[2024-01-24 13:49:33,354] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:33,357] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:33,357] [INFO] DQC Reference Directory: /var/lib/cwl/stg975b813b-4b4b-4c27-9199-9b135f683977/dqc_reference
[2024-01-24 13:49:34,743] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:34,744] [INFO] Task started: Prodigal
[2024-01-24 13:49:34,745] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b14ffb9-18be-40b0-91b5-26919fc53ebb/GCF_016403165.1_ASM1640316v1_genomic.fna.gz | prodigal -d GCF_016403165.1_ASM1640316v1_genomic.fna/cds.fna -a GCF_016403165.1_ASM1640316v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:39,559] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:39,560] [INFO] Task started: HMMsearch
[2024-01-24 13:49:39,560] [INFO] Running command: hmmsearch --tblout GCF_016403165.1_ASM1640316v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg975b813b-4b4b-4c27-9199-9b135f683977/dqc_reference/reference_markers.hmm GCF_016403165.1_ASM1640316v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:39,878] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:39,880] [INFO] Found 6/6 markers.
[2024-01-24 13:49:39,900] [INFO] Query marker FASTA was written to GCF_016403165.1_ASM1640316v1_genomic.fna/markers.fasta
[2024-01-24 13:49:39,901] [INFO] Task started: Blastn
[2024-01-24 13:49:39,901] [INFO] Running command: blastn -query GCF_016403165.1_ASM1640316v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg975b813b-4b4b-4c27-9199-9b135f683977/dqc_reference/reference_markers.fasta -out GCF_016403165.1_ASM1640316v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:40,580] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:40,584] [INFO] Selected 12 target genomes.
[2024-01-24 13:49:40,584] [INFO] Target genome list was writen to GCF_016403165.1_ASM1640316v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:40,591] [INFO] Task started: fastANI
[2024-01-24 13:49:40,592] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b14ffb9-18be-40b0-91b5-26919fc53ebb/GCF_016403165.1_ASM1640316v1_genomic.fna.gz --refList GCF_016403165.1_ASM1640316v1_genomic.fna/target_genomes.txt --output GCF_016403165.1_ASM1640316v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:46,716] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:46,716] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg975b813b-4b4b-4c27-9199-9b135f683977/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:46,717] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg975b813b-4b4b-4c27-9199-9b135f683977/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:46,726] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:49:46,726] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:46,727] [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
Streptococcus lutetiensis	strain=FDAARGOS_1018	GCA_016403165.1	150055	150055	type	True	100.0	651	657	95	conclusive
Streptococcus lutetiensis	strain=NCTC13774	GCA_900475675.1	150055	150055	type	True	99.3147	562	657	95	conclusive
Streptococcus lutetiensis	strain=FDAARGOS_1158	GCA_016725165.1	150055	150055	type	True	99.3019	563	657	95	conclusive
Streptococcus infantarius subsp. infantarius	strain=ATCC BAA-102	GCA_000154985.1	150054	102684	type	True	94.0408	498	657	95	below_threshold
Streptococcus infantarius	strain=NCTC13760	GCA_900459445.1	102684	102684	type	True	93.9769	516	657	95	below_threshold
Streptococcus equinus	strain=NCTC12969	GCA_900459295.1	1335	1335	type	True	88.3678	483	657	95	below_threshold
Streptococcus equinus	strain=ATCC 9812	GCA_000187265.1	1335	1335	type	True	88.1407	475	657	95	below_threshold
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	80.6284	55	657	95	below_threshold
Lactococcus protaetiae	strain=KACC 19320	GCA_006965445.1	2592653	2592653	type	True	79.9478	53	657	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:46,728] [INFO] DFAST Taxonomy check result was written to GCF_016403165.1_ASM1640316v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:46,729] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:46,729] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:46,729] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg975b813b-4b4b-4c27-9199-9b135f683977/dqc_reference/checkm_data
[2024-01-24 13:49:46,731] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:46,753] [INFO] Task started: CheckM
[2024-01-24 13:49:46,753] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016403165.1_ASM1640316v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016403165.1_ASM1640316v1_genomic.fna/checkm_input GCF_016403165.1_ASM1640316v1_genomic.fna/checkm_result
[2024-01-24 13:50:08,499] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:08,501] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:08,531] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:08,532] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:08,532] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016403165.1_ASM1640316v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:08,532] [INFO] Task started: Blastn
[2024-01-24 13:50:08,533] [INFO] Running command: blastn -query GCF_016403165.1_ASM1640316v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg975b813b-4b4b-4c27-9199-9b135f683977/dqc_reference/reference_markers_gtdb.fasta -out GCF_016403165.1_ASM1640316v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:09,400] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:09,403] [INFO] Selected 7 target genomes.
[2024-01-24 13:50:09,403] [INFO] Target genome list was writen to GCF_016403165.1_ASM1640316v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:09,407] [INFO] Task started: fastANI
[2024-01-24 13:50:09,407] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b14ffb9-18be-40b0-91b5-26919fc53ebb/GCF_016403165.1_ASM1640316v1_genomic.fna.gz --refList GCF_016403165.1_ASM1640316v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016403165.1_ASM1640316v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:12,996] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:13,002] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:13,002] [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_900475675.1	s__Streptococcus lutetiensis	99.3298	560	657	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.21	95.22	0.92	0.85	50	conclusive
GCF_000154985.1	s__Streptococcus infantarius	94.0409	498	657	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.67	95.30	0.89	0.82	24	-
GCF_900101445.1	s__Streptococcus equinus_B	93.263	501	657	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.22	0.90	0.87	9	-
GCF_900104225.1	s__Streptococcus equinus_D	88.8365	489	657	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016461705.1	s__Streptococcus vicugnae	88.8141	500	657	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.43	98.30	0.94	0.90	4	-
GCF_000187265.1	s__Streptococcus equinus	88.1407	475	657	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.03	95.86	0.90	0.87	42	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:13,004] [INFO] GTDB search result was written to GCF_016403165.1_ASM1640316v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:13,005] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:13,011] [INFO] DFAST_QC result json was written to GCF_016403165.1_ASM1640316v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:13,011] [INFO] DFAST_QC completed!
[2024-01-24 13:50:13,012] [INFO] Total running time: 0h0m40s