[2024-01-24 14:50:03,879] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:50:03,881] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:50:03,881] [INFO] DQC Reference Directory: /var/lib/cwl/stg19467f7f-99a4-402d-954b-beb4c16a73ae/dqc_reference
[2024-01-24 14:50:05,249] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:50:05,250] [INFO] Task started: Prodigal
[2024-01-24 14:50:05,251] [INFO] Running command: gunzip -c /var/lib/cwl/stg241a700a-5817-4dcc-ba13-91b96bbe3adb/GCF_003545925.1_ASM354592v1_genomic.fna.gz | prodigal -d GCF_003545925.1_ASM354592v1_genomic.fna/cds.fna -a GCF_003545925.1_ASM354592v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:50:16,745] [INFO] Task succeeded: Prodigal
[2024-01-24 14:50:16,745] [INFO] Task started: HMMsearch
[2024-01-24 14:50:16,746] [INFO] Running command: hmmsearch --tblout GCF_003545925.1_ASM354592v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19467f7f-99a4-402d-954b-beb4c16a73ae/dqc_reference/reference_markers.hmm GCF_003545925.1_ASM354592v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:50:16,998] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:50:16,999] [INFO] Found 6/6 markers.
[2024-01-24 14:50:17,037] [INFO] Query marker FASTA was written to GCF_003545925.1_ASM354592v1_genomic.fna/markers.fasta
[2024-01-24 14:50:17,037] [INFO] Task started: Blastn
[2024-01-24 14:50:17,037] [INFO] Running command: blastn -query GCF_003545925.1_ASM354592v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19467f7f-99a4-402d-954b-beb4c16a73ae/dqc_reference/reference_markers.fasta -out GCF_003545925.1_ASM354592v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:50:17,681] [INFO] Task succeeded: Blastn
[2024-01-24 14:50:17,684] [INFO] Selected 11 target genomes.
[2024-01-24 14:50:17,684] [INFO] Target genome list was writen to GCF_003545925.1_ASM354592v1_genomic.fna/target_genomes.txt
[2024-01-24 14:50:17,690] [INFO] Task started: fastANI
[2024-01-24 14:50:17,690] [INFO] Running command: fastANI --query /var/lib/cwl/stg241a700a-5817-4dcc-ba13-91b96bbe3adb/GCF_003545925.1_ASM354592v1_genomic.fna.gz --refList GCF_003545925.1_ASM354592v1_genomic.fna/target_genomes.txt --output GCF_003545925.1_ASM354592v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:50:28,952] [INFO] Task succeeded: fastANI
[2024-01-24 14:50:28,953] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19467f7f-99a4-402d-954b-beb4c16a73ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:50:28,953] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19467f7f-99a4-402d-954b-beb4c16a73ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:50:28,963] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:50:28,963] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:50:28,963] [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
Leptospira yasudae	strain=F1	GCA_003545925.1	2202201	2202201	type	True	100.0	1465	1468	95	conclusive
Leptospira kmetyi	strain=Bejo-Iso9	GCA_000243735.3	408139	408139	type	True	84.5614	1168	1468	95	below_threshold
Leptospira barantonii	strain=FH4-C-A1	GCA_002811925.1	2023184	2023184	type	True	83.901	1172	1468	95	below_threshold
Leptospira alstonii	strain=79601	GCA_000347175.1	28452	28452	type	True	81.9422	924	1468	95	below_threshold
Leptospira adleri	strain=FH2-B-D1	GCA_002811985.1	2023186	2023186	type	True	81.0791	937	1468	95	below_threshold
Leptospira tipperaryensis	strain=GWTS #1	GCA_001729245.1	2564040	2564040	type	True	81.0432	949	1468	95	below_threshold
Leptospira ainazelensis	strain=201903071	GCA_016918785.1	2810034	2810034	type	True	80.8443	952	1468	95	below_threshold
Leptospira ellisii	strain=ATI7-C-A5	GCA_002811955.1	2023197	2023197	type	True	80.6686	719	1468	95	below_threshold
Leptospira alexanderi	strain=L 60	GCA_000243815.3	100053	100053	type	True	80.5781	819	1468	95	below_threshold
Leptospira borgpetersenii	strain=DSM 21538	GCA_003046425.1	174	174	type	True	80.2786	725	1468	95	below_threshold
Leptospira mayottensis	strain=200901116	GCA_000306675.3	1137606	1137606	type	True	80.2219	754	1468	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:50:28,965] [INFO] DFAST Taxonomy check result was written to GCF_003545925.1_ASM354592v1_genomic.fna/tc_result.tsv
[2024-01-24 14:50:28,965] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:50:28,966] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:50:28,966] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19467f7f-99a4-402d-954b-beb4c16a73ae/dqc_reference/checkm_data
[2024-01-24 14:50:28,967] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:50:29,006] [INFO] Task started: CheckM
[2024-01-24 14:50:29,006] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003545925.1_ASM354592v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003545925.1_ASM354592v1_genomic.fna/checkm_input GCF_003545925.1_ASM354592v1_genomic.fna/checkm_result
[2024-01-24 14:51:02,254] [INFO] Task succeeded: CheckM
[2024-01-24 14:51:02,255] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:51:02,275] [INFO] ===== Completeness check finished =====
[2024-01-24 14:51:02,275] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:51:02,275] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003545925.1_ASM354592v1_genomic.fna/markers.fasta)
[2024-01-24 14:51:02,276] [INFO] Task started: Blastn
[2024-01-24 14:51:02,276] [INFO] Running command: blastn -query GCF_003545925.1_ASM354592v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19467f7f-99a4-402d-954b-beb4c16a73ae/dqc_reference/reference_markers_gtdb.fasta -out GCF_003545925.1_ASM354592v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:51:03,103] [INFO] Task succeeded: Blastn
[2024-01-24 14:51:03,106] [INFO] Selected 8 target genomes.
[2024-01-24 14:51:03,106] [INFO] Target genome list was writen to GCF_003545925.1_ASM354592v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:51:03,112] [INFO] Task started: fastANI
[2024-01-24 14:51:03,112] [INFO] Running command: fastANI --query /var/lib/cwl/stg241a700a-5817-4dcc-ba13-91b96bbe3adb/GCF_003545925.1_ASM354592v1_genomic.fna.gz --refList GCF_003545925.1_ASM354592v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003545925.1_ASM354592v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:51:11,104] [INFO] Task succeeded: fastANI
[2024-01-24 14:51:11,111] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:51:11,111] [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_003545925.1	s__Leptospira yasudae	100.0	1465	1468	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	97.33	95.78	0.94	0.93	8	conclusive
GCF_000243735.2	s__Leptospira kmetyi	84.5444	1170	1468	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	99.04	98.99	0.96	0.94	7	-
GCF_002811925.1	s__Leptospira barantonii	83.8959	1173	1468	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	96.36	96.36	0.93	0.93	2	-
GCF_000347175.1	s__Leptospira alstonii	81.9516	924	1468	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	99.79	99.25	0.97	0.95	5	-
GCF_000332415.1	s__Leptospira weilii_A	81.8997	898	1468	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001729245.1	s__Leptospira tipperaryensis	81.0525	947	1468	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002811955.1	s__Leptospira ellisii	80.683	718	1468	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003046425.1	s__Leptospira borgpetersenii	80.2704	726	1468	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	99.13	97.82	0.96	0.92	148	-
--------------------------------------------------------------------------------
[2024-01-24 14:51:11,113] [INFO] GTDB search result was written to GCF_003545925.1_ASM354592v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:51:11,114] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:51:11,116] [INFO] DFAST_QC result json was written to GCF_003545925.1_ASM354592v1_genomic.fna/dqc_result.json
[2024-01-24 14:51:11,117] [INFO] DFAST_QC completed!
[2024-01-24 14:51:11,117] [INFO] Total running time: 0h1m7s