[2024-01-25 19:06:05,507] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:06:05,509] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:06:05,509] [INFO] DQC Reference Directory: /var/lib/cwl/stgd83d5ae7-1d68-4e5c-86df-223199752595/dqc_reference
[2024-01-25 19:06:06,698] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:06:06,699] [INFO] Task started: Prodigal
[2024-01-25 19:06:06,699] [INFO] Running command: gunzip -c /var/lib/cwl/stg80962fc6-f3ff-4cba-825b-06f8cb4099af/GCF_011304355.1_ASM1130435v1_genomic.fna.gz | prodigal -d GCF_011304355.1_ASM1130435v1_genomic.fna/cds.fna -a GCF_011304355.1_ASM1130435v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:06:09,671] [INFO] Task succeeded: Prodigal
[2024-01-25 19:06:09,671] [INFO] Task started: HMMsearch
[2024-01-25 19:06:09,671] [INFO] Running command: hmmsearch --tblout GCF_011304355.1_ASM1130435v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd83d5ae7-1d68-4e5c-86df-223199752595/dqc_reference/reference_markers.hmm GCF_011304355.1_ASM1130435v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:06:09,868] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:06:09,869] [INFO] Found 6/6 markers.
[2024-01-25 19:06:09,884] [INFO] Query marker FASTA was written to GCF_011304355.1_ASM1130435v1_genomic.fna/markers.fasta
[2024-01-25 19:06:09,885] [INFO] Task started: Blastn
[2024-01-25 19:06:09,885] [INFO] Running command: blastn -query GCF_011304355.1_ASM1130435v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd83d5ae7-1d68-4e5c-86df-223199752595/dqc_reference/reference_markers.fasta -out GCF_011304355.1_ASM1130435v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:06:10,477] [INFO] Task succeeded: Blastn
[2024-01-25 19:06:10,480] [INFO] Selected 23 target genomes.
[2024-01-25 19:06:10,480] [INFO] Target genome list was writen to GCF_011304355.1_ASM1130435v1_genomic.fna/target_genomes.txt
[2024-01-25 19:06:10,543] [INFO] Task started: fastANI
[2024-01-25 19:06:10,543] [INFO] Running command: fastANI --query /var/lib/cwl/stg80962fc6-f3ff-4cba-825b-06f8cb4099af/GCF_011304355.1_ASM1130435v1_genomic.fna.gz --refList GCF_011304355.1_ASM1130435v1_genomic.fna/target_genomes.txt --output GCF_011304355.1_ASM1130435v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:06:18,067] [INFO] Task succeeded: fastANI
[2024-01-25 19:06:18,067] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd83d5ae7-1d68-4e5c-86df-223199752595/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:06:18,068] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd83d5ae7-1d68-4e5c-86df-223199752595/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:06:18,075] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:06:18,075] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:06:18,075] [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
Weissella coleopterorum	strain=HDW19	GCA_011304355.1	2714949	2714949	type	True	100.0	539	539	95	conclusive
Weissella koreensis	strain=KCTC 3621	GCA_000277645.1	165096	165096	type	True	81.5048	308	539	95	below_threshold
Weissella ceti	strain=CECT 7719	GCA_018394055.1	759620	759620	suspected-type	True	80.3725	53	539	95	below_threshold
Weissella diestrammenae	strain=KACC 16890	GCA_014397255.1	1162633	1162633	type	True	79.6357	116	539	95	below_threshold
Weissella kandleri	strain=DSM 20593	GCA_001438705.1	1616	1616	type	True	79.485	128	539	95	below_threshold
Weissella viridescens	strain=DSM 20410	GCA_001437355.1	1629	1629	type	True	78.3202	54	539	95	below_threshold
Weissella oryzae	strain=SG25	GCA_000691805.2	1129792	1129792	type	True	78.2693	50	539	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:06:18,078] [INFO] DFAST Taxonomy check result was written to GCF_011304355.1_ASM1130435v1_genomic.fna/tc_result.tsv
[2024-01-25 19:06:18,079] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:06:18,079] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:06:18,079] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd83d5ae7-1d68-4e5c-86df-223199752595/dqc_reference/checkm_data
[2024-01-25 19:06:18,080] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:06:18,101] [INFO] Task started: CheckM
[2024-01-25 19:06:18,101] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011304355.1_ASM1130435v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011304355.1_ASM1130435v1_genomic.fna/checkm_input GCF_011304355.1_ASM1130435v1_genomic.fna/checkm_result
[2024-01-25 19:06:33,379] [INFO] Task succeeded: CheckM
[2024-01-25 19:06:33,381] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:06:33,402] [INFO] ===== Completeness check finished =====
[2024-01-25 19:06:33,402] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:06:33,403] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011304355.1_ASM1130435v1_genomic.fna/markers.fasta)
[2024-01-25 19:06:33,403] [INFO] Task started: Blastn
[2024-01-25 19:06:33,403] [INFO] Running command: blastn -query GCF_011304355.1_ASM1130435v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd83d5ae7-1d68-4e5c-86df-223199752595/dqc_reference/reference_markers_gtdb.fasta -out GCF_011304355.1_ASM1130435v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:06:34,391] [INFO] Task succeeded: Blastn
[2024-01-25 19:06:34,394] [INFO] Selected 19 target genomes.
[2024-01-25 19:06:34,394] [INFO] Target genome list was writen to GCF_011304355.1_ASM1130435v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:06:34,419] [INFO] Task started: fastANI
[2024-01-25 19:06:34,419] [INFO] Running command: fastANI --query /var/lib/cwl/stg80962fc6-f3ff-4cba-825b-06f8cb4099af/GCF_011304355.1_ASM1130435v1_genomic.fna.gz --refList GCF_011304355.1_ASM1130435v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011304355.1_ASM1130435v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:06:40,914] [INFO] Task succeeded: fastANI
[2024-01-25 19:06:40,920] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:06:40,920] [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_011304355.1	s__Weissella coleopterorum	100.0	539	539	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000277645.1	s__Weissella koreensis	81.4996	309	539	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	99.29	98.85	0.93	0.91	5	-
GCF_018394055.1	s__Weissella ceti	79.8225	52	539	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014397255.1	s__Weissella diestrammenae	79.5652	115	539	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000750535.1	s__Weissella ceti_A	79.5613	52	539	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	99.87	99.79	0.99	0.98	5	-
GCF_001438705.1	s__Weissella kandleri	79.485	128	539	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001437355.1	s__Weissella viridescens	78.3202	54	539	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	99.44	98.29	0.96	0.91	6	-
GCF_000691805.2	s__Weissella oryzae	78.2693	50	539	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:06:40,922] [INFO] GTDB search result was written to GCF_011304355.1_ASM1130435v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:06:40,922] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:06:40,926] [INFO] DFAST_QC result json was written to GCF_011304355.1_ASM1130435v1_genomic.fna/dqc_result.json
[2024-01-25 19:06:40,926] [INFO] DFAST_QC completed!
[2024-01-25 19:06:40,926] [INFO] Total running time: 0h0m35s