[2024-01-24 14:12:45,398] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:45,400] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:45,401] [INFO] DQC Reference Directory: /var/lib/cwl/stgf13d4b54-cd34-4d20-ba0a-d9e1ec6ab6cd/dqc_reference
[2024-01-24 14:12:46,619] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:46,620] [INFO] Task started: Prodigal
[2024-01-24 14:12:46,621] [INFO] Running command: gunzip -c /var/lib/cwl/stg901f132d-fa06-4675-8ff0-8c1c6fce4491/GCF_000373345.1_ASM37334v1_genomic.fna.gz | prodigal -d GCF_000373345.1_ASM37334v1_genomic.fna/cds.fna -a GCF_000373345.1_ASM37334v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:50,768] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:50,769] [INFO] Task started: HMMsearch
[2024-01-24 14:12:50,769] [INFO] Running command: hmmsearch --tblout GCF_000373345.1_ASM37334v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf13d4b54-cd34-4d20-ba0a-d9e1ec6ab6cd/dqc_reference/reference_markers.hmm GCF_000373345.1_ASM37334v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:51,043] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:51,045] [INFO] Found 6/6 markers.
[2024-01-24 14:12:51,077] [INFO] Query marker FASTA was written to GCF_000373345.1_ASM37334v1_genomic.fna/markers.fasta
[2024-01-24 14:12:51,077] [INFO] Task started: Blastn
[2024-01-24 14:12:51,078] [INFO] Running command: blastn -query GCF_000373345.1_ASM37334v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf13d4b54-cd34-4d20-ba0a-d9e1ec6ab6cd/dqc_reference/reference_markers.fasta -out GCF_000373345.1_ASM37334v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:51,655] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:51,660] [INFO] Selected 8 target genomes.
[2024-01-24 14:12:51,660] [INFO] Target genome list was writen to GCF_000373345.1_ASM37334v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:51,664] [INFO] Task started: fastANI
[2024-01-24 14:12:51,665] [INFO] Running command: fastANI --query /var/lib/cwl/stg901f132d-fa06-4675-8ff0-8c1c6fce4491/GCF_000373345.1_ASM37334v1_genomic.fna.gz --refList GCF_000373345.1_ASM37334v1_genomic.fna/target_genomes.txt --output GCF_000373345.1_ASM37334v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:56,969] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:56,970] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf13d4b54-cd34-4d20-ba0a-d9e1ec6ab6cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:56,970] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf13d4b54-cd34-4d20-ba0a-d9e1ec6ab6cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:56,980] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:12:56,980] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:56,980] [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
Leptotrichia wadei	strain=DSM 19758	GCA_000373345.1	157687	157687	type	True	100.0	731	735	95	conclusive
Leptotrichia wadei	strain=JCM16777	GCA_007990545.2	157687	157687	type	True	99.9917	729	735	95	conclusive
Leptotrichia shahii	strain=JCM16776	GCA_008327825.1	157691	157691	type	True	90.8619	580	735	95	below_threshold
Leptotrichia shahii	strain=DSM 19757	GCA_000373045.1	157691	157691	type	True	90.8468	586	735	95	below_threshold
Leptotrichia hofstadii	strain=DSM 21651	GCA_000428965.1	157688	157688	type	True	85.3969	566	735	95	below_threshold
Leptotrichia massiliensis	strain=Marseille-P3007	GCA_900104625.1	1852388	1852388	type	True	85.2043	534	735	95	below_threshold
Leptotrichia trevisanii	strain=DSM 22070	GCA_000482505.1	109328	109328	type	True	85.1898	538	735	95	below_threshold
Leptotrichia buccalis	strain=DSM 1135	GCA_000023905.1	40542	40542	type	True	84.9741	526	735	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:56,982] [INFO] DFAST Taxonomy check result was written to GCF_000373345.1_ASM37334v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:56,983] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:56,983] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:56,983] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf13d4b54-cd34-4d20-ba0a-d9e1ec6ab6cd/dqc_reference/checkm_data
[2024-01-24 14:12:56,985] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:57,041] [INFO] Task started: CheckM
[2024-01-24 14:12:57,041] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000373345.1_ASM37334v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000373345.1_ASM37334v1_genomic.fna/checkm_input GCF_000373345.1_ASM37334v1_genomic.fna/checkm_result
[2024-01-24 14:13:16,963] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:16,965] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:16,981] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:16,982] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:16,982] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000373345.1_ASM37334v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:16,982] [INFO] Task started: Blastn
[2024-01-24 14:13:16,983] [INFO] Running command: blastn -query GCF_000373345.1_ASM37334v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf13d4b54-cd34-4d20-ba0a-d9e1ec6ab6cd/dqc_reference/reference_markers_gtdb.fasta -out GCF_000373345.1_ASM37334v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:17,935] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:17,940] [INFO] Selected 11 target genomes.
[2024-01-24 14:13:17,940] [INFO] Target genome list was writen to GCF_000373345.1_ASM37334v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:17,952] [INFO] Task started: fastANI
[2024-01-24 14:13:17,952] [INFO] Running command: fastANI --query /var/lib/cwl/stg901f132d-fa06-4675-8ff0-8c1c6fce4491/GCF_000373345.1_ASM37334v1_genomic.fna.gz --refList GCF_000373345.1_ASM37334v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000373345.1_ASM37334v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:25,181] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:25,200] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:25,200] [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_007990545.2	s__Leptotrichia wadei	99.968	730	735	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia	95.0	97.52	96.88	0.90	0.86	7	conclusive
GCF_007990445.1	s__Leptotrichia wadei_A	91.9675	600	735	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia	95.0	97.03	96.85	0.85	0.83	4	-
GCF_008327825.1	s__Leptotrichia shahii	90.8619	580	735	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia	95.0	99.96	99.96	1.00	1.00	2	-
GCF_002240055.1	s__Leptotrichia sp002240055	85.6871	395	735	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia	95.0	98.99	98.99	0.99	0.99	2	-
GCF_007990525.1	s__Leptotrichia hofstadii	85.3263	561	735	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia	95.0	98.32	96.65	0.96	0.92	3	-
GCF_000469385.1	s__Leptotrichia sp000469385	85.3008	526	735	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104625.1	s__Leptotrichia massiliensis	85.2435	532	735	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia	95.0	96.80	96.21	0.92	0.89	3	-
GCF_007990635.1	s__Leptotrichia hongkongensis	85.2207	538	735	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482505.1	s__Leptotrichia trevisanii	85.1788	539	735	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia	95.0	97.98	97.58	0.90	0.88	4	-
GCF_000023905.1	s__Leptotrichia buccalis	84.9247	528	735	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018128245.1	s__JABCPH02 sp013333235	83.5045	350	735	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__JABCPH02	95.0	97.39	97.39	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:25,202] [INFO] GTDB search result was written to GCF_000373345.1_ASM37334v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:25,202] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:25,206] [INFO] DFAST_QC result json was written to GCF_000373345.1_ASM37334v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:25,206] [INFO] DFAST_QC completed!
[2024-01-24 14:13:25,206] [INFO] Total running time: 0h0m40s