[2024-01-24 11:22:49,491] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:22:49,493] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:22:49,493] [INFO] DQC Reference Directory: /var/lib/cwl/stgaed00b16-2f0d-415b-aad9-bfc20006e986/dqc_reference
[2024-01-24 11:22:50,720] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:22:50,721] [INFO] Task started: Prodigal
[2024-01-24 11:22:50,722] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f13912b-a72a-4a93-9047-2fb225092064/GCF_001434945.1_ASM143494v1_genomic.fna.gz | prodigal -d GCF_001434945.1_ASM143494v1_genomic.fna/cds.fna -a GCF_001434945.1_ASM143494v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:22:53,936] [INFO] Task succeeded: Prodigal
[2024-01-24 11:22:53,936] [INFO] Task started: HMMsearch
[2024-01-24 11:22:53,937] [INFO] Running command: hmmsearch --tblout GCF_001434945.1_ASM143494v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaed00b16-2f0d-415b-aad9-bfc20006e986/dqc_reference/reference_markers.hmm GCF_001434945.1_ASM143494v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:22:54,171] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:22:54,173] [INFO] Found 6/6 markers.
[2024-01-24 11:22:54,196] [INFO] Query marker FASTA was written to GCF_001434945.1_ASM143494v1_genomic.fna/markers.fasta
[2024-01-24 11:22:54,196] [INFO] Task started: Blastn
[2024-01-24 11:22:54,197] [INFO] Running command: blastn -query GCF_001434945.1_ASM143494v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaed00b16-2f0d-415b-aad9-bfc20006e986/dqc_reference/reference_markers.fasta -out GCF_001434945.1_ASM143494v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:22:54,780] [INFO] Task succeeded: Blastn
[2024-01-24 11:22:54,783] [INFO] Selected 13 target genomes.
[2024-01-24 11:22:54,784] [INFO] Target genome list was writen to GCF_001434945.1_ASM143494v1_genomic.fna/target_genomes.txt
[2024-01-24 11:22:56,246] [INFO] Task started: fastANI
[2024-01-24 11:22:56,247] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f13912b-a72a-4a93-9047-2fb225092064/GCF_001434945.1_ASM143494v1_genomic.fna.gz --refList GCF_001434945.1_ASM143494v1_genomic.fna/target_genomes.txt --output GCF_001434945.1_ASM143494v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:23:01,024] [INFO] Task succeeded: fastANI
[2024-01-24 11:23:01,025] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaed00b16-2f0d-415b-aad9-bfc20006e986/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:23:01,025] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaed00b16-2f0d-415b-aad9-bfc20006e986/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:23:01,038] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:23:01,038] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:23:01,038] [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 helveticus	strain=CGMCC 1.1877	GCA_001434945.1	1587	1587	type	True	99.9999	485	492	95	conclusive
Lactobacillus helveticus	strain=JCM 1120	GCA_015698225.1	1587	1587	type	True	99.9954	491	492	95	conclusive
Lactobacillus helveticus	strain=DSM 20075	GCA_000160855.1	1587	1587	type	True	99.9657	489	492	95	conclusive
Lactobacillus gallinarum	strain=DSM 10532	GCA_001434975.1	52242	52242	type	True	89.5719	384	492	95	below_threshold
Lactobacillus kefiranofaciens subsp. kefirgranum	strain=DSM 10550	GCA_001434195.1	190906	267818	type	True	84.3465	319	492	95	below_threshold
Lactobacillus kitasatonis	strain=DSM 16761	GCA_001434435.1	237446	237446	type	True	83.5181	310	492	95	below_threshold
Lactobacillus ultunensis	strain=DSM 16047	GCA_001436305.1	227945	227945	type	True	83.4643	319	492	95	below_threshold
Lactobacillus acidophilus	strain=ATCC 4356	GCA_000786395.1	1579	1579	type	True	82.2809	308	492	95	below_threshold
Lactobacillus intestinalis	strain=DSM 6629	GCA_024397795.1	151781	151781	type	True	80.5246	200	492	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:23:01,040] [INFO] DFAST Taxonomy check result was written to GCF_001434945.1_ASM143494v1_genomic.fna/tc_result.tsv
[2024-01-24 11:23:01,041] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:23:01,041] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:23:01,041] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaed00b16-2f0d-415b-aad9-bfc20006e986/dqc_reference/checkm_data
[2024-01-24 11:23:01,042] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:23:01,067] [INFO] Task started: CheckM
[2024-01-24 11:23:01,068] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001434945.1_ASM143494v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001434945.1_ASM143494v1_genomic.fna/checkm_input GCF_001434945.1_ASM143494v1_genomic.fna/checkm_result
[2024-01-24 11:23:18,962] [INFO] Task succeeded: CheckM
[2024-01-24 11:23:18,964] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:23:18,984] [INFO] ===== Completeness check finished =====
[2024-01-24 11:23:18,984] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:23:18,985] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001434945.1_ASM143494v1_genomic.fna/markers.fasta)
[2024-01-24 11:23:18,985] [INFO] Task started: Blastn
[2024-01-24 11:23:18,985] [INFO] Running command: blastn -query GCF_001434945.1_ASM143494v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaed00b16-2f0d-415b-aad9-bfc20006e986/dqc_reference/reference_markers_gtdb.fasta -out GCF_001434945.1_ASM143494v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:23:19,711] [INFO] Task succeeded: Blastn
[2024-01-24 11:23:19,714] [INFO] Selected 8 target genomes.
[2024-01-24 11:23:19,715] [INFO] Target genome list was writen to GCF_001434945.1_ASM143494v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:23:19,721] [INFO] Task started: fastANI
[2024-01-24 11:23:19,721] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f13912b-a72a-4a93-9047-2fb225092064/GCF_001434945.1_ASM143494v1_genomic.fna.gz --refList GCF_001434945.1_ASM143494v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001434945.1_ASM143494v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:23:23,553] [INFO] Task succeeded: fastANI
[2024-01-24 11:23:23,563] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:23:23,564] [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_000160855.1	s__Lactobacillus helveticus	99.9657	489	492	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.35	96.37	0.85	0.75	146	conclusive
GCF_001434975.1	s__Lactobacillus gallinarum	89.5981	383	492	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.30	97.84	0.88	0.84	17	-
GCF_900103655.1	s__Lactobacillus kefiranofaciens	84.5532	333	492	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.62	99.18	0.95	0.85	9	-
GCF_002706375.1	s__Lactobacillus amylovorus	83.8246	321	492	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.43	96.81	0.87	0.78	24	-
GCF_001436305.1	s__Lactobacillus ultunensis	83.4643	319	492	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.98	99.95	0.99	0.98	4	-
GCF_000615285.1	s__Lactobacillus kitasatonis	83.3978	312	492	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.87	97.76	0.93	0.87	3	-
GCF_018987235.1	s__Lactobacillus crispatus	82.4342	303	492	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.75	96.25	0.84	0.70	161	-
GCF_001591845.1	s__Lactobacillus acidophilus	82.3524	304	492	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.96	99.12	0.99	0.94	59	-
--------------------------------------------------------------------------------
[2024-01-24 11:23:23,565] [INFO] GTDB search result was written to GCF_001434945.1_ASM143494v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:23:23,566] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:23:23,569] [INFO] DFAST_QC result json was written to GCF_001434945.1_ASM143494v1_genomic.fna/dqc_result.json
[2024-01-24 11:23:23,569] [INFO] DFAST_QC completed!
[2024-01-24 11:23:23,569] [INFO] Total running time: 0h0m34s