[2024-01-24 13:31:35,552] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:35,554] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:35,554] [INFO] DQC Reference Directory: /var/lib/cwl/stg9af9b685-7326-45a3-9917-b4d405db895b/dqc_reference
[2024-01-24 13:31:36,949] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:36,950] [INFO] Task started: Prodigal
[2024-01-24 13:31:36,950] [INFO] Running command: gunzip -c /var/lib/cwl/stgc6ccc47f-9ae6-441b-8498-d98e43cc10a8/GCF_002993965.1_ASM299396v1_genomic.fna.gz | prodigal -d GCF_002993965.1_ASM299396v1_genomic.fna/cds.fna -a GCF_002993965.1_ASM299396v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:39,824] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:39,824] [INFO] Task started: HMMsearch
[2024-01-24 13:31:39,824] [INFO] Running command: hmmsearch --tblout GCF_002993965.1_ASM299396v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9af9b685-7326-45a3-9917-b4d405db895b/dqc_reference/reference_markers.hmm GCF_002993965.1_ASM299396v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:40,075] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:40,076] [INFO] Found 6/6 markers.
[2024-01-24 13:31:40,093] [INFO] Query marker FASTA was written to GCF_002993965.1_ASM299396v1_genomic.fna/markers.fasta
[2024-01-24 13:31:40,094] [INFO] Task started: Blastn
[2024-01-24 13:31:40,094] [INFO] Running command: blastn -query GCF_002993965.1_ASM299396v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9af9b685-7326-45a3-9917-b4d405db895b/dqc_reference/reference_markers.fasta -out GCF_002993965.1_ASM299396v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:40,710] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:40,713] [INFO] Selected 10 target genomes.
[2024-01-24 13:31:40,713] [INFO] Target genome list was writen to GCF_002993965.1_ASM299396v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:40,729] [INFO] Task started: fastANI
[2024-01-24 13:31:40,729] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6ccc47f-9ae6-441b-8498-d98e43cc10a8/GCF_002993965.1_ASM299396v1_genomic.fna.gz --refList GCF_002993965.1_ASM299396v1_genomic.fna/target_genomes.txt --output GCF_002993965.1_ASM299396v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:31:44,183] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:44,184] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9af9b685-7326-45a3-9917-b4d405db895b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:31:44,184] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9af9b685-7326-45a3-9917-b4d405db895b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:31:44,193] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:31:44,193] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:31:44,193] [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
Apilactobacillus timberlakei	strain=HV_12	GCA_002993965.1	2008380	2008380	type	True	100.0	503	505	95	conclusive
Apilactobacillus micheneri	strain=Hlig3	GCA_002993975.1	1899430	1899430	type	True	93.8175	427	505	95	below_threshold
Apilactobacillus quenuiae	strain=HV_6	GCA_002994005.1	2008377	2008377	type	True	89.3776	407	505	95	below_threshold
Apilactobacillus apisilvae	strain=SG5_A10	GCA_023380225.1	2923364	2923364	type	True	82.7793	352	505	95	below_threshold
Apilactobacillus bombintestini	strain=BHWM-4	GCA_003627035.1	2419772	2419772	type	True	79.8686	208	505	95	below_threshold
Apilactobacillus zhangqiuensis	strain=F502-1	GCA_019656215.1	2841031	2841031	type	True	79.4192	170	505	95	below_threshold
Apilactobacillus xinyiensis	strain=F575-4	GCA_019656235.1	2841032	2841032	type	True	79.1911	170	505	95	below_threshold
Lentilactobacillus laojiaonis	strain=IM3328	GCA_020616595.1	2883998	2883998	type	True	78.2283	72	505	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:31:44,195] [INFO] DFAST Taxonomy check result was written to GCF_002993965.1_ASM299396v1_genomic.fna/tc_result.tsv
[2024-01-24 13:31:44,197] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:31:44,198] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:31:44,198] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9af9b685-7326-45a3-9917-b4d405db895b/dqc_reference/checkm_data
[2024-01-24 13:31:44,199] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:31:44,216] [INFO] Task started: CheckM
[2024-01-24 13:31:44,216] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002993965.1_ASM299396v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002993965.1_ASM299396v1_genomic.fna/checkm_input GCF_002993965.1_ASM299396v1_genomic.fna/checkm_result
[2024-01-24 13:32:01,281] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:01,282] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:01,302] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:01,302] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:01,303] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002993965.1_ASM299396v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:01,303] [INFO] Task started: Blastn
[2024-01-24 13:32:01,303] [INFO] Running command: blastn -query GCF_002993965.1_ASM299396v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9af9b685-7326-45a3-9917-b4d405db895b/dqc_reference/reference_markers_gtdb.fasta -out GCF_002993965.1_ASM299396v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:02,097] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:02,101] [INFO] Selected 9 target genomes.
[2024-01-24 13:32:02,101] [INFO] Target genome list was writen to GCF_002993965.1_ASM299396v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:02,116] [INFO] Task started: fastANI
[2024-01-24 13:32:02,116] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6ccc47f-9ae6-441b-8498-d98e43cc10a8/GCF_002993965.1_ASM299396v1_genomic.fna.gz --refList GCF_002993965.1_ASM299396v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002993965.1_ASM299396v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:04,952] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:04,960] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:04,961] [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_002993965.1	s__Apilactobacillus timberlakei	100.0	503	505	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	98.96	98.30	0.93	0.87	9	conclusive
GCF_002993975.1	s__Apilactobacillus micheneri	93.8175	427	505	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	98.16	96.49	0.93	0.89	21	-
GCF_002994005.1	s__Apilactobacillus quenuiae	89.3776	407	505	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003627035.1	s__Apilactobacillus bombintestini	79.8686	208	505	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001281175.1	s__Apilactobacillus apinorum	79.6032	188	505	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001949975.2	s__Apilactobacillus kunkeei_A	79.5713	153	505	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	96.15	95.05	0.91	0.88	13	-
GCF_001308205.1	s__Apilactobacillus kunkeei_B	79.5529	166	505	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:04,965] [INFO] GTDB search result was written to GCF_002993965.1_ASM299396v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:04,966] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:04,969] [INFO] DFAST_QC result json was written to GCF_002993965.1_ASM299396v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:04,969] [INFO] DFAST_QC completed!
[2024-01-24 13:32:04,969] [INFO] Total running time: 0h0m29s