[2024-01-25 18:02:50,707] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:02:50,710] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:02:50,710] [INFO] DQC Reference Directory: /var/lib/cwl/stge8275358-234c-4de8-a457-fb0a636511d0/dqc_reference
[2024-01-25 18:02:51,856] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:02:51,857] [INFO] Task started: Prodigal
[2024-01-25 18:02:51,857] [INFO] Running command: gunzip -c /var/lib/cwl/stgd002d822-db89-4445-82c2-98af6256c2ff/GCF_000306675.2_ASM30667v3_genomic.fna.gz | prodigal -d GCF_000306675.2_ASM30667v3_genomic.fna/cds.fna -a GCF_000306675.2_ASM30667v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:02:59,995] [INFO] Task succeeded: Prodigal
[2024-01-25 18:02:59,996] [INFO] Task started: HMMsearch
[2024-01-25 18:02:59,996] [INFO] Running command: hmmsearch --tblout GCF_000306675.2_ASM30667v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8275358-234c-4de8-a457-fb0a636511d0/dqc_reference/reference_markers.hmm GCF_000306675.2_ASM30667v3_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:03:00,236] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:03:00,237] [INFO] Found 6/6 markers.
[2024-01-25 18:03:00,273] [INFO] Query marker FASTA was written to GCF_000306675.2_ASM30667v3_genomic.fna/markers.fasta
[2024-01-25 18:03:00,273] [INFO] Task started: Blastn
[2024-01-25 18:03:00,273] [INFO] Running command: blastn -query GCF_000306675.2_ASM30667v3_genomic.fna/markers.fasta -db /var/lib/cwl/stge8275358-234c-4de8-a457-fb0a636511d0/dqc_reference/reference_markers.fasta -out GCF_000306675.2_ASM30667v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:00,817] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:00,822] [INFO] Selected 8 target genomes.
[2024-01-25 18:03:00,822] [INFO] Target genome list was writen to GCF_000306675.2_ASM30667v3_genomic.fna/target_genomes.txt
[2024-01-25 18:03:00,831] [INFO] Task started: fastANI
[2024-01-25 18:03:00,832] [INFO] Running command: fastANI --query /var/lib/cwl/stgd002d822-db89-4445-82c2-98af6256c2ff/GCF_000306675.2_ASM30667v3_genomic.fna.gz --refList GCF_000306675.2_ASM30667v3_genomic.fna/target_genomes.txt --output GCF_000306675.2_ASM30667v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:03:11,254] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:11,255] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8275358-234c-4de8-a457-fb0a636511d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:03:11,255] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8275358-234c-4de8-a457-fb0a636511d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:03:11,263] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:03:11,263] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:03:11,263] [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 mayottensis	strain=200901116	GCA_000306675.3	1137606	1137606	type	True	100.0	1398	1404	95	conclusive
Leptospira alexanderi	strain=L 60	GCA_000243815.3	100053	100053	type	True	91.923	1123	1404	95	below_threshold
Leptospira borgpetersenii	strain=DSM 21538	GCA_003046425.1	174	174	type	True	90.988	1131	1404	95	below_threshold
Leptospira santarosai	strain=LT 821	GCA_000313175.2	28183	28183	type	True	86.7104	1054	1404	95	below_threshold
Leptospira alstonii	strain=79601	GCA_000347175.1	28452	28452	type	True	82.8938	963	1404	95	below_threshold
Leptospira yasudae	strain=F1	GCA_003545925.1	2202201	2202201	type	True	80.1756	767	1404	95	below_threshold
Leptospira kirschneri	strain=3522 CT	GCA_000243695.3	29507	29507	type	True	80.0921	878	1404	95	below_threshold
Leptospira interrogans	strain=ATCC 43642	GCA_900156205.1	173	173	type	True	79.9644	827	1404	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:03:11,265] [INFO] DFAST Taxonomy check result was written to GCF_000306675.2_ASM30667v3_genomic.fna/tc_result.tsv
[2024-01-25 18:03:11,265] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:03:11,265] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:03:11,265] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8275358-234c-4de8-a457-fb0a636511d0/dqc_reference/checkm_data
[2024-01-25 18:03:11,266] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:03:11,308] [INFO] Task started: CheckM
[2024-01-25 18:03:11,308] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000306675.2_ASM30667v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000306675.2_ASM30667v3_genomic.fna/checkm_input GCF_000306675.2_ASM30667v3_genomic.fna/checkm_result
[2024-01-25 18:03:39,643] [INFO] Task succeeded: CheckM
[2024-01-25 18:03:39,644] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:03:39,678] [INFO] ===== Completeness check finished =====
[2024-01-25 18:03:39,678] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:03:39,678] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000306675.2_ASM30667v3_genomic.fna/markers.fasta)
[2024-01-25 18:03:39,678] [INFO] Task started: Blastn
[2024-01-25 18:03:39,678] [INFO] Running command: blastn -query GCF_000306675.2_ASM30667v3_genomic.fna/markers.fasta -db /var/lib/cwl/stge8275358-234c-4de8-a457-fb0a636511d0/dqc_reference/reference_markers_gtdb.fasta -out GCF_000306675.2_ASM30667v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:40,466] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:40,470] [INFO] Selected 6 target genomes.
[2024-01-25 18:03:40,470] [INFO] Target genome list was writen to GCF_000306675.2_ASM30667v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:03:40,477] [INFO] Task started: fastANI
[2024-01-25 18:03:40,477] [INFO] Running command: fastANI --query /var/lib/cwl/stgd002d822-db89-4445-82c2-98af6256c2ff/GCF_000306675.2_ASM30667v3_genomic.fna.gz --refList GCF_000306675.2_ASM30667v3_genomic.fna/target_genomes_gtdb.txt --output GCF_000306675.2_ASM30667v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:03:49,620] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:49,625] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:03:49,626] [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_000306675.2	s__Leptospira mayottensis	100.0	1401	1404	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	99.59	98.88	0.95	0.90	6	conclusive
GCF_000243815.2	s__Leptospira alexanderi	91.9036	1125	1404	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	90.999	1130	1404	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	99.13	97.82	0.96	0.92	148	-
GCF_000244815.1	s__Leptospira weilii	90.7416	1147	1404	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	95.50	95.12	0.87	0.84	20	-
GCF_000313175.2	s__Leptospira santarosai	86.7225	1051	1404	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	98.62	96.47	0.92	0.90	43	-
GCF_000347175.1	s__Leptospira alstonii	82.9126	958	1404	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	99.79	99.25	0.97	0.95	5	-
--------------------------------------------------------------------------------
[2024-01-25 18:03:49,628] [INFO] GTDB search result was written to GCF_000306675.2_ASM30667v3_genomic.fna/result_gtdb.tsv
[2024-01-25 18:03:49,628] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:03:49,632] [INFO] DFAST_QC result json was written to GCF_000306675.2_ASM30667v3_genomic.fna/dqc_result.json
[2024-01-25 18:03:49,632] [INFO] DFAST_QC completed!
[2024-01-25 18:03:49,632] [INFO] Total running time: 0h0m59s