[2024-01-25 17:38:05,483] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:38:05,492] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:38:05,493] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b684396-13a6-4639-9335-8e078ba446b0/dqc_reference
[2024-01-25 17:38:06,672] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:38:06,673] [INFO] Task started: Prodigal
[2024-01-25 17:38:06,673] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a452d07-bf83-40a5-b1b7-053c50b975ee/GCF_002088015.1_ASM208801v1_genomic.fna.gz | prodigal -d GCF_002088015.1_ASM208801v1_genomic.fna/cds.fna -a GCF_002088015.1_ASM208801v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:38:10,058] [INFO] Task succeeded: Prodigal
[2024-01-25 17:38:10,058] [INFO] Task started: HMMsearch
[2024-01-25 17:38:10,059] [INFO] Running command: hmmsearch --tblout GCF_002088015.1_ASM208801v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b684396-13a6-4639-9335-8e078ba446b0/dqc_reference/reference_markers.hmm GCF_002088015.1_ASM208801v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:38:10,261] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:38:10,262] [INFO] Found 6/6 markers.
[2024-01-25 17:38:10,281] [INFO] Query marker FASTA was written to GCF_002088015.1_ASM208801v1_genomic.fna/markers.fasta
[2024-01-25 17:38:10,281] [INFO] Task started: Blastn
[2024-01-25 17:38:10,282] [INFO] Running command: blastn -query GCF_002088015.1_ASM208801v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b684396-13a6-4639-9335-8e078ba446b0/dqc_reference/reference_markers.fasta -out GCF_002088015.1_ASM208801v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:38:10,834] [INFO] Task succeeded: Blastn
[2024-01-25 17:38:10,841] [INFO] Selected 12 target genomes.
[2024-01-25 17:38:10,841] [INFO] Target genome list was writen to GCF_002088015.1_ASM208801v1_genomic.fna/target_genomes.txt
[2024-01-25 17:38:10,845] [INFO] Task started: fastANI
[2024-01-25 17:38:10,845] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a452d07-bf83-40a5-b1b7-053c50b975ee/GCF_002088015.1_ASM208801v1_genomic.fna.gz --refList GCF_002088015.1_ASM208801v1_genomic.fna/target_genomes.txt --output GCF_002088015.1_ASM208801v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:38:17,083] [INFO] Task succeeded: fastANI
[2024-01-25 17:38:17,084] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b684396-13a6-4639-9335-8e078ba446b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:38:17,084] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b684396-13a6-4639-9335-8e078ba446b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:38:17,092] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 17:38:17,092] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:38:17,092] [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 crispatus	strain=ATCC 33820	GCA_002088015.1	47770	47770	type	True	100.0	626	631	95	conclusive
Lactobacillus crispatus	strain=ATCC 33820	GCA_018987235.1	47770	47770	suspected-type	True	99.9908	631	631	95	conclusive
Lactobacillus crispatus	strain=NCK2488	GCA_008694755.1	47770	47770	type	True	99.9726	577	631	95	conclusive
Lactobacillus crispatus	strain=DSM 20584	GCA_001434005.1	47770	47770	type	True	99.9593	579	631	95	conclusive
Lactobacillus amylovorus	strain=DSM 20531	GCA_002706375.1	1604	1604	type	True	82.6491	364	631	95	below_threshold
Lactobacillus kefiranofaciens subsp. kefirgranum	strain=DSM 10550	GCA_001434195.1	190906	267818	type	True	81.8871	339	631	95	below_threshold
Lactobacillus ultunensis	strain=DSM 16047	GCA_001436305.1	227945	227945	type	True	81.7137	359	631	95	below_threshold
Lactobacillus intestinalis	strain=DSM 6629	GCA_024397795.1	151781	151781	type	True	80.2089	222	631	95	below_threshold
Lactobacillus rodentium	strain=DSM 24759	GCA_024622425.1	947835	947835	type	True	78.7877	103	631	95	below_threshold
Lactobacillus apis	strain=LMG 26964	GCA_002837055.1	303541	303541	type	True	78.109	122	631	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:38:17,094] [INFO] DFAST Taxonomy check result was written to GCF_002088015.1_ASM208801v1_genomic.fna/tc_result.tsv
[2024-01-25 17:38:17,095] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:38:17,095] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:38:17,095] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b684396-13a6-4639-9335-8e078ba446b0/dqc_reference/checkm_data
[2024-01-25 17:38:17,096] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:38:17,122] [INFO] Task started: CheckM
[2024-01-25 17:38:17,122] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002088015.1_ASM208801v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002088015.1_ASM208801v1_genomic.fna/checkm_input GCF_002088015.1_ASM208801v1_genomic.fna/checkm_result
[2024-01-25 17:38:33,172] [INFO] Task succeeded: CheckM
[2024-01-25 17:38:33,173] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:38:33,223] [INFO] ===== Completeness check finished =====
[2024-01-25 17:38:33,223] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:38:33,223] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002088015.1_ASM208801v1_genomic.fna/markers.fasta)
[2024-01-25 17:38:33,224] [INFO] Task started: Blastn
[2024-01-25 17:38:33,224] [INFO] Running command: blastn -query GCF_002088015.1_ASM208801v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b684396-13a6-4639-9335-8e078ba446b0/dqc_reference/reference_markers_gtdb.fasta -out GCF_002088015.1_ASM208801v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:38:34,000] [INFO] Task succeeded: Blastn
[2024-01-25 17:38:34,003] [INFO] Selected 12 target genomes.
[2024-01-25 17:38:34,003] [INFO] Target genome list was writen to GCF_002088015.1_ASM208801v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:38:34,006] [INFO] Task started: fastANI
[2024-01-25 17:38:34,006] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a452d07-bf83-40a5-b1b7-053c50b975ee/GCF_002088015.1_ASM208801v1_genomic.fna.gz --refList GCF_002088015.1_ASM208801v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002088015.1_ASM208801v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:38:39,490] [INFO] Task succeeded: fastANI
[2024-01-25 17:38:39,498] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:38:39,498] [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_018987235.1	s__Lactobacillus crispatus	99.9908	631	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.75	96.25	0.84	0.70	161	conclusive
GCF_001434975.1	s__Lactobacillus gallinarum	82.8278	359	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.30	97.84	0.88	0.84	17	-
GCF_000615285.1	s__Lactobacillus kitasatonis	82.7654	349	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.87	97.76	0.93	0.87	3	-
GCF_002706375.1	s__Lactobacillus amylovorus	82.6062	366	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.43	96.81	0.87	0.78	24	-
GCF_000160855.1	s__Lactobacillus helveticus	82.1904	350	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.35	96.37	0.85	0.75	146	-
GCF_001591845.1	s__Lactobacillus acidophilus	81.9453	342	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.96	99.12	0.99	0.94	59	-
GCF_900103655.1	s__Lactobacillus kefiranofaciens	81.8776	339	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.62	99.18	0.95	0.85	9	-
GCF_001436305.1	s__Lactobacillus ultunensis	81.7436	358	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.98	99.95	0.99	0.98	4	-
GCF_000615445.1	s__Lactobacillus hamsteri	80.3978	242	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.97	99.97	0.99	0.99	2	-
GCA_014803905.1	s__Lactobacillus sp014803905	78.5724	66	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:38:39,499] [INFO] GTDB search result was written to GCF_002088015.1_ASM208801v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:38:39,500] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:38:39,503] [INFO] DFAST_QC result json was written to GCF_002088015.1_ASM208801v1_genomic.fna/dqc_result.json
[2024-01-25 17:38:39,503] [INFO] DFAST_QC completed!
[2024-01-25 17:38:39,504] [INFO] Total running time: 0h0m34s