[2024-01-24 14:53:50,419] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:53:50,421] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:53:50,421] [INFO] DQC Reference Directory: /var/lib/cwl/stge643c1db-8e28-40c5-9c84-d07c360cd10d/dqc_reference
[2024-01-24 14:53:51,600] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:53:51,600] [INFO] Task started: Prodigal
[2024-01-24 14:53:51,601] [INFO] Running command: gunzip -c /var/lib/cwl/stg75c38c84-a33c-4fbc-ba4b-e0f633fe2c0b/GCF_003397705.1_ASM339770v1_genomic.fna.gz | prodigal -d GCF_003397705.1_ASM339770v1_genomic.fna/cds.fna -a GCF_003397705.1_ASM339770v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:53:55,621] [INFO] Task succeeded: Prodigal
[2024-01-24 14:53:55,622] [INFO] Task started: HMMsearch
[2024-01-24 14:53:55,622] [INFO] Running command: hmmsearch --tblout GCF_003397705.1_ASM339770v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge643c1db-8e28-40c5-9c84-d07c360cd10d/dqc_reference/reference_markers.hmm GCF_003397705.1_ASM339770v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:53:55,854] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:53:55,856] [INFO] Found 6/6 markers.
[2024-01-24 14:53:55,872] [INFO] Query marker FASTA was written to GCF_003397705.1_ASM339770v1_genomic.fna/markers.fasta
[2024-01-24 14:53:55,873] [INFO] Task started: Blastn
[2024-01-24 14:53:55,873] [INFO] Running command: blastn -query GCF_003397705.1_ASM339770v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge643c1db-8e28-40c5-9c84-d07c360cd10d/dqc_reference/reference_markers.fasta -out GCF_003397705.1_ASM339770v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:53:56,484] [INFO] Task succeeded: Blastn
[2024-01-24 14:53:56,488] [INFO] Selected 13 target genomes.
[2024-01-24 14:53:56,488] [INFO] Target genome list was writen to GCF_003397705.1_ASM339770v1_genomic.fna/target_genomes.txt
[2024-01-24 14:53:56,508] [INFO] Task started: fastANI
[2024-01-24 14:53:56,508] [INFO] Running command: fastANI --query /var/lib/cwl/stg75c38c84-a33c-4fbc-ba4b-e0f633fe2c0b/GCF_003397705.1_ASM339770v1_genomic.fna.gz --refList GCF_003397705.1_ASM339770v1_genomic.fna/target_genomes.txt --output GCF_003397705.1_ASM339770v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:54:00,861] [INFO] Task succeeded: fastANI
[2024-01-24 14:54:00,862] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge643c1db-8e28-40c5-9c84-d07c360cd10d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:54:00,862] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge643c1db-8e28-40c5-9c84-d07c360cd10d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:54:00,869] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:54:00,869] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:54:00,870] [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
Gardnerella swidsinskii	strain=GS 9838-1	GCA_003397705.1	2792979	2792979	type	True	100.0	537	537	95	inconclusive
Gardnerella leopoldii	strain=UGent 06.41	GCA_003293675.1	2792978	2792978	type	True	95.6616	459	537	95	inconclusive
Gardnerella vaginalis	strain=DSM 4944	GCA_900105405.1	2702	2702	suspected-type	True	84.0571	298	537	95	below_threshold
Gardnerella vaginalis	strain=JCM 11026	GCA_001042655.1	2702	2702	suspected-type	True	83.9785	299	537	95	below_threshold
Gardnerella vaginalis	strain=ATCC 14018	GCA_003397685.1	2702	2702	suspected-type	True	83.8517	306	537	95	below_threshold
Gardnerella vaginalis	strain=ATCC 14018	GCA_000178355.1	2702	2702	suspected-type	True	83.6215	254	537	95	below_threshold
Gardnerella piotii	strain=UGent 18.01	GCA_003397585.1	2792977	2792977	type	True	82.4699	288	537	95	below_threshold
Galliscardovia ingluviei	strain=CCM 8606	GCA_014635685.1	1769422	1769422	type	True	77.956	55	537	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:54:00,871] [INFO] DFAST Taxonomy check result was written to GCF_003397705.1_ASM339770v1_genomic.fna/tc_result.tsv
[2024-01-24 14:54:00,871] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:54:00,872] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:54:00,872] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge643c1db-8e28-40c5-9c84-d07c360cd10d/dqc_reference/checkm_data
[2024-01-24 14:54:00,873] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:54:00,897] [INFO] Task started: CheckM
[2024-01-24 14:54:00,897] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003397705.1_ASM339770v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003397705.1_ASM339770v1_genomic.fna/checkm_input GCF_003397705.1_ASM339770v1_genomic.fna/checkm_result
[2024-01-24 14:54:20,097] [INFO] Task succeeded: CheckM
[2024-01-24 14:54:20,098] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:54:20,119] [INFO] ===== Completeness check finished =====
[2024-01-24 14:54:20,120] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:54:20,120] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003397705.1_ASM339770v1_genomic.fna/markers.fasta)
[2024-01-24 14:54:20,121] [INFO] Task started: Blastn
[2024-01-24 14:54:20,121] [INFO] Running command: blastn -query GCF_003397705.1_ASM339770v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge643c1db-8e28-40c5-9c84-d07c360cd10d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003397705.1_ASM339770v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:54:20,892] [INFO] Task succeeded: Blastn
[2024-01-24 14:54:20,896] [INFO] Selected 10 target genomes.
[2024-01-24 14:54:20,896] [INFO] Target genome list was writen to GCF_003397705.1_ASM339770v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:54:20,906] [INFO] Task started: fastANI
[2024-01-24 14:54:20,906] [INFO] Running command: fastANI --query /var/lib/cwl/stg75c38c84-a33c-4fbc-ba4b-e0f633fe2c0b/GCF_003397705.1_ASM339770v1_genomic.fna.gz --refList GCF_003397705.1_ASM339770v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003397705.1_ASM339770v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:54:25,411] [INFO] Task succeeded: fastANI
[2024-01-24 14:54:25,420] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:54:25,420] [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_003397705.1	s__Bifidobacterium swidsinskii	100.0	537	537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.6629	98.35	97.96	0.94	0.90	18	conclusive
GCF_003293675.1	s__Bifidobacterium leopoldii	95.6616	459	537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.706	98.89	98.40	0.95	0.92	16	-
GCA_003585845.1	s__Bifidobacterium sp003585845	94.5338	469	537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.706	N/A	N/A	N/A	N/A	1	-
GCF_000263635.1	s__Bifidobacterium vaginale_C	87.2676	404	537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.53	95.52	0.94	0.93	5	-
GCF_000263595.1	s__Bifidobacterium vaginale_E	87.0967	411	537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	95.68	95.61	0.91	0.90	4	-
GCF_002896555.1	s__Bifidobacterium vaginale_F	86.4447	329	537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003585735.1	s__Bifidobacterium sp003585735	86.2337	407	537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.73	99.73	0.99	0.99	2	-
GCF_001546485.1	s__Bifidobacterium vaginale_D	86.2223	382	537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.87	98.82	0.95	0.94	3	-
GCF_003408845.1	s__Bifidobacterium vaginale_H	85.287	382	537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:54:25,422] [INFO] GTDB search result was written to GCF_003397705.1_ASM339770v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:54:25,422] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:54:25,426] [INFO] DFAST_QC result json was written to GCF_003397705.1_ASM339770v1_genomic.fna/dqc_result.json
[2024-01-24 14:54:25,426] [INFO] DFAST_QC completed!
[2024-01-24 14:54:25,426] [INFO] Total running time: 0h0m35s