_ASM2275263v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 18:12:36,343] [INFO] Task succeeded: HMMsearch
[2023-06-13 18:12:36,344] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg57e488bb-a1c9-4a35-8c24-0e0ebb0a757c/GCA_022752635.1_ASM2275263v1_genomic.fna.gz]
[2023-06-13 18:12:36,361] [INFO] Query marker FASTA was written to GCA_022752635.1_ASM2275263v1_genomic.fna/markers.fasta
[2023-06-13 18:12:36,362] [INFO] Task started: Blastn
[2023-06-13 18:12:36,362] [INFO] Running command: blastn -query GCA_022752635.1_ASM2275263v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfde14a3c-f322-4667-b18d-f1f890213fe5/dqc_reference/reference_markers.fasta -out GCA_022752635.1_ASM2275263v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 18:12:37,471] [INFO] Task succeeded: Blastn
[2023-06-13 18:12:37,496] [INFO] Selected 5 target genomes.
[2023-06-13 18:12:37,496] [INFO] Target genome list was writen to GCA_022752635.1_ASM2275263v1_genomic.fna/target_genomes.txt
[2023-06-13 18:12:37,498] [INFO] Task started: fastANI
[2023-06-13 18:12:37,498] [INFO] Running command: fastANI --query /var/lib/cwl/stg57e488bb-a1c9-4a35-8c24-0e0ebb0a757c/GCA_022752635.1_ASM2275263v1_genomic.fna.gz --refList GCA_022752635.1_ASM2275263v1_genomic.fna/target_genomes.txt --output GCA_022752635.1_ASM2275263v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 18:12:39,197] [INFO] Task succeeded: fastANI
[2023-06-13 18:12:39,197] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfde14a3c-f322-4667-b18d-f1f890213fe5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 18:12:39,198] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfde14a3c-f322-4667-b18d-f1f890213fe5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 18:12:39,204] [INFO] Found 5 fastANI hits (3 hits with ANI > threshold)
[2023-06-13 18:12:39,204] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 18:12:39,204] [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 gasseri	strain=ATCC 33323	GCA_008868295.1	1596	1596	type	True	98.7566	337	355	95	conclusive
Lactobacillus gasseri	strain=ATCC 33323	GCA_000014425.1	1596	1596	type	True	98.6855	341	355	95	conclusive
Lactobacillus gasseri	strain=NCTC13722	GCA_900452355.1	1596	1596	type	True	98.642	342	355	95	conclusive
Lactobacillus paragasseri	strain=JCM 5343	GCA_003307275.1	2107999	2107999	type	True	94.8743	322	355	95	below_threshold
Lactobacillus paragasseri	strain=JCM 5343	GCA_003584685.1	2107999	2107999	type	True	94.8743	324	355	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 18:12:39,206] [INFO] DFAST Taxonomy check result was written to GCA_022752635.1_ASM2275263v1_genomic.fna/tc_result.tsv
[2023-06-13 18:12:39,207] [INFO] ===== Taxonomy check completed =====
[2023-06-13 18:12:39,207] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 18:12:39,207] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfde14a3c-f322-4667-b18d-f1f890213fe5/dqc_reference/checkm_data
[2023-06-13 18:12:39,208] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 18:12:39,224] [INFO] Task started: CheckM
[2023-06-13 18:12:39,224] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022752635.1_ASM2275263v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022752635.1_ASM2275263v1_genomic.fna/checkm_input GCA_022752635.1_ASM2275263v1_genomic.fna/checkm_result
[2023-06-13 18:12:53,029] [INFO] Task succeeded: CheckM
[2023-06-13 18:12:53,031] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 18:12:53,056] [INFO] ===== Completeness check finished =====
[2023-06-13 18:12:53,057] [INFO] ===== Start GTDB Search =====
[2023-06-13 18:12:53,057] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022752635.1_ASM2275263v1_genomic.fna/markers.fasta)
[2023-06-13 18:12:53,057] [INFO] Task started: Blastn
[2023-06-13 18:12:53,057] [INFO] Running command: blastn -query GCA_022752635.1_ASM2275263v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfde14a3c-f322-4667-b18d-f1f890213fe5/dqc_reference/reference_markers_gtdb.fasta -out GCA_022752635.1_ASM2275263v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 18:12:53,762] [INFO] Task succeeded: Blastn
[2023-06-13 18:12:53,766] [INFO] Selected 8 target genomes.
[2023-06-13 18:12:53,766] [INFO] Target genome list was writen to GCA_022752635.1_ASM2275263v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 18:12:53,766] [INFO] Task started: fastANI
[2023-06-13 18:12:53,767] [INFO] Running command: fastANI --query /var/lib/cwl/stg57e488bb-a1c9-4a35-8c24-0e0ebb0a757c/GCA_022752635.1_ASM2275263v1_genomic.fna.gz --refList GCA_022752635.1_ASM2275263v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022752635.1_ASM2275263v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 18:12:56,357] [INFO] Task succeeded: fastANI
[2023-06-13 18:12:56,364] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 18:12:56,365] [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_000014425.1	s__Lactobacillus gasseri	98.6855	341	355	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.12	96.79	0.93	0.86	41	conclusive
GCF_003584685.1	s__Lactobacillus paragasseri	94.8743	324	355	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.70	97.96	0.91	0.84	40	-
GCF_001436695.1	s__Lactobacillus taiwanensis	86.4877	280	355	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.80	98.01	0.90	0.86	31	-
GCF_000159355.1	s__Lactobacillus johnsonii	85.9524	273	355	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.89	95.28	0.86	0.57	61	-
GCA_910589175.1	s__Lactobacillus sp910589175	85.7827	268	355	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910589675.1	s__Lactobacillus sp910589675	84.6187	136	355	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.72	97.13	0.73	0.71	7	-
GCA_014803905.1	s__Lactobacillus sp014803905	79.5716	91	355	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001436305.1	s__Lactobacillus ultunensis	78.7679	89	355	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.98	99.95	0.99	0.98	4	-
--------------------------------------------------------------------------------
[2023-06-13 18:12:56,366] [INFO] GTDB search result was written to GCA_022752635.1_ASM2275263v1_genomic.fna/result_gtdb.tsv
[2023-06-13 18:12:56,368] [INFO] ===== GTDB Search completed =====
[2023-06-13 18:12:56,370] [INFO] DFAST_QC result json was written to GCA_022752635.1_ASM2275263v1_genomic.fna/dqc_result.json
[2023-06-13 18:12:56,371] [INFO] DFAST_QC completed!
[2023-06-13 18:12:56,371] [INFO] Total running time: 0h0m24s