[2024-01-24 14:40:02,547] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:40:02,549] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:40:02,549] [INFO] DQC Reference Directory: /var/lib/cwl/stg9e79296d-fd05-468e-8b9b-82730d1c8554/dqc_reference
[2024-01-24 14:40:03,906] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:40:03,907] [INFO] Task started: Prodigal
[2024-01-24 14:40:03,908] [INFO] Running command: gunzip -c /var/lib/cwl/stg00a73d31-6014-41fc-a637-f208749f3ce2/GCF_001437405.1_ASM143740v1_genomic.fna.gz | prodigal -d GCF_001437405.1_ASM143740v1_genomic.fna/cds.fna -a GCF_001437405.1_ASM143740v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:40:08,982] [INFO] Task succeeded: Prodigal
[2024-01-24 14:40:08,983] [INFO] Task started: HMMsearch
[2024-01-24 14:40:08,983] [INFO] Running command: hmmsearch --tblout GCF_001437405.1_ASM143740v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9e79296d-fd05-468e-8b9b-82730d1c8554/dqc_reference/reference_markers.hmm GCF_001437405.1_ASM143740v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:40:09,232] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:40:09,233] [INFO] Found 6/6 markers.
[2024-01-24 14:40:09,263] [INFO] Query marker FASTA was written to GCF_001437405.1_ASM143740v1_genomic.fna/markers.fasta
[2024-01-24 14:40:09,263] [INFO] Task started: Blastn
[2024-01-24 14:40:09,264] [INFO] Running command: blastn -query GCF_001437405.1_ASM143740v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e79296d-fd05-468e-8b9b-82730d1c8554/dqc_reference/reference_markers.fasta -out GCF_001437405.1_ASM143740v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:09,896] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:09,899] [INFO] Selected 14 target genomes.
[2024-01-24 14:40:09,900] [INFO] Target genome list was writen to GCF_001437405.1_ASM143740v1_genomic.fna/target_genomes.txt
[2024-01-24 14:40:09,905] [INFO] Task started: fastANI
[2024-01-24 14:40:09,905] [INFO] Running command: fastANI --query /var/lib/cwl/stg00a73d31-6014-41fc-a637-f208749f3ce2/GCF_001437405.1_ASM143740v1_genomic.fna.gz --refList GCF_001437405.1_ASM143740v1_genomic.fna/target_genomes.txt --output GCF_001437405.1_ASM143740v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:16,088] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:16,089] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9e79296d-fd05-468e-8b9b-82730d1c8554/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:16,089] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9e79296d-fd05-468e-8b9b-82730d1c8554/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:16,097] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:40:16,097] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:16,097] [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 ethanolidurans	strain=DSM 22301	GCA_001437405.1	319653	319653	type	True	100.0	719	721	95	conclusive
Pediococcus ethanolidurans	strain=CGMCC 1.3889	GCA_900111205.1	319653	319653	type	True	99.9949	717	721	95	conclusive
Pediococcus parvulus	strain=JCM 5889	GCA_014651215.1	54062	54062	type	True	82.4376	421	721	95	below_threshold
Pediococcus cellicola	strain=DSM 17757	GCA_001438655.1	319652	319652	type	True	82.2538	364	721	95	below_threshold
Pediococcus parvulus	strain=NBRC 100673	GCA_007990205.1	54062	54062	type	True	82.2441	405	721	95	below_threshold
Pediococcus damnosus	strain=DSM 20331	GCA_001437255.1	51663	51663	type	True	80.0215	306	721	95	below_threshold
Pediococcus inopinatus	strain=DSM 20285	GCA_002982135.1	114090	114090	type	True	79.9353	316	721	95	below_threshold
Lactiplantibacillus paraplantarum	strain=DSM 10667	GCA_003641145.1	60520	60520	type	True	78.3432	53	721	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:16,099] [INFO] DFAST Taxonomy check result was written to GCF_001437405.1_ASM143740v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:16,100] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:16,100] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:16,100] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9e79296d-fd05-468e-8b9b-82730d1c8554/dqc_reference/checkm_data
[2024-01-24 14:40:16,101] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:16,130] [INFO] Task started: CheckM
[2024-01-24 14:40:16,131] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001437405.1_ASM143740v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001437405.1_ASM143740v1_genomic.fna/checkm_input GCF_001437405.1_ASM143740v1_genomic.fna/checkm_result
[2024-01-24 14:40:38,635] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:38,636] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:38,656] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:38,656] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:38,656] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001437405.1_ASM143740v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:38,657] [INFO] Task started: Blastn
[2024-01-24 14:40:38,657] [INFO] Running command: blastn -query GCF_001437405.1_ASM143740v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e79296d-fd05-468e-8b9b-82730d1c8554/dqc_reference/reference_markers_gtdb.fasta -out GCF_001437405.1_ASM143740v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:39,491] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:39,494] [INFO] Selected 15 target genomes.
[2024-01-24 14:40:39,495] [INFO] Target genome list was writen to GCF_001437405.1_ASM143740v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:39,503] [INFO] Task started: fastANI
[2024-01-24 14:40:39,503] [INFO] Running command: fastANI --query /var/lib/cwl/stg00a73d31-6014-41fc-a637-f208749f3ce2/GCF_001437405.1_ASM143740v1_genomic.fna.gz --refList GCF_001437405.1_ASM143740v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001437405.1_ASM143740v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:45,331] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:45,340] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:45,340] [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_001437405.1	s__Pediococcus ethanolidurans	100.0	719	721	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	98.63	97.25	0.91	0.81	5	conclusive
GCF_001438655.1	s__Pediococcus cellicola	82.2538	364	721	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007990205.1	s__Pediococcus parvulus	82.2319	406	721	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	80.0451	304	721	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	99.57	99.19	0.93	0.88	12	-
GCF_002982135.1	s__Pediococcus inopinatus	79.9524	315	721	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	99.47	98.95	0.96	0.92	3	-
GCF_001434225.1	s__Liquorilactobacillus nagelii	78.4408	51	721	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	98.67	98.67	0.89	0.89	2	-
GCF_001437075.1	s__Pediococcus stilesii	78.4408	56	721	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	97.68	97.68	0.92	0.92	2	-
GCF_000237995.1	s__Pediococcus claussenii	78.1915	78	721	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	99.87	99.79	0.97	0.95	4	-
GCF_001437605.1	s__Pediococcus argentinicus	78.0458	97	721	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	99.99	99.98	0.98	0.97	3	-
GCF_001437285.1	s__Pediococcus pentosaceus	77.8158	75	721	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	98.80	98.32	0.92	0.90	75	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:45,342] [INFO] GTDB search result was written to GCF_001437405.1_ASM143740v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:45,343] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:45,346] [INFO] DFAST_QC result json was written to GCF_001437405.1_ASM143740v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:45,346] [INFO] DFAST_QC completed!
[2024-01-24 14:40:45,346] [INFO] Total running time: 0h0m43s