[2024-01-25 18:53:05,776] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:53:05,777] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:53:05,778] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f5fdff1-f124-47fb-b66d-85d916e2ffc0/dqc_reference
[2024-01-25 18:53:06,913] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:53:06,914] [INFO] Task started: Prodigal
[2024-01-25 18:53:06,914] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b9053c3-68b1-489b-b11c-19c258b94e4b/GCF_001435995.1_ASM143599v1_genomic.fna.gz | prodigal -d GCF_001435995.1_ASM143599v1_genomic.fna/cds.fna -a GCF_001435995.1_ASM143599v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:53:09,075] [INFO] Task succeeded: Prodigal
[2024-01-25 18:53:09,076] [INFO] Task started: HMMsearch
[2024-01-25 18:53:09,076] [INFO] Running command: hmmsearch --tblout GCF_001435995.1_ASM143599v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f5fdff1-f124-47fb-b66d-85d916e2ffc0/dqc_reference/reference_markers.hmm GCF_001435995.1_ASM143599v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:53:09,289] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:53:09,290] [INFO] Found 6/6 markers.
[2024-01-25 18:53:09,306] [INFO] Query marker FASTA was written to GCF_001435995.1_ASM143599v1_genomic.fna/markers.fasta
[2024-01-25 18:53:09,306] [INFO] Task started: Blastn
[2024-01-25 18:53:09,306] [INFO] Running command: blastn -query GCF_001435995.1_ASM143599v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f5fdff1-f124-47fb-b66d-85d916e2ffc0/dqc_reference/reference_markers.fasta -out GCF_001435995.1_ASM143599v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:53:09,897] [INFO] Task succeeded: Blastn
[2024-01-25 18:53:09,899] [INFO] Selected 15 target genomes.
[2024-01-25 18:53:09,900] [INFO] Target genome list was writen to GCF_001435995.1_ASM143599v1_genomic.fna/target_genomes.txt
[2024-01-25 18:53:09,914] [INFO] Task started: fastANI
[2024-01-25 18:53:09,914] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b9053c3-68b1-489b-b11c-19c258b94e4b/GCF_001435995.1_ASM143599v1_genomic.fna.gz --refList GCF_001435995.1_ASM143599v1_genomic.fna/target_genomes.txt --output GCF_001435995.1_ASM143599v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:53:14,415] [INFO] Task succeeded: fastANI
[2024-01-25 18:53:14,415] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f5fdff1-f124-47fb-b66d-85d916e2ffc0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:53:14,416] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f5fdff1-f124-47fb-b66d-85d916e2ffc0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:53:14,422] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:53:14,422] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:53:14,422] [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 ozensis	strain=DSM 23829	GCA_001435995.1	866801	866801	type	True	100.0	478	479	95	conclusive
Apilactobacillus ozensis	strain=JCM 17196	GCA_001311485.1	866801	866801	type	True	99.7993	458	479	95	conclusive
Apilactobacillus xinyiensis	strain=F575-4	GCA_019656235.1	2841032	2841032	type	True	84.5862	352	479	95	below_threshold
Apilactobacillus micheneri	strain=Hlig3	GCA_002993975.1	1899430	1899430	type	True	79.3095	149	479	95	below_threshold
Apilactobacillus timberlakei	strain=HV_12	GCA_002993965.1	2008380	2008380	type	True	79.0372	156	479	95	below_threshold
Apilactobacillus apisilvae	strain=SG5_A10	GCA_023380225.1	2923364	2923364	type	True	78.9815	171	479	95	below_threshold
Apilactobacillus quenuiae	strain=HV_6	GCA_002994005.1	2008377	2008377	type	True	78.7455	155	479	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:53:14,424] [INFO] DFAST Taxonomy check result was written to GCF_001435995.1_ASM143599v1_genomic.fna/tc_result.tsv
[2024-01-25 18:53:14,425] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:53:14,425] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:53:14,425] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f5fdff1-f124-47fb-b66d-85d916e2ffc0/dqc_reference/checkm_data
[2024-01-25 18:53:14,426] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:53:14,443] [INFO] Task started: CheckM
[2024-01-25 18:53:14,443] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001435995.1_ASM143599v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001435995.1_ASM143599v1_genomic.fna/checkm_input GCF_001435995.1_ASM143599v1_genomic.fna/checkm_result
[2024-01-25 18:53:28,186] [INFO] Task succeeded: CheckM
[2024-01-25 18:53:28,187] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:53:28,201] [INFO] ===== Completeness check finished =====
[2024-01-25 18:53:28,202] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:53:28,202] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001435995.1_ASM143599v1_genomic.fna/markers.fasta)
[2024-01-25 18:53:28,202] [INFO] Task started: Blastn
[2024-01-25 18:53:28,202] [INFO] Running command: blastn -query GCF_001435995.1_ASM143599v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f5fdff1-f124-47fb-b66d-85d916e2ffc0/dqc_reference/reference_markers_gtdb.fasta -out GCF_001435995.1_ASM143599v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:53:28,932] [INFO] Task succeeded: Blastn
[2024-01-25 18:53:28,935] [INFO] Selected 20 target genomes.
[2024-01-25 18:53:28,935] [INFO] Target genome list was writen to GCF_001435995.1_ASM143599v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:53:28,970] [INFO] Task started: fastANI
[2024-01-25 18:53:28,970] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b9053c3-68b1-489b-b11c-19c258b94e4b/GCF_001435995.1_ASM143599v1_genomic.fna.gz --refList GCF_001435995.1_ASM143599v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001435995.1_ASM143599v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:53:34,846] [INFO] Task succeeded: fastANI
[2024-01-25 18:53:34,853] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:53:34,853] [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_001435995.1	s__Apilactobacillus ozensis	100.0	478	479	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	99.83	99.83	1.00	1.00	2	conclusive
GCF_002993975.1	s__Apilactobacillus micheneri	79.3095	149	479	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	98.16	96.49	0.93	0.89	21	-
GCF_002993965.1	s__Apilactobacillus timberlakei	79.0372	156	479	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	98.96	98.30	0.93	0.87	9	-
GCF_005930975.1	s__Apilactobacillus kunkeei_E	78.9719	98	479	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001308205.1	s__Apilactobacillus kunkeei_B	78.7509	100	479	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002994005.1	s__Apilactobacillus quenuiae	78.7455	155	479	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	78.6505	131	479	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	78.6481	124	479	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001436555.1	s__Lentilactobacillus senioris	76.8953	57	479	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.88	99.77	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:53:34,859] [INFO] GTDB search result was written to GCF_001435995.1_ASM143599v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:53:34,859] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:53:34,863] [INFO] DFAST_QC result json was written to GCF_001435995.1_ASM143599v1_genomic.fna/dqc_result.json
[2024-01-25 18:53:34,863] [INFO] DFAST_QC completed!
[2024-01-25 18:53:34,863] [INFO] Total running time: 0h0m29s