[2024-01-24 12:30:52,708] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:52,710] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:52,710] [INFO] DQC Reference Directory: /var/lib/cwl/stg21bba76b-c3fc-4abc-9a27-e8044a2e6837/dqc_reference
[2024-01-24 12:30:53,989] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:53,990] [INFO] Task started: Prodigal
[2024-01-24 12:30:53,990] [INFO] Running command: gunzip -c /var/lib/cwl/stgd0cbcbfa-0ded-4e44-b560-dbd8f5455691/GCF_004354495.1_ASM435449v1_genomic.fna.gz | prodigal -d GCF_004354495.1_ASM435449v1_genomic.fna/cds.fna -a GCF_004354495.1_ASM435449v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:57,597] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:57,598] [INFO] Task started: HMMsearch
[2024-01-24 12:30:57,598] [INFO] Running command: hmmsearch --tblout GCF_004354495.1_ASM435449v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg21bba76b-c3fc-4abc-9a27-e8044a2e6837/dqc_reference/reference_markers.hmm GCF_004354495.1_ASM435449v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:57,816] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:57,818] [INFO] Found 6/6 markers.
[2024-01-24 12:30:57,842] [INFO] Query marker FASTA was written to GCF_004354495.1_ASM435449v1_genomic.fna/markers.fasta
[2024-01-24 12:30:57,842] [INFO] Task started: Blastn
[2024-01-24 12:30:57,843] [INFO] Running command: blastn -query GCF_004354495.1_ASM435449v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21bba76b-c3fc-4abc-9a27-e8044a2e6837/dqc_reference/reference_markers.fasta -out GCF_004354495.1_ASM435449v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:58,419] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:58,423] [INFO] Selected 17 target genomes.
[2024-01-24 12:30:58,424] [INFO] Target genome list was writen to GCF_004354495.1_ASM435449v1_genomic.fna/target_genomes.txt
[2024-01-24 12:30:58,435] [INFO] Task started: fastANI
[2024-01-24 12:30:58,435] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0cbcbfa-0ded-4e44-b560-dbd8f5455691/GCF_004354495.1_ASM435449v1_genomic.fna.gz --refList GCF_004354495.1_ASM435449v1_genomic.fna/target_genomes.txt --output GCF_004354495.1_ASM435449v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:03,720] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:03,721] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg21bba76b-c3fc-4abc-9a27-e8044a2e6837/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:03,721] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg21bba76b-c3fc-4abc-9a27-e8044a2e6837/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:03,732] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:31:03,733] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:03,733] [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
Pediococcus pentosaceus	strain=ATCC 33316	GCA_004354495.1	1255	1255	type	True	100.0	578	580	95	conclusive
Pediococcus pentosaceus	strain=FDAARGOS_1009	GCA_016127775.1	1255	1255	type	True	99.9896	572	580	95	conclusive
Pediococcus pentosaceus	strain=DSM 20336	GCA_001437285.1	1255	1255	type	True	99.9622	564	580	95	conclusive
Pediococcus acidilactici	strain=DSM 20284	GCA_000146325.1	1254	1254	neotype	True	79.7706	178	580	95	below_threshold
Pediococcus acidilactici	strain=CCUG 32235	GCA_012396515.1	1254	1254	neotype	True	79.7388	178	580	95	below_threshold
Pediococcus argentinicus	strain=DSM 23026	GCA_001437605.1	480391	480391	type	True	79.2152	131	580	95	below_threshold
Companilactobacillus pabuli	strain=NFFJ11	GCA_014058425.1	2714036	2714036	type	True	79.0661	55	580	95	below_threshold
Pediococcus argentinicus	strain=CCUG 54535	GCA_012396535.1	480391	480391	type	True	79.0288	124	580	95	below_threshold
Pediococcus parvulus	strain=JCM 5889	GCA_014651215.1	54062	54062	type	True	78.9962	68	580	95	below_threshold
Pediococcus parvulus	strain=NBRC 100673	GCA_007990205.1	54062	54062	type	True	78.8075	67	580	95	below_threshold
Lentilactobacillus kosonis	strain=NBRC111893	GCA_003864335.1	2810561	2810561	type	True	77.4333	55	580	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:03,734] [INFO] DFAST Taxonomy check result was written to GCF_004354495.1_ASM435449v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:03,735] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:03,735] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:03,736] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg21bba76b-c3fc-4abc-9a27-e8044a2e6837/dqc_reference/checkm_data
[2024-01-24 12:31:03,737] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:03,758] [INFO] Task started: CheckM
[2024-01-24 12:31:03,758] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004354495.1_ASM435449v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004354495.1_ASM435449v1_genomic.fna/checkm_input GCF_004354495.1_ASM435449v1_genomic.fna/checkm_result
[2024-01-24 12:31:22,610] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:22,611] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:22,629] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:22,629] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:22,629] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004354495.1_ASM435449v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:22,630] [INFO] Task started: Blastn
[2024-01-24 12:31:22,630] [INFO] Running command: blastn -query GCF_004354495.1_ASM435449v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21bba76b-c3fc-4abc-9a27-e8044a2e6837/dqc_reference/reference_markers_gtdb.fasta -out GCF_004354495.1_ASM435449v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:23,424] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:23,427] [INFO] Selected 19 target genomes.
[2024-01-24 12:31:23,427] [INFO] Target genome list was writen to GCF_004354495.1_ASM435449v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:23,437] [INFO] Task started: fastANI
[2024-01-24 12:31:23,437] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0cbcbfa-0ded-4e44-b560-dbd8f5455691/GCF_004354495.1_ASM435449v1_genomic.fna.gz --refList GCF_004354495.1_ASM435449v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004354495.1_ASM435449v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:30,326] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:30,335] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:30,336] [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_001437285.1	s__Pediococcus pentosaceus	99.9622	564	580	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	98.80	98.32	0.92	0.90	75	conclusive
GCF_001437075.1	s__Pediococcus stilesii	80.1901	250	580	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	97.68	97.68	0.92	0.92	2	-
GCA_009809575.1	s__Pediococcus acidilactici_A	79.9014	178	580	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000146325.1	s__Pediococcus acidilactici	79.7706	178	580	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	97.64	96.71	0.89	0.81	172	-
GCF_001437605.1	s__Pediococcus argentinicus	79.2152	131	580	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	99.99	99.98	0.98	0.97	3	-
GCF_014058425.1	s__Companilactobacillus pabuli	79.0661	55	580	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.23	98.09	0.94	0.87	5	-
GCF_007990205.1	s__Pediococcus parvulus	78.8075	67	580	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	99.29	98.77	0.93	0.88	4	-
GCF_001437255.1	s__Pediococcus damnosus	78.5458	67	580	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	99.57	99.19	0.93	0.88	12	-
GCF_001437405.1	s__Pediococcus ethanolidurans	78.3386	74	580	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	98.63	97.25	0.91	0.81	5	-
GCF_001438655.1	s__Pediococcus cellicola	77.841	68	580	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:30,337] [INFO] GTDB search result was written to GCF_004354495.1_ASM435449v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:30,337] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:30,341] [INFO] DFAST_QC result json was written to GCF_004354495.1_ASM435449v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:30,341] [INFO] DFAST_QC completed!
[2024-01-24 12:31:30,342] [INFO] Total running time: 0h0m38s