[2024-01-24 12:23:04,484] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:04,486] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:04,486] [INFO] DQC Reference Directory: /var/lib/cwl/stg42de66d5-e8fe-4922-8fc8-307954de0a52/dqc_reference
[2024-01-24 12:23:05,845] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:05,847] [INFO] Task started: Prodigal
[2024-01-24 12:23:05,847] [INFO] Running command: gunzip -c /var/lib/cwl/stg524d3c9c-7976-4609-8e51-f061d40f5892/GCF_003114835.2_ASM311483v3_genomic.fna.gz | prodigal -d GCF_003114835.2_ASM311483v3_genomic.fna/cds.fna -a GCF_003114835.2_ASM311483v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:16,566] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:16,566] [INFO] Task started: HMMsearch
[2024-01-24 12:23:16,566] [INFO] Running command: hmmsearch --tblout GCF_003114835.2_ASM311483v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg42de66d5-e8fe-4922-8fc8-307954de0a52/dqc_reference/reference_markers.hmm GCF_003114835.2_ASM311483v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:16,859] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:16,861] [INFO] Found 6/6 markers.
[2024-01-24 12:23:16,904] [INFO] Query marker FASTA was written to GCF_003114835.2_ASM311483v3_genomic.fna/markers.fasta
[2024-01-24 12:23:16,904] [INFO] Task started: Blastn
[2024-01-24 12:23:16,904] [INFO] Running command: blastn -query GCF_003114835.2_ASM311483v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg42de66d5-e8fe-4922-8fc8-307954de0a52/dqc_reference/reference_markers.fasta -out GCF_003114835.2_ASM311483v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:17,486] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:17,489] [INFO] Selected 15 target genomes.
[2024-01-24 12:23:17,490] [INFO] Target genome list was writen to GCF_003114835.2_ASM311483v3_genomic.fna/target_genomes.txt
[2024-01-24 12:23:17,495] [INFO] Task started: fastANI
[2024-01-24 12:23:17,496] [INFO] Running command: fastANI --query /var/lib/cwl/stg524d3c9c-7976-4609-8e51-f061d40f5892/GCF_003114835.2_ASM311483v3_genomic.fna.gz --refList GCF_003114835.2_ASM311483v3_genomic.fna/target_genomes.txt --output GCF_003114835.2_ASM311483v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:28,732] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:28,732] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg42de66d5-e8fe-4922-8fc8-307954de0a52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:28,733] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg42de66d5-e8fe-4922-8fc8-307954de0a52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:28,748] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:28,748] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:28,748] [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 kobayashii	strain=E30	GCA_003114835.3	1917830	1917830	type	True	100.0	1434	1434	95	conclusive
Leptospira ilyithenensis	strain=201400974	GCA_004771005.1	2484901	2484901	type	True	88.0348	1209	1434	95	below_threshold
Leptospira wolbachii	strain=CDC	GCA_000332515.2	29511	29511	type	True	77.5225	242	1434	95	below_threshold
Leptospira harrisiae	strain=FH2-B-A1	GCA_002811945.1	2023189	2023189	type	True	77.452	241	1434	95	below_threshold
Leptospira biflexa	strain=Patoc 1 (Paris)	GCA_000017685.1	172	172	type	True	77.3852	212	1434	95	below_threshold
Leptospira ognonensis	strain=201702476	GCA_004770745.1	2484945	2484945	type	True	77.3735	205	1434	95	below_threshold
Leptospira levettii	strain=MCA2-B-A1	GCA_002812085.1	2023178	2023178	type	True	77.33	220	1434	95	below_threshold
Leptospira vanthielii	strain=Waz Holland	GCA_000332455.2	293085	293085	type	True	77.3147	237	1434	95	below_threshold
Leptospira abararensis	strain=201903074	GCA_016918735.1	2810036	2810036	type	True	77.3024	247	1434	95	below_threshold
Leptospira brenneri	strain=JW2-C-A2	GCA_002812125.1	2023182	2023182	type	True	77.2472	234	1434	95	below_threshold
Leptospira chreensis	strain=201903075	GCA_016919165.1	2810035	2810035	type	True	77.2269	242	1434	95	below_threshold
Leptospira yanagawae	strain=Sao Paulo	GCA_000332475.2	293069	293069	type	True	77.1592	227	1434	95	below_threshold
Leptospira ellinghausenii	strain=E18	GCA_003114815.1	1917822	1917822	type	True	77.1269	223	1434	95	below_threshold
Leptospira ainlahdjerensis	strain=201903070	GCA_016919175.1	2810033	2810033	type	True	76.3099	55	1434	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:28,750] [INFO] DFAST Taxonomy check result was written to GCF_003114835.2_ASM311483v3_genomic.fna/tc_result.tsv
[2024-01-24 12:23:28,751] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:28,751] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:28,751] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg42de66d5-e8fe-4922-8fc8-307954de0a52/dqc_reference/checkm_data
[2024-01-24 12:23:28,752] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:28,800] [INFO] Task started: CheckM
[2024-01-24 12:23:28,801] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003114835.2_ASM311483v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003114835.2_ASM311483v3_genomic.fna/checkm_input GCF_003114835.2_ASM311483v3_genomic.fna/checkm_result
[2024-01-24 12:24:04,336] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:04,337] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:04,358] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:04,359] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:04,359] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003114835.2_ASM311483v3_genomic.fna/markers.fasta)
[2024-01-24 12:24:04,359] [INFO] Task started: Blastn
[2024-01-24 12:24:04,360] [INFO] Running command: blastn -query GCF_003114835.2_ASM311483v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg42de66d5-e8fe-4922-8fc8-307954de0a52/dqc_reference/reference_markers_gtdb.fasta -out GCF_003114835.2_ASM311483v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:05,114] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:05,118] [INFO] Selected 14 target genomes.
[2024-01-24 12:24:05,118] [INFO] Target genome list was writen to GCF_003114835.2_ASM311483v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:05,128] [INFO] Task started: fastANI
[2024-01-24 12:24:05,128] [INFO] Running command: fastANI --query /var/lib/cwl/stg524d3c9c-7976-4609-8e51-f061d40f5892/GCF_003114835.2_ASM311483v3_genomic.fna.gz --refList GCF_003114835.2_ASM311483v3_genomic.fna/target_genomes_gtdb.txt --output GCF_003114835.2_ASM311483v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:15,396] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:15,420] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:15,420] [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_003114835.1	s__Leptospira_A kobayashii	99.9848	1417	1434	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004771005.1	s__Leptospira_A ilyithenensis	88.032	1210	1434	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004770995.1	s__Leptospira_A idonii	78.4756	516	1434	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004769575.1	s__Leptospira_A perdikensis	77.4946	242	1434	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004770145.1	s__Leptospira_A bourretii	77.4908	243	1434	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	99.12	99.11	0.96	0.96	4	-
GCF_004770745.1	s__Leptospira_A ognonensis	77.359	206	1434	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000332455.1	s__Leptospira_A vanthielii	77.3584	238	1434	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	98.49	98.49	0.94	0.94	2	-
GCF_002812085.1	s__Leptospira_A levettii	77.33	220	1434	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	98.63	98.25	0.94	0.91	14	-
GCF_004770475.1	s__Leptospira_A mtsangambouensis	77.3244	246	1434	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016918735.1	s__Leptospira_A sp016918735	77.3	248	1434	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002812125.1	s__Leptospira_A brenneri	77.269	232	1434	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	99.47	99.47	0.99	0.99	2	-
GCF_016919165.1	s__Leptospira_A sp016919165	77.2278	242	1434	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004770905.1	s__Leptospira_A bandrabouensis	77.1004	250	1434	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	99.97	99.97	0.99	0.99	2	-
GCF_004769235.1	s__Leptospira_A kanakyensis	77.0871	263	1434	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	99.99	99.99	1.00	0.99	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:15,421] [INFO] GTDB search result was written to GCF_003114835.2_ASM311483v3_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:15,422] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:15,425] [INFO] DFAST_QC result json was written to GCF_003114835.2_ASM311483v3_genomic.fna/dqc_result.json
[2024-01-24 12:24:15,426] [INFO] DFAST_QC completed!
[2024-01-24 12:24:15,426] [INFO] Total running time: 0h1m11s