[2024-01-25 20:19:20,659] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:19:20,660] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:19:20,660] [INFO] DQC Reference Directory: /var/lib/cwl/stgd7a81d0f-0e8b-4ad5-ad5d-652038efdd17/dqc_reference
[2024-01-25 20:19:21,838] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:19:21,840] [INFO] Task started: Prodigal
[2024-01-25 20:19:21,840] [INFO] Running command: gunzip -c /var/lib/cwl/stg403f94c8-df0b-4533-be37-86767381cb47/GCF_000296855.1_ASM29685v1_genomic.fna.gz | prodigal -d GCF_000296855.1_ASM29685v1_genomic.fna/cds.fna -a GCF_000296855.1_ASM29685v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:19:25,094] [INFO] Task succeeded: Prodigal
[2024-01-25 20:19:25,095] [INFO] Task started: HMMsearch
[2024-01-25 20:19:25,095] [INFO] Running command: hmmsearch --tblout GCF_000296855.1_ASM29685v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd7a81d0f-0e8b-4ad5-ad5d-652038efdd17/dqc_reference/reference_markers.hmm GCF_000296855.1_ASM29685v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:19:25,273] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:19:25,274] [INFO] Found 6/6 markers.
[2024-01-25 20:19:25,294] [INFO] Query marker FASTA was written to GCF_000296855.1_ASM29685v1_genomic.fna/markers.fasta
[2024-01-25 20:19:25,294] [INFO] Task started: Blastn
[2024-01-25 20:19:25,294] [INFO] Running command: blastn -query GCF_000296855.1_ASM29685v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7a81d0f-0e8b-4ad5-ad5d-652038efdd17/dqc_reference/reference_markers.fasta -out GCF_000296855.1_ASM29685v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:25,854] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:25,858] [INFO] Selected 18 target genomes.
[2024-01-25 20:19:25,858] [INFO] Target genome list was writen to GCF_000296855.1_ASM29685v1_genomic.fna/target_genomes.txt
[2024-01-25 20:19:25,864] [INFO] Task started: fastANI
[2024-01-25 20:19:25,865] [INFO] Running command: fastANI --query /var/lib/cwl/stg403f94c8-df0b-4533-be37-86767381cb47/GCF_000296855.1_ASM29685v1_genomic.fna.gz --refList GCF_000296855.1_ASM29685v1_genomic.fna/target_genomes.txt --output GCF_000296855.1_ASM29685v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:19:31,844] [INFO] Task succeeded: fastANI
[2024-01-25 20:19:31,845] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd7a81d0f-0e8b-4ad5-ad5d-652038efdd17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:19:31,845] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd7a81d0f-0e8b-4ad5-ad5d-652038efdd17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:19:31,853] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:19:31,853] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:19:31,854] [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 gigeriorum	strain=type strain: CRBIP 24.85	GCA_000296855.1	1203069	1203069	type	True	100.0	589	591	95	conclusive
Lactobacillus gigeriorum	strain=DSM 23908	GCA_001436575.1	1203069	1203069	type	True	99.9155	557	591	95	conclusive
Lactobacillus pasteurii	strain=DSM 23907	GCA_004354755.1	872327	872327	type	True	80.7643	271	591	95	below_threshold
Lactobacillus pasteurii	strain=DSM 23907	GCA_001433915.1	872327	872327	type	True	80.7555	263	591	95	below_threshold
Lactobacillus pasteurii	strain=type strain:CRBIP 24.76	GCA_000297025.1	872327	872327	type	True	80.6082	271	591	95	below_threshold
Lactobacillus hamsteri	strain=DSM 5661	GCA_001434515.1	96565	96565	type	True	79.7742	178	591	95	below_threshold
Lactobacillus hamsteri	strain=JCM 6256	GCA_000615445.1	96565	96565	type	True	79.5913	181	591	95	below_threshold
Lactobacillus intestinalis	strain=DSM 6629	GCA_001435325.1	151781	151781	type	True	79.2926	173	591	95	below_threshold
Lactobacillus helveticus	strain=DSM 20075	GCA_000160855.1	1587	1587	type	True	79.2729	160	591	95	below_threshold
Lactobacillus intestinalis	strain=DSM 6629	GCA_024397795.1	151781	151781	type	True	79.2498	180	591	95	below_threshold
Lactobacillus helveticus	strain=CGMCC 1.1877	GCA_001434945.1	1587	1587	type	True	79.149	151	591	95	below_threshold
Lactobacillus helveticus	strain=JCM 1120	GCA_015698225.1	1587	1587	type	True	79.1378	158	591	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:19:31,855] [INFO] DFAST Taxonomy check result was written to GCF_000296855.1_ASM29685v1_genomic.fna/tc_result.tsv
[2024-01-25 20:19:31,855] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:19:31,856] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:19:31,856] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd7a81d0f-0e8b-4ad5-ad5d-652038efdd17/dqc_reference/checkm_data
[2024-01-25 20:19:31,857] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:19:31,879] [INFO] Task started: CheckM
[2024-01-25 20:19:31,879] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000296855.1_ASM29685v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000296855.1_ASM29685v1_genomic.fna/checkm_input GCF_000296855.1_ASM29685v1_genomic.fna/checkm_result
[2024-01-25 20:19:47,988] [INFO] Task succeeded: CheckM
[2024-01-25 20:19:47,989] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:19:48,008] [INFO] ===== Completeness check finished =====
[2024-01-25 20:19:48,008] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:19:48,009] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000296855.1_ASM29685v1_genomic.fna/markers.fasta)
[2024-01-25 20:19:48,009] [INFO] Task started: Blastn
[2024-01-25 20:19:48,009] [INFO] Running command: blastn -query GCF_000296855.1_ASM29685v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7a81d0f-0e8b-4ad5-ad5d-652038efdd17/dqc_reference/reference_markers_gtdb.fasta -out GCF_000296855.1_ASM29685v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:48,762] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:48,766] [INFO] Selected 16 target genomes.
[2024-01-25 20:19:48,767] [INFO] Target genome list was writen to GCF_000296855.1_ASM29685v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:19:48,779] [INFO] Task started: fastANI
[2024-01-25 20:19:48,779] [INFO] Running command: fastANI --query /var/lib/cwl/stg403f94c8-df0b-4533-be37-86767381cb47/GCF_000296855.1_ASM29685v1_genomic.fna.gz --refList GCF_000296855.1_ASM29685v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000296855.1_ASM29685v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:19:54,123] [INFO] Task succeeded: fastANI
[2024-01-25 20:19:54,134] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:19:54,134] [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_000296855.1	s__Lactobacillus gigeriorum	100.0	589	591	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.96	99.96	0.96	0.96	2	conclusive
GCF_000297025.1	s__Lactobacillus pasteurii	80.6057	272	591	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.99	99.98	0.99	0.99	3	-
GCF_001434975.1	s__Lactobacillus gallinarum	79.8067	168	591	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.30	97.84	0.88	0.84	17	-
GCA_014803915.1	s__Lactobacillus sp014803915	79.7356	131	591	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000615445.1	s__Lactobacillus hamsteri	79.5589	184	591	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.97	99.97	0.99	0.99	2	-
GCF_000178475.1	s__Lactobacillus amylolyticus	79.5051	167	591	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.45	98.00	0.96	0.87	8	-
GCF_004009905.1	s__Lactobacillus xujianguonis	79.4524	182	591	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.83	99.82	0.94	0.92	3	-
GCF_001435325.1	s__Lactobacillus intestinalis	79.2926	173	591	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.33	96.07	0.89	0.82	9	-
GCF_000160855.1	s__Lactobacillus helveticus	79.2292	162	591	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.35	96.37	0.85	0.75	146	-
GCF_001434335.1	s__Lactobacillus kalixensis	78.8807	175	591	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	78.8524	114	591	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.72	97.13	0.73	0.71	7	-
GCA_018883635.1	s__Lactobacillus pullistercoris	78.6993	168	591	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001436695.1	s__Lactobacillus taiwanensis	78.3438	115	591	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.80	98.01	0.90	0.86	31	-
GCA_014803895.1	s__Lactobacillus sp014803895	78.3161	99	591	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000970855.1	s__Lactobacillus helsingborgensis	77.949	86	591	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.65	97.05	0.93	0.90	6	-
--------------------------------------------------------------------------------
[2024-01-25 20:19:54,140] [INFO] GTDB search result was written to GCF_000296855.1_ASM29685v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:19:54,140] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:19:54,144] [INFO] DFAST_QC result json was written to GCF_000296855.1_ASM29685v1_genomic.fna/dqc_result.json
[2024-01-25 20:19:54,144] [INFO] DFAST_QC completed!
[2024-01-25 20:19:54,144] [INFO] Total running time: 0h0m33s