[2024-01-24 12:15:03,985] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:03,987] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:03,987] [INFO] DQC Reference Directory: /var/lib/cwl/stg09cad90d-0493-4f1e-9785-3283d86a5140/dqc_reference
[2024-01-24 12:15:05,240] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:05,240] [INFO] Task started: Prodigal
[2024-01-24 12:15:05,241] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c8f56d5-ff25-4ed1-9f76-e4299bfddb2b/GCF_016919175.1_ASM1691917v1_genomic.fna.gz | prodigal -d GCF_016919175.1_ASM1691917v1_genomic.fna/cds.fna -a GCF_016919175.1_ASM1691917v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:15,855] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:15,856] [INFO] Task started: HMMsearch
[2024-01-24 12:15:15,856] [INFO] Running command: hmmsearch --tblout GCF_016919175.1_ASM1691917v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09cad90d-0493-4f1e-9785-3283d86a5140/dqc_reference/reference_markers.hmm GCF_016919175.1_ASM1691917v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:16,213] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:16,215] [INFO] Found 6/6 markers.
[2024-01-24 12:15:16,261] [INFO] Query marker FASTA was written to GCF_016919175.1_ASM1691917v1_genomic.fna/markers.fasta
[2024-01-24 12:15:16,262] [INFO] Task started: Blastn
[2024-01-24 12:15:16,262] [INFO] Running command: blastn -query GCF_016919175.1_ASM1691917v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09cad90d-0493-4f1e-9785-3283d86a5140/dqc_reference/reference_markers.fasta -out GCF_016919175.1_ASM1691917v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:16,876] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:16,880] [INFO] Selected 7 target genomes.
[2024-01-24 12:15:16,880] [INFO] Target genome list was writen to GCF_016919175.1_ASM1691917v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:16,883] [INFO] Task started: fastANI
[2024-01-24 12:15:16,884] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c8f56d5-ff25-4ed1-9f76-e4299bfddb2b/GCF_016919175.1_ASM1691917v1_genomic.fna.gz --refList GCF_016919175.1_ASM1691917v1_genomic.fna/target_genomes.txt --output GCF_016919175.1_ASM1691917v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:25,265] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:25,266] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09cad90d-0493-4f1e-9785-3283d86a5140/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:25,266] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09cad90d-0493-4f1e-9785-3283d86a5140/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:25,274] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:25,274] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:25,274] [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 ainlahdjerensis	strain=201903070	GCA_016919175.1	2810033	2810033	type	True	100.0	1558	1570	95	conclusive
Leptospira tipperaryensis	strain=GWTS #1	GCA_001729245.1	2564040	2564040	type	True	87.8338	1286	1570	95	below_threshold
Leptospira ainazelensis	strain=201903071	GCA_016918785.1	2810034	2810034	type	True	87.1502	1332	1570	95	below_threshold
Leptospira adleri	strain=FH2-B-D1	GCA_002811985.1	2023186	2023186	type	True	84.385	1199	1570	95	below_threshold
Leptospira kmetyi	strain=Bejo-Iso9	GCA_000243735.3	408139	408139	type	True	81.1109	946	1570	95	below_threshold
Leptospira yasudae	strain=F1	GCA_003545925.1	2202201	2202201	type	True	80.7653	889	1570	95	below_threshold
Leptospira alstonii	strain=79601	GCA_000347175.1	28452	28452	type	True	80.3598	766	1570	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:25,275] [INFO] DFAST Taxonomy check result was written to GCF_016919175.1_ASM1691917v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:25,276] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:25,276] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:25,276] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09cad90d-0493-4f1e-9785-3283d86a5140/dqc_reference/checkm_data
[2024-01-24 12:15:25,277] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:25,324] [INFO] Task started: CheckM
[2024-01-24 12:15:25,324] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016919175.1_ASM1691917v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016919175.1_ASM1691917v1_genomic.fna/checkm_input GCF_016919175.1_ASM1691917v1_genomic.fna/checkm_result
[2024-01-24 12:16:01,982] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:01,985] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:02,010] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:02,010] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:02,011] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016919175.1_ASM1691917v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:02,011] [INFO] Task started: Blastn
[2024-01-24 12:16:02,011] [INFO] Running command: blastn -query GCF_016919175.1_ASM1691917v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09cad90d-0493-4f1e-9785-3283d86a5140/dqc_reference/reference_markers_gtdb.fasta -out GCF_016919175.1_ASM1691917v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:02,848] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:02,852] [INFO] Selected 6 target genomes.
[2024-01-24 12:16:02,852] [INFO] Target genome list was writen to GCF_016919175.1_ASM1691917v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:02,858] [INFO] Task started: fastANI
[2024-01-24 12:16:02,858] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c8f56d5-ff25-4ed1-9f76-e4299bfddb2b/GCF_016919175.1_ASM1691917v1_genomic.fna.gz --refList GCF_016919175.1_ASM1691917v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016919175.1_ASM1691917v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:10,422] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:10,433] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:10,433] [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_016919175.1	s__Leptospira sp016919175	100.0	1559	1570	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001729245.1	s__Leptospira tipperaryensis	87.823	1288	1570	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016918785.1	s__Leptospira sp016918785	87.1553	1331	1570	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003545885.1	s__Leptospira stimsonii	86.187	1228	1570	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.7414	N/A	N/A	N/A	N/A	1	-
GCF_003545875.1	s__Leptospira stimsonii_A	85.5292	1219	1570	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.7414	99.10	99.09	0.95	0.94	3	-
GCF_002811985.1	s__Leptospira adleri	84.3851	1199	1570	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	99.11	98.26	0.94	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:10,435] [INFO] GTDB search result was written to GCF_016919175.1_ASM1691917v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:10,435] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:10,438] [INFO] DFAST_QC result json was written to GCF_016919175.1_ASM1691917v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:10,438] [INFO] DFAST_QC completed!
[2024-01-24 12:16:10,438] [INFO] Total running time: 0h1m6s