[2024-01-24 13:57:00,885] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:00,886] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:00,887] [INFO] DQC Reference Directory: /var/lib/cwl/stgde86130f-615b-4fd0-99fa-78ab75ad1fda/dqc_reference
[2024-01-24 13:57:02,174] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:02,175] [INFO] Task started: Prodigal
[2024-01-24 13:57:02,176] [INFO] Running command: gunzip -c /var/lib/cwl/stg2996b729-36fc-4834-9ea8-b5c1b6adb15c/GCF_002993975.1_ASM299397v1_genomic.fna.gz | prodigal -d GCF_002993975.1_ASM299397v1_genomic.fna/cds.fna -a GCF_002993975.1_ASM299397v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:04,801] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:04,801] [INFO] Task started: HMMsearch
[2024-01-24 13:57:04,801] [INFO] Running command: hmmsearch --tblout GCF_002993975.1_ASM299397v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde86130f-615b-4fd0-99fa-78ab75ad1fda/dqc_reference/reference_markers.hmm GCF_002993975.1_ASM299397v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:05,081] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:05,083] [INFO] Found 6/6 markers.
[2024-01-24 13:57:05,103] [INFO] Query marker FASTA was written to GCF_002993975.1_ASM299397v1_genomic.fna/markers.fasta
[2024-01-24 13:57:05,104] [INFO] Task started: Blastn
[2024-01-24 13:57:05,104] [INFO] Running command: blastn -query GCF_002993975.1_ASM299397v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde86130f-615b-4fd0-99fa-78ab75ad1fda/dqc_reference/reference_markers.fasta -out GCF_002993975.1_ASM299397v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:05,727] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:05,730] [INFO] Selected 11 target genomes.
[2024-01-24 13:57:05,731] [INFO] Target genome list was writen to GCF_002993975.1_ASM299397v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:05,764] [INFO] Task started: fastANI
[2024-01-24 13:57:05,764] [INFO] Running command: fastANI --query /var/lib/cwl/stg2996b729-36fc-4834-9ea8-b5c1b6adb15c/GCF_002993975.1_ASM299397v1_genomic.fna.gz --refList GCF_002993975.1_ASM299397v1_genomic.fna/target_genomes.txt --output GCF_002993975.1_ASM299397v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:09,424] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:09,425] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde86130f-615b-4fd0-99fa-78ab75ad1fda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:09,426] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde86130f-615b-4fd0-99fa-78ab75ad1fda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:09,441] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:09,441] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:09,441] [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 micheneri	strain=Hlig3	GCA_002993975.1	1899430	1899430	type	True	100.0	482	482	95	conclusive
Apilactobacillus timberlakei	strain=HV_12	GCA_002993965.1	2008380	2008380	type	True	93.8929	425	482	95	below_threshold
Apilactobacillus quenuiae	strain=HV_6	GCA_002994005.1	2008377	2008377	type	True	88.7542	407	482	95	below_threshold
Apilactobacillus apisilvae	strain=SG5_A10	GCA_023380225.1	2923364	2923364	type	True	83.1668	366	482	95	below_threshold
Apilactobacillus bombintestini	strain=BHWM-4	GCA_003627035.1	2419772	2419772	type	True	80.1177	218	482	95	below_threshold
Apilactobacillus zhangqiuensis	strain=F502-1	GCA_019656215.1	2841031	2841031	type	True	79.5457	169	482	95	below_threshold
Apilactobacillus xinyiensis	strain=F575-4	GCA_019656235.1	2841032	2841032	type	True	79.4937	177	482	95	below_threshold
Apilactobacillus waqarii	strain=HBW1	GCA_019061205.1	2851006	2851006	type	True	79.4198	168	482	95	below_threshold
Lentilactobacillus kosonis	strain=NBRC111893	GCA_003864335.1	2810561	2810561	type	True	77.8026	60	482	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:09,443] [INFO] DFAST Taxonomy check result was written to GCF_002993975.1_ASM299397v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:09,444] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:09,444] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:09,444] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde86130f-615b-4fd0-99fa-78ab75ad1fda/dqc_reference/checkm_data
[2024-01-24 13:57:09,445] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:09,467] [INFO] Task started: CheckM
[2024-01-24 13:57:09,467] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002993975.1_ASM299397v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002993975.1_ASM299397v1_genomic.fna/checkm_input GCF_002993975.1_ASM299397v1_genomic.fna/checkm_result
[2024-01-24 13:57:26,228] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:26,230] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:26,249] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:26,249] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:26,250] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002993975.1_ASM299397v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:26,250] [INFO] Task started: Blastn
[2024-01-24 13:57:26,250] [INFO] Running command: blastn -query GCF_002993975.1_ASM299397v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde86130f-615b-4fd0-99fa-78ab75ad1fda/dqc_reference/reference_markers_gtdb.fasta -out GCF_002993975.1_ASM299397v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:27,046] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:27,057] [INFO] Selected 10 target genomes.
[2024-01-24 13:57:27,057] [INFO] Target genome list was writen to GCF_002993975.1_ASM299397v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:27,065] [INFO] Task started: fastANI
[2024-01-24 13:57:27,065] [INFO] Running command: fastANI --query /var/lib/cwl/stg2996b729-36fc-4834-9ea8-b5c1b6adb15c/GCF_002993975.1_ASM299397v1_genomic.fna.gz --refList GCF_002993975.1_ASM299397v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002993975.1_ASM299397v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:30,585] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:30,595] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:30,596] [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_002993975.1	s__Apilactobacillus micheneri	100.0	482	482	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	98.16	96.49	0.93	0.89	21	conclusive
GCF_002993965.1	s__Apilactobacillus timberlakei	93.8929	425	482	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	98.96	98.30	0.93	0.87	9	-
GCF_002994005.1	s__Apilactobacillus quenuiae	88.7542	407	482	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	80.2033	217	482	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	79.9124	187	482	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	79.698	152	482	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	96.15	95.05	0.91	0.88	13	-
GCF_005930975.1	s__Apilactobacillus kunkeei_E	79.3756	185	482	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	79.3223	179	482	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 13:57:30,597] [INFO] GTDB search result was written to GCF_002993975.1_ASM299397v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:30,598] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:30,601] [INFO] DFAST_QC result json was written to GCF_002993975.1_ASM299397v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:30,601] [INFO] DFAST_QC completed!
[2024-01-24 13:57:30,601] [INFO] Total running time: 0h0m30s