[2024-01-25 19:51:05,446] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:51:05,447] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:51:05,447] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b7d00a0-7b11-4185-a1eb-b8dfb2298306/dqc_reference
[2024-01-25 19:51:06,600] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:51:06,601] [INFO] Task started: Prodigal
[2024-01-25 19:51:06,601] [INFO] Running command: gunzip -c /var/lib/cwl/stg9a927996-8f7c-4878-8de9-19cf88213073/GCF_001592065.1_ASM159206v1_genomic.fna.gz | prodigal -d GCF_001592065.1_ASM159206v1_genomic.fna/cds.fna -a GCF_001592065.1_ASM159206v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:51:11,841] [INFO] Task succeeded: Prodigal
[2024-01-25 19:51:11,841] [INFO] Task started: HMMsearch
[2024-01-25 19:51:11,841] [INFO] Running command: hmmsearch --tblout GCF_001592065.1_ASM159206v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b7d00a0-7b11-4185-a1eb-b8dfb2298306/dqc_reference/reference_markers.hmm GCF_001592065.1_ASM159206v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:51:12,038] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:51:12,039] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9a927996-8f7c-4878-8de9-19cf88213073/GCF_001592065.1_ASM159206v1_genomic.fna.gz]
[2024-01-25 19:51:12,063] [INFO] Query marker FASTA was written to GCF_001592065.1_ASM159206v1_genomic.fna/markers.fasta
[2024-01-25 19:51:12,063] [INFO] Task started: Blastn
[2024-01-25 19:51:12,063] [INFO] Running command: blastn -query GCF_001592065.1_ASM159206v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b7d00a0-7b11-4185-a1eb-b8dfb2298306/dqc_reference/reference_markers.fasta -out GCF_001592065.1_ASM159206v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:51:12,615] [INFO] Task succeeded: Blastn
[2024-01-25 19:51:12,618] [INFO] Selected 11 target genomes.
[2024-01-25 19:51:12,618] [INFO] Target genome list was writen to GCF_001592065.1_ASM159206v1_genomic.fna/target_genomes.txt
[2024-01-25 19:51:12,622] [INFO] Task started: fastANI
[2024-01-25 19:51:12,623] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a927996-8f7c-4878-8de9-19cf88213073/GCF_001592065.1_ASM159206v1_genomic.fna.gz --refList GCF_001592065.1_ASM159206v1_genomic.fna/target_genomes.txt --output GCF_001592065.1_ASM159206v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:51:18,534] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:18,535] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b7d00a0-7b11-4185-a1eb-b8dfb2298306/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:51:18,535] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b7d00a0-7b11-4185-a1eb-b8dfb2298306/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:51:18,542] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 19:51:18,542] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:51:18,542] [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
Companilactobacillus nodensis	strain=NBRC 107160	GCA_001592065.1	460870	460870	type	True	100.0	881	882	95	conclusive
Companilactobacillus nodensis	strain=DSM 19682	GCA_001435555.1	460870	460870	type	True	99.9987	882	882	95	conclusive
Companilactobacillus nodensis	strain=JCM 14932	GCA_000615905.1	460870	460870	type	True	99.9476	860	882	95	conclusive
Companilactobacillus jidongensis	strain=204-8	GCA_003946575.1	2486006	2486006	type	True	88.1532	697	882	95	below_threshold
Companilactobacillus insicii	strain=DSM 29801	GCA_003946015.1	1732567	1732567	type	True	84.4237	592	882	95	below_threshold
Companilactobacillus hulinensis	strain=8-1(1)	GCA_003946555.1	2486007	2486007	type	True	83.2135	504	882	95	below_threshold
Companilactobacillus allii	strain=WiKim39	GCA_023923085.1	1847728	1847728	type	True	81.8702	423	882	95	below_threshold
Companilactobacillus kimchii	strain=DSM 13961	GCA_009764365.1	2801452	2801452	type	True	80.3015	260	882	95	below_threshold
Companilactobacillus paralimentarius	strain=DSM 13238	GCA_009764345.1	83526	83526	type	True	79.8749	250	882	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:51:18,544] [INFO] DFAST Taxonomy check result was written to GCF_001592065.1_ASM159206v1_genomic.fna/tc_result.tsv
[2024-01-25 19:51:18,544] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:51:18,544] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:51:18,544] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b7d00a0-7b11-4185-a1eb-b8dfb2298306/dqc_reference/checkm_data
[2024-01-25 19:51:18,545] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:51:18,576] [INFO] Task started: CheckM
[2024-01-25 19:51:18,576] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001592065.1_ASM159206v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001592065.1_ASM159206v1_genomic.fna/checkm_input GCF_001592065.1_ASM159206v1_genomic.fna/checkm_result
[2024-01-25 19:51:39,639] [INFO] Task succeeded: CheckM
[2024-01-25 19:51:39,640] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:51:39,666] [INFO] ===== Completeness check finished =====
[2024-01-25 19:51:39,666] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:51:39,667] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001592065.1_ASM159206v1_genomic.fna/markers.fasta)
[2024-01-25 19:51:39,667] [INFO] Task started: Blastn
[2024-01-25 19:51:39,667] [INFO] Running command: blastn -query GCF_001592065.1_ASM159206v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b7d00a0-7b11-4185-a1eb-b8dfb2298306/dqc_reference/reference_markers_gtdb.fasta -out GCF_001592065.1_ASM159206v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:51:40,431] [INFO] Task succeeded: Blastn
[2024-01-25 19:51:40,434] [INFO] Selected 8 target genomes.
[2024-01-25 19:51:40,434] [INFO] Target genome list was writen to GCF_001592065.1_ASM159206v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:51:40,443] [INFO] Task started: fastANI
[2024-01-25 19:51:40,443] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a927996-8f7c-4878-8de9-19cf88213073/GCF_001592065.1_ASM159206v1_genomic.fna.gz --refList GCF_001592065.1_ASM159206v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001592065.1_ASM159206v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:51:45,335] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:45,341] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:51:45,341] [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_000615905.1	s__Companilactobacillus nodensis	99.9476	860	882	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.98	99.98	1.00	1.00	3	conclusive
GCF_003946575.1	s__Companilactobacillus jidongensis	88.1532	697	882	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946015.1	s__Companilactobacillus insicii	84.4018	594	882	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946555.1	s__Companilactobacillus hulinensis	83.2294	503	882	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001971585.1	s__Companilactobacillus allii	81.9152	426	882	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001435505.1	s__Companilactobacillus futsaii	80.0332	267	882	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.20	98.55	0.91	0.87	7	-
GCF_001435815.1	s__Companilactobacillus nantensis	79.6464	301	882	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003946505.1	s__Companilactobacillus mishanensis	79.1289	236	882	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	98.34	97.53	0.96	0.93	4	-
--------------------------------------------------------------------------------
[2024-01-25 19:51:45,342] [INFO] GTDB search result was written to GCF_001592065.1_ASM159206v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:51:45,343] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:51:45,345] [INFO] DFAST_QC result json was written to GCF_001592065.1_ASM159206v1_genomic.fna/dqc_result.json
[2024-01-25 19:51:45,346] [INFO] DFAST_QC completed!
[2024-01-25 19:51:45,346] [INFO] Total running time: 0h0m40s