[2024-01-24 13:28:02,026] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:02,028] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:02,028] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a84838d-b10e-4aeb-8656-d953469b0977/dqc_reference
[2024-01-24 13:28:03,416] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:03,418] [INFO] Task started: Prodigal
[2024-01-24 13:28:03,418] [INFO] Running command: gunzip -c /var/lib/cwl/stgbfedfe5c-cf12-4be5-8734-468b70e888fc/GCF_000243695.2_gls454049v02_genomic.fna.gz | prodigal -d GCF_000243695.2_gls454049v02_genomic.fna/cds.fna -a GCF_000243695.2_gls454049v02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:12,037] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:12,037] [INFO] Task started: HMMsearch
[2024-01-24 13:28:12,037] [INFO] Running command: hmmsearch --tblout GCF_000243695.2_gls454049v02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a84838d-b10e-4aeb-8656-d953469b0977/dqc_reference/reference_markers.hmm GCF_000243695.2_gls454049v02_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:12,313] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:12,315] [INFO] Found 6/6 markers.
[2024-01-24 13:28:12,351] [INFO] Query marker FASTA was written to GCF_000243695.2_gls454049v02_genomic.fna/markers.fasta
[2024-01-24 13:28:12,351] [INFO] Task started: Blastn
[2024-01-24 13:28:12,351] [INFO] Running command: blastn -query GCF_000243695.2_gls454049v02_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a84838d-b10e-4aeb-8656-d953469b0977/dqc_reference/reference_markers.fasta -out GCF_000243695.2_gls454049v02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:12,962] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:12,965] [INFO] Selected 7 target genomes.
[2024-01-24 13:28:12,966] [INFO] Target genome list was writen to GCF_000243695.2_gls454049v02_genomic.fna/target_genomes.txt
[2024-01-24 13:28:12,969] [INFO] Task started: fastANI
[2024-01-24 13:28:12,969] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfedfe5c-cf12-4be5-8734-468b70e888fc/GCF_000243695.2_gls454049v02_genomic.fna.gz --refList GCF_000243695.2_gls454049v02_genomic.fna/target_genomes.txt --output GCF_000243695.2_gls454049v02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:32,119] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:32,120] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a84838d-b10e-4aeb-8656-d953469b0977/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:32,120] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a84838d-b10e-4aeb-8656-d953469b0977/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:32,128] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:32,128] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:32,128] [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 kirschneri	strain=3522 CT	GCA_000243695.3	29507	29507	type	True	100.0	1456	1457	95	conclusive
Leptospira interrogans	strain=ATCC 43642	GCA_900156205.1	173	173	type	True	90.8215	1304	1457	95	below_threshold
Leptospira interrogans	strain=RGA	GCA_000343165.1	173	173	type	True	90.8133	1291	1457	95	below_threshold
Leptospira noguchii	strain=CZ214	GCA_000306255.2	28182	28182	suspected-type	True	89.7202	1281	1457	95	below_threshold
Leptospira alstonii	strain=79601	GCA_000347175.1	28452	28452	type	True	80.7938	926	1457	95	below_threshold
Leptospira alexanderi	strain=L 60	GCA_000243815.3	100053	100053	type	True	80.2712	869	1457	95	below_threshold
Leptospira kmetyi	strain=Bejo-Iso9	GCA_000243735.3	408139	408139	type	True	79.7421	775	1457	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:32,130] [INFO] DFAST Taxonomy check result was written to GCF_000243695.2_gls454049v02_genomic.fna/tc_result.tsv
[2024-01-24 13:28:32,131] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:32,131] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:32,131] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a84838d-b10e-4aeb-8656-d953469b0977/dqc_reference/checkm_data
[2024-01-24 13:28:32,132] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:32,178] [INFO] Task started: CheckM
[2024-01-24 13:28:32,179] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000243695.2_gls454049v02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000243695.2_gls454049v02_genomic.fna/checkm_input GCF_000243695.2_gls454049v02_genomic.fna/checkm_result
[2024-01-24 13:29:01,316] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:01,320] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:01,337] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:01,338] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:01,338] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000243695.2_gls454049v02_genomic.fna/markers.fasta)
[2024-01-24 13:29:01,338] [INFO] Task started: Blastn
[2024-01-24 13:29:01,338] [INFO] Running command: blastn -query GCF_000243695.2_gls454049v02_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a84838d-b10e-4aeb-8656-d953469b0977/dqc_reference/reference_markers_gtdb.fasta -out GCF_000243695.2_gls454049v02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:02,098] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:02,101] [INFO] Selected 9 target genomes.
[2024-01-24 13:29:02,101] [INFO] Target genome list was writen to GCF_000243695.2_gls454049v02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:02,111] [INFO] Task started: fastANI
[2024-01-24 13:29:02,111] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfedfe5c-cf12-4be5-8734-468b70e888fc/GCF_000243695.2_gls454049v02_genomic.fna.gz --refList GCF_000243695.2_gls454049v02_genomic.fna/target_genomes_gtdb.txt --output GCF_000243695.2_gls454049v02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:19,832] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:19,840] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:19,841] [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_000243695.2	s__Leptospira kirschneri	100.0	1456	1457	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	98.95	97.03	0.96	0.91	36	conclusive
GCF_900156205.1	s__Leptospira interrogans	90.8264	1303	1457	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	99.34	97.40	0.96	0.89	353	-
GCF_000306255.2	s__Leptospira noguchii	89.7274	1280	1457	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	96.46	95.50	0.89	0.81	18	-
GCF_000332415.1	s__Leptospira weilii_A	80.864	923	1457	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000347175.1	s__Leptospira alstonii	80.8103	930	1457	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	99.79	99.25	0.97	0.95	5	-
GCF_000243815.2	s__Leptospira alexanderi	80.2674	868	1457	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	99.22	97.61	0.97	0.93	6	-
GCF_000313175.2	s__Leptospira santarosai	80.1289	835	1457	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	98.62	96.47	0.92	0.90	43	-
GCF_000243735.2	s__Leptospira kmetyi	79.7422	775	1457	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	79.6342	763	1457	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	96.36	96.36	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:19,842] [INFO] GTDB search result was written to GCF_000243695.2_gls454049v02_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:19,842] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:19,845] [INFO] DFAST_QC result json was written to GCF_000243695.2_gls454049v02_genomic.fna/dqc_result.json
[2024-01-24 13:29:19,845] [INFO] DFAST_QC completed!
[2024-01-24 13:29:19,845] [INFO] Total running time: 0h1m18s