[2024-01-24 14:31:29,085] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:29,087] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:29,088] [INFO] DQC Reference Directory: /var/lib/cwl/stg8362804e-3ae7-41b4-aa55-1ed1f094a9b7/dqc_reference
[2024-01-24 14:31:30,185] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:30,185] [INFO] Task started: Prodigal
[2024-01-24 14:31:30,186] [INFO] Running command: gunzip -c /var/lib/cwl/stge9f4a206-1c85-43e0-9225-60e9e1e03025/GCF_015698225.1_ASM1569822v1_genomic.fna.gz | prodigal -d GCF_015698225.1_ASM1569822v1_genomic.fna/cds.fna -a GCF_015698225.1_ASM1569822v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:33,436] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:33,436] [INFO] Task started: HMMsearch
[2024-01-24 14:31:33,436] [INFO] Running command: hmmsearch --tblout GCF_015698225.1_ASM1569822v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8362804e-3ae7-41b4-aa55-1ed1f094a9b7/dqc_reference/reference_markers.hmm GCF_015698225.1_ASM1569822v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:33,631] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:33,632] [INFO] Found 6/6 markers.
[2024-01-24 14:31:33,651] [INFO] Query marker FASTA was written to GCF_015698225.1_ASM1569822v1_genomic.fna/markers.fasta
[2024-01-24 14:31:33,651] [INFO] Task started: Blastn
[2024-01-24 14:31:33,651] [INFO] Running command: blastn -query GCF_015698225.1_ASM1569822v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8362804e-3ae7-41b4-aa55-1ed1f094a9b7/dqc_reference/reference_markers.fasta -out GCF_015698225.1_ASM1569822v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:34,245] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:34,248] [INFO] Selected 13 target genomes.
[2024-01-24 14:31:34,248] [INFO] Target genome list was writen to GCF_015698225.1_ASM1569822v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:34,275] [INFO] Task started: fastANI
[2024-01-24 14:31:34,275] [INFO] Running command: fastANI --query /var/lib/cwl/stge9f4a206-1c85-43e0-9225-60e9e1e03025/GCF_015698225.1_ASM1569822v1_genomic.fna.gz --refList GCF_015698225.1_ASM1569822v1_genomic.fna/target_genomes.txt --output GCF_015698225.1_ASM1569822v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:39,896] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:39,897] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8362804e-3ae7-41b4-aa55-1ed1f094a9b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:39,897] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8362804e-3ae7-41b4-aa55-1ed1f094a9b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:39,938] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:31:39,938] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:39,938] [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=JCM 1120	GCA_015698225.1	1587	1587	type	True	100.0	561	569	95	conclusive
Lactobacillus helveticus	strain=CGMCC 1.1877	GCA_001434945.1	1587	1587	type	True	99.7381	462	569	95	conclusive
Lactobacillus helveticus	strain=DSM 20075	GCA_000160855.1	1587	1587	type	True	99.7205	553	569	95	conclusive
Lactobacillus gallinarum	strain=DSM 10532	GCA_001434975.1	52242	52242	type	True	89.4988	410	569	95	below_threshold
Lactobacillus kefiranofaciens subsp. kefirgranum	strain=DSM 10550	GCA_001434195.1	190906	267818	type	True	84.6674	344	569	95	below_threshold
Lactobacillus ultunensis	strain=DSM 16047	GCA_001436305.1	227945	227945	type	True	83.3385	345	569	95	below_threshold
Lactobacillus kitasatonis	strain=DSM 16761	GCA_001434435.1	237446	237446	type	True	83.0091	356	569	95	below_threshold
Lactobacillus acidophilus	strain=ATCC 4356	GCA_000786395.1	1579	1579	type	True	82.2914	326	569	95	below_threshold
Lactobacillus intestinalis	strain=DSM 6629	GCA_024397795.1	151781	151781	type	True	80.4885	215	569	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:39,939] [INFO] DFAST Taxonomy check result was written to GCF_015698225.1_ASM1569822v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:39,940] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:39,940] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:39,940] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8362804e-3ae7-41b4-aa55-1ed1f094a9b7/dqc_reference/checkm_data
[2024-01-24 14:31:39,946] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:39,971] [INFO] Task started: CheckM
[2024-01-24 14:31:39,972] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015698225.1_ASM1569822v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015698225.1_ASM1569822v1_genomic.fna/checkm_input GCF_015698225.1_ASM1569822v1_genomic.fna/checkm_result
[2024-01-24 14:31:58,907] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:58,908] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:58,923] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:58,923] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:58,923] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015698225.1_ASM1569822v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:58,924] [INFO] Task started: Blastn
[2024-01-24 14:31:58,924] [INFO] Running command: blastn -query GCF_015698225.1_ASM1569822v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8362804e-3ae7-41b4-aa55-1ed1f094a9b7/dqc_reference/reference_markers_gtdb.fasta -out GCF_015698225.1_ASM1569822v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:59,829] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:59,831] [INFO] Selected 8 target genomes.
[2024-01-24 14:31:59,831] [INFO] Target genome list was writen to GCF_015698225.1_ASM1569822v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:59,837] [INFO] Task started: fastANI
[2024-01-24 14:31:59,837] [INFO] Running command: fastANI --query /var/lib/cwl/stge9f4a206-1c85-43e0-9225-60e9e1e03025/GCF_015698225.1_ASM1569822v1_genomic.fna.gz --refList GCF_015698225.1_ASM1569822v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015698225.1_ASM1569822v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:03,893] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:03,917] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:03,917] [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	99.7205	553	569	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	89.4804	410	569	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	85.1555	357	569	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	83.758	344	569	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	83.3167	347	569	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	83.0014	357	569	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	82.5338	334	569	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	82.2758	324	569	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 14:32:03,918] [INFO] GTDB search result was written to GCF_015698225.1_ASM1569822v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:03,918] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:03,921] [INFO] DFAST_QC result json was written to GCF_015698225.1_ASM1569822v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:03,921] [INFO] DFAST_QC completed!
[2024-01-24 14:32:03,921] [INFO] Total running time: 0h0m35s