[2024-01-24 14:23:04,942] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:23:04,944] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:23:04,944] [INFO] DQC Reference Directory: /var/lib/cwl/stg24c3960a-9e3e-45b2-a451-1d5f2dd736e8/dqc_reference
[2024-01-24 14:23:06,287] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:23:06,288] [INFO] Task started: Prodigal
[2024-01-24 14:23:06,288] [INFO] Running command: gunzip -c /var/lib/cwl/stg3d545475-7ca5-49ea-8b43-7ac9ab929498/GCF_000306255.2_gls454059v02_genomic.fna.gz | prodigal -d GCF_000306255.2_gls454059v02_genomic.fna/cds.fna -a GCF_000306255.2_gls454059v02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:15,058] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:15,059] [INFO] Task started: HMMsearch
[2024-01-24 14:23:15,059] [INFO] Running command: hmmsearch --tblout GCF_000306255.2_gls454059v02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24c3960a-9e3e-45b2-a451-1d5f2dd736e8/dqc_reference/reference_markers.hmm GCF_000306255.2_gls454059v02_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:15,408] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:15,412] [INFO] Found 6/6 markers.
[2024-01-24 14:23:15,492] [INFO] Query marker FASTA was written to GCF_000306255.2_gls454059v02_genomic.fna/markers.fasta
[2024-01-24 14:23:15,492] [INFO] Task started: Blastn
[2024-01-24 14:23:15,493] [INFO] Running command: blastn -query GCF_000306255.2_gls454059v02_genomic.fna/markers.fasta -db /var/lib/cwl/stg24c3960a-9e3e-45b2-a451-1d5f2dd736e8/dqc_reference/reference_markers.fasta -out GCF_000306255.2_gls454059v02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:16,169] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:16,172] [INFO] Selected 7 target genomes.
[2024-01-24 14:23:16,173] [INFO] Target genome list was writen to GCF_000306255.2_gls454059v02_genomic.fna/target_genomes.txt
[2024-01-24 14:23:16,176] [INFO] Task started: fastANI
[2024-01-24 14:23:16,177] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d545475-7ca5-49ea-8b43-7ac9ab929498/GCF_000306255.2_gls454059v02_genomic.fna.gz --refList GCF_000306255.2_gls454059v02_genomic.fna/target_genomes.txt --output GCF_000306255.2_gls454059v02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:29,593] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:29,593] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24c3960a-9e3e-45b2-a451-1d5f2dd736e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:29,594] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24c3960a-9e3e-45b2-a451-1d5f2dd736e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:29,601] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:23:29,601] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:29,601] [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 noguchii	strain=CZ214	GCA_000306255.2	28182	28182	suspected-type	True	100.0	1537	1554	95	conclusive
Leptospira kirschneri	strain=3522 CT	GCA_000243695.3	29507	29507	type	True	89.6421	1282	1554	95	below_threshold
Leptospira interrogans	strain=RGA	GCA_000343165.1	173	173	type	True	88.7815	1257	1554	95	below_threshold
Leptospira interrogans	strain=ATCC 43642	GCA_900156205.1	173	173	type	True	88.7757	1290	1554	95	below_threshold
Leptospira alstonii	strain=79601	GCA_000347175.1	28452	28452	type	True	80.3208	905	1554	95	below_threshold
Leptospira alexanderi	strain=L 60	GCA_000243815.3	100053	100053	type	True	79.9547	862	1554	95	below_threshold
Leptospira barantonii	strain=FH4-C-A1	GCA_002811925.1	2023184	2023184	type	True	79.5559	709	1554	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:29,603] [INFO] DFAST Taxonomy check result was written to GCF_000306255.2_gls454059v02_genomic.fna/tc_result.tsv
[2024-01-24 14:23:29,603] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:29,604] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:29,604] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24c3960a-9e3e-45b2-a451-1d5f2dd736e8/dqc_reference/checkm_data
[2024-01-24 14:23:29,605] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:29,654] [INFO] Task started: CheckM
[2024-01-24 14:23:29,654] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000306255.2_gls454059v02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000306255.2_gls454059v02_genomic.fna/checkm_input GCF_000306255.2_gls454059v02_genomic.fna/checkm_result
[2024-01-24 14:24:02,545] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:02,547] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:02,569] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:02,570] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:02,570] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000306255.2_gls454059v02_genomic.fna/markers.fasta)
[2024-01-24 14:24:02,570] [INFO] Task started: Blastn
[2024-01-24 14:24:02,571] [INFO] Running command: blastn -query GCF_000306255.2_gls454059v02_genomic.fna/markers.fasta -db /var/lib/cwl/stg24c3960a-9e3e-45b2-a451-1d5f2dd736e8/dqc_reference/reference_markers_gtdb.fasta -out GCF_000306255.2_gls454059v02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:03,502] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:03,510] [INFO] Selected 8 target genomes.
[2024-01-24 14:24:03,511] [INFO] Target genome list was writen to GCF_000306255.2_gls454059v02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:03,519] [INFO] Task started: fastANI
[2024-01-24 14:24:03,519] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d545475-7ca5-49ea-8b43-7ac9ab929498/GCF_000306255.2_gls454059v02_genomic.fna.gz --refList GCF_000306255.2_gls454059v02_genomic.fna/target_genomes_gtdb.txt --output GCF_000306255.2_gls454059v02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:16,684] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:16,698] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:16,698] [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_000306255.2	s__Leptospira noguchii	100.0	1539	1554	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	96.46	95.50	0.89	0.81	18	conclusive
GCF_000243695.2	s__Leptospira kirschneri	89.6663	1280	1554	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	98.95	97.03	0.96	0.91	36	-
GCF_900156205.1	s__Leptospira interrogans	88.7792	1291	1554	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	99.34	97.40	0.96	0.89	353	-
GCF_000332415.1	s__Leptospira weilii_A	80.4208	896	1554	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	80.3214	903	1554	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	79.9788	857	1554	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	99.22	97.61	0.97	0.93	6	-
GCF_003046425.1	s__Leptospira borgpetersenii	79.7941	812	1554	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	99.13	97.82	0.96	0.92	148	-
GCF_002811925.1	s__Leptospira barantonii	79.5627	708	1554	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 14:24:16,700] [INFO] GTDB search result was written to GCF_000306255.2_gls454059v02_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:16,702] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:16,706] [INFO] DFAST_QC result json was written to GCF_000306255.2_gls454059v02_genomic.fna/dqc_result.json
[2024-01-24 14:24:16,707] [INFO] DFAST_QC completed!
[2024-01-24 14:24:16,707] [INFO] Total running time: 0h1m12s