[2024-01-24 13:48:57,239] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:57,241] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:57,241] [INFO] DQC Reference Directory: /var/lib/cwl/stgd8f34c42-c5bd-4868-b459-de926b4e26bd/dqc_reference
[2024-01-24 13:48:58,479] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:48:58,480] [INFO] Task started: Prodigal
[2024-01-24 13:48:58,480] [INFO] Running command: gunzip -c /var/lib/cwl/stg4029be4e-34e2-40e5-b422-b6dd3b98e04a/GCF_002150035.1_ASM215003v1_genomic.fna.gz | prodigal -d GCF_002150035.1_ASM215003v1_genomic.fna/cds.fna -a GCF_002150035.1_ASM215003v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:07,155] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:07,155] [INFO] Task started: HMMsearch
[2024-01-24 13:49:07,155] [INFO] Running command: hmmsearch --tblout GCF_002150035.1_ASM215003v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd8f34c42-c5bd-4868-b459-de926b4e26bd/dqc_reference/reference_markers.hmm GCF_002150035.1_ASM215003v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:07,463] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:07,465] [INFO] Found 6/6 markers.
[2024-01-24 13:49:07,503] [INFO] Query marker FASTA was written to GCF_002150035.1_ASM215003v1_genomic.fna/markers.fasta
[2024-01-24 13:49:07,504] [INFO] Task started: Blastn
[2024-01-24 13:49:07,504] [INFO] Running command: blastn -query GCF_002150035.1_ASM215003v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8f34c42-c5bd-4868-b459-de926b4e26bd/dqc_reference/reference_markers.fasta -out GCF_002150035.1_ASM215003v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:08,078] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:08,082] [INFO] Selected 8 target genomes.
[2024-01-24 13:49:08,082] [INFO] Target genome list was writen to GCF_002150035.1_ASM215003v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:08,140] [INFO] Task started: fastANI
[2024-01-24 13:49:08,141] [INFO] Running command: fastANI --query /var/lib/cwl/stg4029be4e-34e2-40e5-b422-b6dd3b98e04a/GCF_002150035.1_ASM215003v1_genomic.fna.gz --refList GCF_002150035.1_ASM215003v1_genomic.fna/target_genomes.txt --output GCF_002150035.1_ASM215003v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:16,503] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:16,504] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd8f34c42-c5bd-4868-b459-de926b4e26bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:16,504] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd8f34c42-c5bd-4868-b459-de926b4e26bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:16,515] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:16,515] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:16,515] [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 venezuelensis	strain=CLM-U50	GCA_002150035.1	1958811	1958811	type	True	100.0	1426	1426	95	conclusive
Leptospira saintgironsiae	strain=FH4-C-A2	GCA_002811765.1	2023183	2023183	type	True	88.2308	1232	1426	95	below_threshold
Leptospira selangorensis	strain=SSW17	GCA_004769405.1	2484982	2484982	type	True	88.0238	1243	1426	95	below_threshold
Leptospira haakeii	strain=ATI7-C-A4	GCA_002812045.1	2023198	2023198	type	True	87.7391	1245	1426	95	below_threshold
Leptospira hartskeerlii	strain=MCA2-B-A3	GCA_002811475.1	2023177	2023177	type	True	87.3376	1210	1426	95	below_threshold
Leptospira licerasiae	strain=VAR 010	GCA_000244755.3	447106	447106	type	True	86.813	1229	1426	95	below_threshold
Leptospira licerasiae	strain=ATCC BAA-1110	GCA_000526875.1	447106	447106	type	True	86.7727	1222	1426	95	below_threshold
Leptospira neocaledonica	strain=ES4-C-A1	GCA_002812205.1	2023192	2023192	type	True	86.6396	1199	1426	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:16,519] [INFO] DFAST Taxonomy check result was written to GCF_002150035.1_ASM215003v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:16,520] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:16,520] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:16,520] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd8f34c42-c5bd-4868-b459-de926b4e26bd/dqc_reference/checkm_data
[2024-01-24 13:49:16,521] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:16,563] [INFO] Task started: CheckM
[2024-01-24 13:49:16,564] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002150035.1_ASM215003v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002150035.1_ASM215003v1_genomic.fna/checkm_input GCF_002150035.1_ASM215003v1_genomic.fna/checkm_result
[2024-01-24 13:49:47,365] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:47,367] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:47,391] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:47,392] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:47,392] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002150035.1_ASM215003v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:47,393] [INFO] Task started: Blastn
[2024-01-24 13:49:47,393] [INFO] Running command: blastn -query GCF_002150035.1_ASM215003v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8f34c42-c5bd-4868-b459-de926b4e26bd/dqc_reference/reference_markers_gtdb.fasta -out GCF_002150035.1_ASM215003v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:48,169] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:48,172] [INFO] Selected 9 target genomes.
[2024-01-24 13:49:48,172] [INFO] Target genome list was writen to GCF_002150035.1_ASM215003v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:48,212] [INFO] Task started: fastANI
[2024-01-24 13:49:48,212] [INFO] Running command: fastANI --query /var/lib/cwl/stg4029be4e-34e2-40e5-b422-b6dd3b98e04a/GCF_002150035.1_ASM215003v1_genomic.fna.gz --refList GCF_002150035.1_ASM215003v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002150035.1_ASM215003v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:57,763] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:57,772] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:57,773] [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_002150035.1	s__Leptospira_B venezuelensis	100.0	1426	1426	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_004769555.1	s__Leptospira_B koniambonensis	88.6621	1258	1426	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004770895.1	s__Leptospira_B dzoumogneensis	88.3874	1240	1426	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002811765.1	s__Leptospira_B saintgironsiae	88.2236	1233	1426	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004770105.1	s__Leptospira_B andrefontaineae	88.2234	1222	1426	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004769405.1	s__Leptospira_B selangorensis	88.0151	1244	1426	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B	95.0	97.97	97.97	0.98	0.97	3	-
GCF_002812045.1	s__Leptospira_B haakeii	87.7462	1244	1426	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002811475.1	s__Leptospira_B hartskeerlii	87.3324	1211	1426	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000244755.1	s__Leptospira_B licerasiae	86.8044	1230	1426	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B	95.0	99.34	97.39	0.98	0.94	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:49:57,775] [INFO] GTDB search result was written to GCF_002150035.1_ASM215003v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:57,776] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:57,780] [INFO] DFAST_QC result json was written to GCF_002150035.1_ASM215003v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:57,781] [INFO] DFAST_QC completed!
[2024-01-24 13:49:57,781] [INFO] Total running time: 0h1m1s