[2024-01-24 13:46:09,920] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:09,922] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:09,922] [INFO] DQC Reference Directory: /var/lib/cwl/stg00074440-7a2a-4b79-aa66-63d4b9937c8c/dqc_reference
[2024-01-24 13:46:11,236] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:11,237] [INFO] Task started: Prodigal
[2024-01-24 13:46:11,238] [INFO] Running command: gunzip -c /var/lib/cwl/stgba07117d-10a1-473c-bf9c-0b190f76d4e9/GCF_009600985.1_ASM960098v1_genomic.fna.gz | prodigal -d GCF_009600985.1_ASM960098v1_genomic.fna/cds.fna -a GCF_009600985.1_ASM960098v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:16,988] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:16,988] [INFO] Task started: HMMsearch
[2024-01-24 13:46:16,988] [INFO] Running command: hmmsearch --tblout GCF_009600985.1_ASM960098v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg00074440-7a2a-4b79-aa66-63d4b9937c8c/dqc_reference/reference_markers.hmm GCF_009600985.1_ASM960098v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:17,275] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:17,276] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgba07117d-10a1-473c-bf9c-0b190f76d4e9/GCF_009600985.1_ASM960098v1_genomic.fna.gz]
[2024-01-24 13:46:17,301] [INFO] Query marker FASTA was written to GCF_009600985.1_ASM960098v1_genomic.fna/markers.fasta
[2024-01-24 13:46:17,302] [INFO] Task started: Blastn
[2024-01-24 13:46:17,302] [INFO] Running command: blastn -query GCF_009600985.1_ASM960098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg00074440-7a2a-4b79-aa66-63d4b9937c8c/dqc_reference/reference_markers.fasta -out GCF_009600985.1_ASM960098v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:17,952] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:17,956] [INFO] Selected 18 target genomes.
[2024-01-24 13:46:17,956] [INFO] Target genome list was writen to GCF_009600985.1_ASM960098v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:17,962] [INFO] Task started: fastANI
[2024-01-24 13:46:17,962] [INFO] Running command: fastANI --query /var/lib/cwl/stgba07117d-10a1-473c-bf9c-0b190f76d4e9/GCF_009600985.1_ASM960098v1_genomic.fna.gz --refList GCF_009600985.1_ASM960098v1_genomic.fna/target_genomes.txt --output GCF_009600985.1_ASM960098v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:27,589] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:27,589] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg00074440-7a2a-4b79-aa66-63d4b9937c8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:27,589] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg00074440-7a2a-4b79-aa66-63d4b9937c8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:27,603] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:27,603] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:27,604] [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 halodurans	strain=TMW 1.2172	GCA_009600985.1	2584183	2584183	type	True	100.0	804	808	95	conclusive
Companilactobacillus pabuli	strain=NFFJ11	GCA_014058425.1	2714036	2714036	type	True	82.2236	488	808	95	below_threshold
Companilactobacillus musae	strain=313	GCA_003573575.1	1903258	1903258	type	True	82.1938	434	808	95	below_threshold
Companilactobacillus farciminis	strain=DSM 20184	GCA_002706745.1	1612	1612	suspected-type	True	82.1776	470	808	95	below_threshold
Companilactobacillus musae	strain=NBRC 112868	GCA_003967595.1	1903258	1903258	type	True	82.169	439	808	95	below_threshold
Companilactobacillus futsaii	strain=JCM 17355	GCA_001435505.1	938155	938155	type	True	81.9131	466	808	95	below_threshold
Companilactobacillus formosensis	strain=NBRC 109509	GCA_005405305.1	1617889	1617889	type	True	81.8901	477	808	95	below_threshold
Companilactobacillus nuruki	strain=SYF10-1a	GCA_002872255.1	1993540	1993540	type	True	81.7788	404	808	95	below_threshold
Companilactobacillus paralimentarius	strain=DSM 13238	GCA_009764345.1	83526	83526	type	True	81.6232	395	808	95	below_threshold
Companilactobacillus zhachilii	strain=HBUAS52074	GCA_003606365.2	2304606	2304606	type	True	81.61	428	808	95	below_threshold
Companilactobacillus heilongjiangensis	strain=S4-3	GCA_005405325.1	1074467	1074467	type	True	81.5473	426	808	95	below_threshold
Companilactobacillus nantensis	strain=DSM 16982	GCA_001435815.1	305793	305793	type	True	81.5312	439	808	95	below_threshold
Companilactobacillus heilongjiangensis	strain=DSM 28069	GCA_000831645.3	1074467	1074467	type	True	81.4564	438	808	95	below_threshold
Companilactobacillus kimchii	strain=DSM 13961	GCA_009764365.1	2801452	2801452	type	True	81.4416	405	808	95	below_threshold
Companilactobacillus huachuanensis	strain=395-6.2	GCA_005404815.1	2559914	2559914	type	True	81.2464	421	808	95	below_threshold
Companilactobacillus allii	strain=WiKim39	GCA_023923085.1	1847728	1847728	type	True	79.1825	247	808	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:27,605] [INFO] DFAST Taxonomy check result was written to GCF_009600985.1_ASM960098v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:27,606] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:27,606] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:27,606] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg00074440-7a2a-4b79-aa66-63d4b9937c8c/dqc_reference/checkm_data
[2024-01-24 13:46:27,608] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:27,645] [INFO] Task started: CheckM
[2024-01-24 13:46:27,645] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009600985.1_ASM960098v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009600985.1_ASM960098v1_genomic.fna/checkm_input GCF_009600985.1_ASM960098v1_genomic.fna/checkm_result
[2024-01-24 13:46:51,398] [INFO] Task succeeded: CheckM
[2024-01-24 13:46:51,400] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:46:51,420] [INFO] ===== Completeness check finished =====
[2024-01-24 13:46:51,421] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:46:51,421] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009600985.1_ASM960098v1_genomic.fna/markers.fasta)
[2024-01-24 13:46:51,421] [INFO] Task started: Blastn
[2024-01-24 13:46:51,422] [INFO] Running command: blastn -query GCF_009600985.1_ASM960098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg00074440-7a2a-4b79-aa66-63d4b9937c8c/dqc_reference/reference_markers_gtdb.fasta -out GCF_009600985.1_ASM960098v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:52,221] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:52,225] [INFO] Selected 14 target genomes.
[2024-01-24 13:46:52,225] [INFO] Target genome list was writen to GCF_009600985.1_ASM960098v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:46:52,245] [INFO] Task started: fastANI
[2024-01-24 13:46:52,245] [INFO] Running command: fastANI --query /var/lib/cwl/stgba07117d-10a1-473c-bf9c-0b190f76d4e9/GCF_009600985.1_ASM960098v1_genomic.fna.gz --refList GCF_009600985.1_ASM960098v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009600985.1_ASM960098v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:00,936] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:00,948] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:00,948] [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_009600985.1	s__Companilactobacillus halodurans	100.0	804	808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.75	99.75	0.93	0.93	2	conclusive
GCF_014058425.1	s__Companilactobacillus pabuli	82.198	490	808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.23	98.09	0.94	0.87	5	-
GCF_002706745.1	s__Companilactobacillus farciminis	82.1805	470	808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	98.95	96.63	0.97	0.92	6	-
GCF_003967595.1	s__Companilactobacillus musae	82.169	439	808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005405305.1	s__Companilactobacillus formosensis	81.9156	475	808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001435505.1	s__Companilactobacillus futsaii	81.9014	465	808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.20	98.55	0.91	0.87	7	-
GCF_002872255.1	s__Companilactobacillus nuruki	81.7917	403	808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003606365.2	s__Companilactobacillus zhachilii	81.61	428	808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	97.75	97.75	0.87	0.87	2	-
GCF_009764355.1	s__Companilactobacillus paralimentarius_A	81.5706	404	808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.92	99.92	1.00	0.99	4	-
GCF_001435815.1	s__Companilactobacillus nantensis	81.5421	438	808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001438805.1	s__Companilactobacillus kimchiensis	81.5269	431	808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000831645.3	s__Companilactobacillus heilongjiangensis	81.4405	439	808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005404815.1	s__Companilactobacillus huachuanensis	81.2403	421	808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745525.1	s__Companilactobacillus suantsaicola	81.119	385	808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:00,950] [INFO] GTDB search result was written to GCF_009600985.1_ASM960098v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:00,951] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:00,955] [INFO] DFAST_QC result json was written to GCF_009600985.1_ASM960098v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:00,956] [INFO] DFAST_QC completed!
[2024-01-24 13:47:00,956] [INFO] Total running time: 0h0m51s