[2024-01-24 13:12:55,879] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:55,892] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:55,892] [INFO] DQC Reference Directory: /var/lib/cwl/stg44771b15-d701-4e33-a0e6-4690bcec05d7/dqc_reference
[2024-01-24 13:12:57,412] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:57,414] [INFO] Task started: Prodigal
[2024-01-24 13:12:57,415] [INFO] Running command: gunzip -c /var/lib/cwl/stg44f3df7d-040b-44df-bc72-b30740d60c3f/GCF_001435835.1_ASM143583v1_genomic.fna.gz | prodigal -d GCF_001435835.1_ASM143583v1_genomic.fna/cds.fna -a GCF_001435835.1_ASM143583v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:01,917] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:01,918] [INFO] Task started: HMMsearch
[2024-01-24 13:13:01,918] [INFO] Running command: hmmsearch --tblout GCF_001435835.1_ASM143583v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44771b15-d701-4e33-a0e6-4690bcec05d7/dqc_reference/reference_markers.hmm GCF_001435835.1_ASM143583v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:02,145] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:02,146] [INFO] Found 6/6 markers.
[2024-01-24 13:13:02,167] [INFO] Query marker FASTA was written to GCF_001435835.1_ASM143583v1_genomic.fna/markers.fasta
[2024-01-24 13:13:02,167] [INFO] Task started: Blastn
[2024-01-24 13:13:02,167] [INFO] Running command: blastn -query GCF_001435835.1_ASM143583v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44771b15-d701-4e33-a0e6-4690bcec05d7/dqc_reference/reference_markers.fasta -out GCF_001435835.1_ASM143583v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:02,789] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:02,794] [INFO] Selected 21 target genomes.
[2024-01-24 13:13:02,794] [INFO] Target genome list was writen to GCF_001435835.1_ASM143583v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:02,818] [INFO] Task started: fastANI
[2024-01-24 13:13:02,819] [INFO] Running command: fastANI --query /var/lib/cwl/stg44f3df7d-040b-44df-bc72-b30740d60c3f/GCF_001435835.1_ASM143583v1_genomic.fna.gz --refList GCF_001435835.1_ASM143583v1_genomic.fna/target_genomes.txt --output GCF_001435835.1_ASM143583v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:10,968] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:10,968] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44771b15-d701-4e33-a0e6-4690bcec05d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:10,969] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44771b15-d701-4e33-a0e6-4690bcec05d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:10,976] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:10,976] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:10,976] [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
Lapidilactobacillus concavus	strain=DSM 17758	GCA_001435835.1	287844	287844	type	True	100.0	586	592	95	conclusive
Lapidilactobacillus mulanensis	strain=143-6	GCA_003946215.1	2485999	2485999	type	True	80.2347	247	592	95	below_threshold
Lapidilactobacillus gannanensis	strain=143-1	GCA_003946675.1	2486002	2486002	type	True	79.6638	102	592	95	below_threshold
Lapidilactobacillus bayanensis	strain=54-5	GCA_003946695.1	2485998	2485998	type	True	79.1829	140	592	95	below_threshold
Lapidilactobacillus dextrinicus	strain=DSM 20335	GCA_001436095.1	51664	51664	type	True	78.9194	117	592	95	below_threshold
Lapidilactobacillus wuchangensis	strain=17-4	GCA_003946645.1	2486001	2486001	type	True	78.6702	83	592	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:10,977] [INFO] DFAST Taxonomy check result was written to GCF_001435835.1_ASM143583v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:10,978] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:10,978] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:10,978] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44771b15-d701-4e33-a0e6-4690bcec05d7/dqc_reference/checkm_data
[2024-01-24 13:13:10,979] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:11,005] [INFO] Task started: CheckM
[2024-01-24 13:13:11,005] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001435835.1_ASM143583v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001435835.1_ASM143583v1_genomic.fna/checkm_input GCF_001435835.1_ASM143583v1_genomic.fna/checkm_result
[2024-01-24 13:13:32,496] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:32,497] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:32,512] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:32,512] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:32,513] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001435835.1_ASM143583v1_genomic.fna/markers.fasta)
[2024-01-24 13:13:32,513] [INFO] Task started: Blastn
[2024-01-24 13:13:32,513] [INFO] Running command: blastn -query GCF_001435835.1_ASM143583v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44771b15-d701-4e33-a0e6-4690bcec05d7/dqc_reference/reference_markers_gtdb.fasta -out GCF_001435835.1_ASM143583v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:33,516] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:33,520] [INFO] Selected 21 target genomes.
[2024-01-24 13:13:33,521] [INFO] Target genome list was writen to GCF_001435835.1_ASM143583v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:33,553] [INFO] Task started: fastANI
[2024-01-24 13:13:33,553] [INFO] Running command: fastANI --query /var/lib/cwl/stg44f3df7d-040b-44df-bc72-b30740d60c3f/GCF_001435835.1_ASM143583v1_genomic.fna.gz --refList GCF_001435835.1_ASM143583v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001435835.1_ASM143583v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:13:42,693] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:42,705] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:13:42,705] [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_001435835.1	s__Lapidilactobacillus concavus	100.0	586	592	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lapidilactobacillus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003946215.1	s__Lapidilactobacillus mulanensis	80.28	245	592	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lapidilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946675.1	s__Lapidilactobacillus gannanensis	79.6167	103	592	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lapidilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946695.1	s__Lapidilactobacillus bayanensis	79.1829	140	592	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lapidilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001436095.1	s__Lapidilactobacillus dextrinicus	78.9194	117	592	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lapidilactobacillus	95.0	97.98	95.96	0.93	0.87	3	-
GCF_003946645.1	s__Lapidilactobacillus wuchangensis	78.6702	83	592	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 13:13:42,707] [INFO] GTDB search result was written to GCF_001435835.1_ASM143583v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:13:42,707] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:13:42,710] [INFO] DFAST_QC result json was written to GCF_001435835.1_ASM143583v1_genomic.fna/dqc_result.json
[2024-01-24 13:13:42,710] [INFO] DFAST_QC completed!
[2024-01-24 13:13:42,710] [INFO] Total running time: 0h0m47s