[2024-01-24 15:10:53,977] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:53,983] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:53,984] [INFO] DQC Reference Directory: /var/lib/cwl/stg6424cbe4-d68d-413e-a496-90d1a9f2dd74/dqc_reference
[2024-01-24 15:10:56,634] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:56,635] [INFO] Task started: Prodigal
[2024-01-24 15:10:56,636] [INFO] Running command: gunzip -c /var/lib/cwl/stga1281fc2-342a-4e96-9659-297b5ad8ea6e/GCF_001434005.1_ASM143400v1_genomic.fna.gz | prodigal -d GCF_001434005.1_ASM143400v1_genomic.fna/cds.fna -a GCF_001434005.1_ASM143400v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:00,581] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:00,581] [INFO] Task started: HMMsearch
[2024-01-24 15:11:00,581] [INFO] Running command: hmmsearch --tblout GCF_001434005.1_ASM143400v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6424cbe4-d68d-413e-a496-90d1a9f2dd74/dqc_reference/reference_markers.hmm GCF_001434005.1_ASM143400v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:00,846] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:00,847] [INFO] Found 6/6 markers.
[2024-01-24 15:11:00,869] [INFO] Query marker FASTA was written to GCF_001434005.1_ASM143400v1_genomic.fna/markers.fasta
[2024-01-24 15:11:00,869] [INFO] Task started: Blastn
[2024-01-24 15:11:00,869] [INFO] Running command: blastn -query GCF_001434005.1_ASM143400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6424cbe4-d68d-413e-a496-90d1a9f2dd74/dqc_reference/reference_markers.fasta -out GCF_001434005.1_ASM143400v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:02,423] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:02,428] [INFO] Selected 12 target genomes.
[2024-01-24 15:11:02,429] [INFO] Target genome list was writen to GCF_001434005.1_ASM143400v1_genomic.fna/target_genomes.txt
[2024-01-24 15:11:02,491] [INFO] Task started: fastANI
[2024-01-24 15:11:02,491] [INFO] Running command: fastANI --query /var/lib/cwl/stga1281fc2-342a-4e96-9659-297b5ad8ea6e/GCF_001434005.1_ASM143400v1_genomic.fna.gz --refList GCF_001434005.1_ASM143400v1_genomic.fna/target_genomes.txt --output GCF_001434005.1_ASM143400v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:08,565] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:08,566] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6424cbe4-d68d-413e-a496-90d1a9f2dd74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:08,567] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6424cbe4-d68d-413e-a496-90d1a9f2dd74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:08,589] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 15:11:08,590] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:08,590] [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=DSM 20584	GCA_001434005.1	47770	47770	type	True	100.0	609	616	95	conclusive
Lactobacillus crispatus	strain=ATCC 33820	GCA_002088015.1	47770	47770	type	True	99.9956	615	616	95	conclusive
Lactobacillus crispatus	strain=ATCC 33820	GCA_018987235.1	47770	47770	suspected-type	True	99.9897	616	616	95	conclusive
Lactobacillus crispatus	strain=NCK2488	GCA_008694755.1	47770	47770	type	True	99.9835	566	616	95	conclusive
Lactobacillus amylovorus	strain=DSM 20531	GCA_002706375.1	1604	1604	type	True	82.4312	362	616	95	below_threshold
Lactobacillus ultunensis	strain=DSM 16047	GCA_001436305.1	227945	227945	type	True	81.7681	355	616	95	below_threshold
Lactobacillus kefiranofaciens subsp. kefirgranum	strain=DSM 10550	GCA_001434195.1	190906	267818	type	True	81.7255	342	616	95	below_threshold
Lactobacillus intestinalis	strain=DSM 6629	GCA_024397795.1	151781	151781	type	True	80.0682	226	616	95	below_threshold
Lactobacillus rodentium	strain=DSM 24759	GCA_024622425.1	947835	947835	type	True	78.7749	100	616	95	below_threshold
Lactobacillus apis	strain=LMG 26964	GCA_002837055.1	303541	303541	type	True	78.3112	115	616	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:08,592] [INFO] DFAST Taxonomy check result was written to GCF_001434005.1_ASM143400v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:08,593] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:08,594] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:08,594] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6424cbe4-d68d-413e-a496-90d1a9f2dd74/dqc_reference/checkm_data
[2024-01-24 15:11:08,596] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:08,626] [INFO] Task started: CheckM
[2024-01-24 15:11:08,626] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001434005.1_ASM143400v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001434005.1_ASM143400v1_genomic.fna/checkm_input GCF_001434005.1_ASM143400v1_genomic.fna/checkm_result
[2024-01-24 15:11:28,098] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:28,100] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:28,121] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:28,122] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:28,123] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001434005.1_ASM143400v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:28,123] [INFO] Task started: Blastn
[2024-01-24 15:11:28,123] [INFO] Running command: blastn -query GCF_001434005.1_ASM143400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6424cbe4-d68d-413e-a496-90d1a9f2dd74/dqc_reference/reference_markers_gtdb.fasta -out GCF_001434005.1_ASM143400v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:28,894] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:28,898] [INFO] Selected 12 target genomes.
[2024-01-24 15:11:28,899] [INFO] Target genome list was writen to GCF_001434005.1_ASM143400v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:28,909] [INFO] Task started: fastANI
[2024-01-24 15:11:28,909] [INFO] Running command: fastANI --query /var/lib/cwl/stga1281fc2-342a-4e96-9659-297b5ad8ea6e/GCF_001434005.1_ASM143400v1_genomic.fna.gz --refList GCF_001434005.1_ASM143400v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001434005.1_ASM143400v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:34,369] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:34,378] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:34,379] [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	99.9897	616	616	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	82.9508	345	616	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	82.6967	345	616	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	82.4057	366	616	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	82.1792	347	616	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	82.0193	341	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.96	99.12	0.99	0.94	59	-
GCF_001436305.1	s__Lactobacillus ultunensis	81.7676	355	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.98	99.95	0.99	0.98	4	-
GCF_900103655.1	s__Lactobacillus kefiranofaciens	81.7615	344	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.62	99.18	0.95	0.85	9	-
GCF_000615445.1	s__Lactobacillus hamsteri	80.2375	244	616	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	78.9408	62	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:11:34,388] [INFO] GTDB search result was written to GCF_001434005.1_ASM143400v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:34,389] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:34,392] [INFO] DFAST_QC result json was written to GCF_001434005.1_ASM143400v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:34,392] [INFO] DFAST_QC completed!
[2024-01-24 15:11:34,392] [INFO] Total running time: 0h0m40s