[2024-01-24 11:42:20,327] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:42:20,329] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:42:20,329] [INFO] DQC Reference Directory: /var/lib/cwl/stgeadbb250-3f17-46bb-b8f0-50e81f011162/dqc_reference
[2024-01-24 11:42:24,522] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:42:24,524] [INFO] Task started: Prodigal
[2024-01-24 11:42:24,524] [INFO] Running command: gunzip -c /var/lib/cwl/stg228a8ab8-5e42-4955-9ead-0a336faf5015/GCF_021030645.1_ASM2103064v1_genomic.fna.gz | prodigal -d GCF_021030645.1_ASM2103064v1_genomic.fna/cds.fna -a GCF_021030645.1_ASM2103064v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:42:29,961] [INFO] Task succeeded: Prodigal
[2024-01-24 11:42:29,961] [INFO] Task started: HMMsearch
[2024-01-24 11:42:29,961] [INFO] Running command: hmmsearch --tblout GCF_021030645.1_ASM2103064v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeadbb250-3f17-46bb-b8f0-50e81f011162/dqc_reference/reference_markers.hmm GCF_021030645.1_ASM2103064v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:42:30,198] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:42:30,199] [INFO] Found 6/6 markers.
[2024-01-24 11:42:30,223] [INFO] Query marker FASTA was written to GCF_021030645.1_ASM2103064v1_genomic.fna/markers.fasta
[2024-01-24 11:42:30,223] [INFO] Task started: Blastn
[2024-01-24 11:42:30,224] [INFO] Running command: blastn -query GCF_021030645.1_ASM2103064v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeadbb250-3f17-46bb-b8f0-50e81f011162/dqc_reference/reference_markers.fasta -out GCF_021030645.1_ASM2103064v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:42:30,832] [INFO] Task succeeded: Blastn
[2024-01-24 11:42:30,837] [INFO] Selected 28 target genomes.
[2024-01-24 11:42:30,837] [INFO] Target genome list was writen to GCF_021030645.1_ASM2103064v1_genomic.fna/target_genomes.txt
[2024-01-24 11:42:32,282] [INFO] Task started: fastANI
[2024-01-24 11:42:32,283] [INFO] Running command: fastANI --query /var/lib/cwl/stg228a8ab8-5e42-4955-9ead-0a336faf5015/GCF_021030645.1_ASM2103064v1_genomic.fna.gz --refList GCF_021030645.1_ASM2103064v1_genomic.fna/target_genomes.txt --output GCF_021030645.1_ASM2103064v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:42:43,203] [INFO] Task succeeded: fastANI
[2024-01-24 11:42:43,204] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeadbb250-3f17-46bb-b8f0-50e81f011162/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:42:43,204] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeadbb250-3f17-46bb-b8f0-50e81f011162/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:42:43,212] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:42:43,213] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:42:43,213] [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
Agrilactobacillus fermenti	strain=CC-MHH1034	GCA_021030645.1	2586909	2586909	type	True	100.0	824	827	95	conclusive
Agrilactobacillus composti	strain=DSM 18527	GCA_001436375.1	398555	398555	type	True	77.6312	134	827	95	below_threshold
Loigolactobacillus coryniformis subsp. coryniformis	strain=KCTC 3167	GCA_000166795.1	115541	1610	type	True	76.778	54	827	95	below_threshold
Loigolactobacillus jiayinensis	strain=257-1	GCA_003946445.1	2486016	2486016	type	True	76.741	54	827	95	below_threshold
Lapidilactobacillus gannanensis	strain=143-1	GCA_003946675.1	2486002	2486002	type	True	76.7305	55	827	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:42:43,215] [INFO] DFAST Taxonomy check result was written to GCF_021030645.1_ASM2103064v1_genomic.fna/tc_result.tsv
[2024-01-24 11:42:43,215] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:42:43,215] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:42:43,216] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeadbb250-3f17-46bb-b8f0-50e81f011162/dqc_reference/checkm_data
[2024-01-24 11:42:43,216] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:42:43,242] [INFO] Task started: CheckM
[2024-01-24 11:42:43,242] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021030645.1_ASM2103064v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021030645.1_ASM2103064v1_genomic.fna/checkm_input GCF_021030645.1_ASM2103064v1_genomic.fna/checkm_result
[2024-01-24 11:43:06,341] [INFO] Task succeeded: CheckM
[2024-01-24 11:43:06,342] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:43:06,357] [INFO] ===== Completeness check finished =====
[2024-01-24 11:43:06,358] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:43:06,358] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021030645.1_ASM2103064v1_genomic.fna/markers.fasta)
[2024-01-24 11:43:06,359] [INFO] Task started: Blastn
[2024-01-24 11:43:06,359] [INFO] Running command: blastn -query GCF_021030645.1_ASM2103064v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeadbb250-3f17-46bb-b8f0-50e81f011162/dqc_reference/reference_markers_gtdb.fasta -out GCF_021030645.1_ASM2103064v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:07,134] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:07,140] [INFO] Selected 32 target genomes.
[2024-01-24 11:43:07,140] [INFO] Target genome list was writen to GCF_021030645.1_ASM2103064v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:43:07,179] [INFO] Task started: fastANI
[2024-01-24 11:43:07,179] [INFO] Running command: fastANI --query /var/lib/cwl/stg228a8ab8-5e42-4955-9ead-0a336faf5015/GCF_021030645.1_ASM2103064v1_genomic.fna.gz --refList GCF_021030645.1_ASM2103064v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021030645.1_ASM2103064v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:43:18,230] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:18,235] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:43:18,235] [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_001436375.1	s__Agrilactobacillus composti	77.6312	134	827	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Agrilactobacillus	95.0	99.95	99.95	0.99	0.99	2	-
GCF_002706425.1	s__Loigolactobacillus coryniformis	76.9591	54	827	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Loigolactobacillus	95.0	98.39	97.42	0.89	0.81	10	-
GCF_003946445.1	s__Loigolactobacillus jiayinensis	76.741	54	827	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Loigolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946675.1	s__Lapidilactobacillus gannanensis	76.7305	55	827	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lapidilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:43:18,238] [INFO] GTDB search result was written to GCF_021030645.1_ASM2103064v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:43:18,238] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:43:18,240] [INFO] DFAST_QC result json was written to GCF_021030645.1_ASM2103064v1_genomic.fna/dqc_result.json
[2024-01-24 11:43:18,241] [INFO] DFAST_QC completed!
[2024-01-24 11:43:18,241] [INFO] Total running time: 0h0m58s