[2024-01-24 12:31:19,125] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:19,127] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:19,128] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c199e95-e89d-4af8-827e-ddfbdc7af57a/dqc_reference
[2024-01-24 12:31:20,514] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:20,515] [INFO] Task started: Prodigal
[2024-01-24 12:31:20,515] [INFO] Running command: gunzip -c /var/lib/cwl/stgdab8b155-39ea-4410-af53-bcd34b0a2e1e/GCF_005341425.1_ASM534142v1_genomic.fna.gz | prodigal -d GCF_005341425.1_ASM534142v1_genomic.fna/cds.fna -a GCF_005341425.1_ASM534142v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:25,686] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:25,687] [INFO] Task started: HMMsearch
[2024-01-24 12:31:25,687] [INFO] Running command: hmmsearch --tblout GCF_005341425.1_ASM534142v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c199e95-e89d-4af8-827e-ddfbdc7af57a/dqc_reference/reference_markers.hmm GCF_005341425.1_ASM534142v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:25,942] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:25,943] [INFO] Found 6/6 markers.
[2024-01-24 12:31:25,968] [INFO] Query marker FASTA was written to GCF_005341425.1_ASM534142v1_genomic.fna/markers.fasta
[2024-01-24 12:31:25,969] [INFO] Task started: Blastn
[2024-01-24 12:31:25,969] [INFO] Running command: blastn -query GCF_005341425.1_ASM534142v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c199e95-e89d-4af8-827e-ddfbdc7af57a/dqc_reference/reference_markers.fasta -out GCF_005341425.1_ASM534142v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:26,541] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:26,544] [INFO] Selected 16 target genomes.
[2024-01-24 12:31:26,545] [INFO] Target genome list was writen to GCF_005341425.1_ASM534142v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:26,573] [INFO] Task started: fastANI
[2024-01-24 12:31:26,573] [INFO] Running command: fastANI --query /var/lib/cwl/stgdab8b155-39ea-4410-af53-bcd34b0a2e1e/GCF_005341425.1_ASM534142v1_genomic.fna.gz --refList GCF_005341425.1_ASM534142v1_genomic.fna/target_genomes.txt --output GCF_005341425.1_ASM534142v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:34,546] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:34,546] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c199e95-e89d-4af8-827e-ddfbdc7af57a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:34,546] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c199e95-e89d-4af8-827e-ddfbdc7af57a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:34,555] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:31:34,555] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:34,555] [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
Limosilactobacillus fermentum	strain=B1 28	GCA_005341425.1	1613	1613	type	True	100.0	635	635	95	conclusive
Limosilactobacillus fermentum	strain=DSM 20052	GCA_013394085.1	1613	1613	type	True	99.9354	622	635	95	conclusive
Limosilactobacillus fermentum	strain=ATCC 14931	GCA_000159215.1	1613	1613	type	True	99.7657	596	635	95	conclusive
Limosilactobacillus gorillae	strain=KZ01	GCA_001293735.1	1450649	1450649	type	True	81.4814	330	635	95	below_threshold
Limosilactobacillus antri	strain=DSM 16041	GCA_000160835.1	227943	227943	type	True	78.5192	101	635	95	below_threshold
Limosilactobacillus antri	strain=DSM 16041	GCA_001435475.1	227943	227943	type	True	78.3688	97	635	95	below_threshold
Limosilactobacillus ingluviei	strain=DSM 15946	GCA_001435775.1	148604	148604	type	True	78.0946	142	635	95	below_threshold
Limosilactobacillus panis	strain=DSM 6035	GCA_001027985.1	47493	47493	type	True	77.9319	94	635	95	below_threshold
Limosilactobacillus oris	strain=DSM 4864	GCA_001434465.1	1632	1632	type	True	77.642	100	635	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:34,557] [INFO] DFAST Taxonomy check result was written to GCF_005341425.1_ASM534142v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:34,557] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:34,558] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:34,558] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c199e95-e89d-4af8-827e-ddfbdc7af57a/dqc_reference/checkm_data
[2024-01-24 12:31:34,559] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:34,582] [INFO] Task started: CheckM
[2024-01-24 12:31:34,582] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005341425.1_ASM534142v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005341425.1_ASM534142v1_genomic.fna/checkm_input GCF_005341425.1_ASM534142v1_genomic.fna/checkm_result
[2024-01-24 12:31:56,280] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:56,281] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:56,301] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:56,301] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:56,302] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005341425.1_ASM534142v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:56,302] [INFO] Task started: Blastn
[2024-01-24 12:31:56,303] [INFO] Running command: blastn -query GCF_005341425.1_ASM534142v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c199e95-e89d-4af8-827e-ddfbdc7af57a/dqc_reference/reference_markers_gtdb.fasta -out GCF_005341425.1_ASM534142v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:57,100] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:57,105] [INFO] Selected 18 target genomes.
[2024-01-24 12:31:57,105] [INFO] Target genome list was writen to GCF_005341425.1_ASM534142v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:57,130] [INFO] Task started: fastANI
[2024-01-24 12:31:57,131] [INFO] Running command: fastANI --query /var/lib/cwl/stgdab8b155-39ea-4410-af53-bcd34b0a2e1e/GCF_005341425.1_ASM534142v1_genomic.fna.gz --refList GCF_005341425.1_ASM534142v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005341425.1_ASM534142v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:03,794] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:03,810] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:03,810] [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_013394085.1	s__Limosilactobacillus fermentum	99.9354	622	635	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.65	97.32	0.90	0.60	102	conclusive
GCF_001293735.1	s__Limosilactobacillus gorillae	81.4817	330	635	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001436025.1	s__Limosilactobacillus mucosae	78.5257	83	635	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.05	95.70	0.88	0.73	22	-
GCF_000160835.1	s__Limosilactobacillus antri	78.4802	102	635	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.98	99.98	0.99	0.99	3	-
GCF_001435775.1	s__Limosilactobacillus ingluviei	78.0946	142	635	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.51	97.11	0.84	0.81	5	-
GCF_002940945.1	s__Limosilactobacillus pontis_A	77.8753	85	635	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012843675.1	s__Limosilactobacillus sp012843675	77.6747	92	635	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.07	98.07	0.86	0.86	2	-
GCF_001434465.1	s__Limosilactobacillus oris	77.642	100	635	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.39	95.80	0.88	0.80	8	-
GCA_905214235.1	s__Limosilactobacillus sp905214235	77.6151	103	635	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001435935.1	s__Limosilactobacillus panis	77.5338	97	635	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.95	99.95	0.95	0.95	2	-
GCA_019117285.1	s__Limosilactobacillus intestinigallinarum	77.4866	91	635	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.99	99.99	0.94	0.94	2	-
GCA_019117185.1	s__Limosilactobacillus intestinipullorum	76.6863	87	635	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.21	99.14	0.84	0.80	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:03,813] [INFO] GTDB search result was written to GCF_005341425.1_ASM534142v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:03,814] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:03,818] [INFO] DFAST_QC result json was written to GCF_005341425.1_ASM534142v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:03,818] [INFO] DFAST_QC completed!
[2024-01-24 12:32:03,819] [INFO] Total running time: 0h0m45s