[2024-01-25 18:59:50,713] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:59:50,715] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:59:50,715] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f5293eb-a0d4-4566-86c1-d617820690b3/dqc_reference
[2024-01-25 18:59:51,845] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:59:51,846] [INFO] Task started: Prodigal
[2024-01-25 18:59:51,846] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5eff735-5a14-4805-8391-724675c3a7b0/GCF_000413055.1_Trep_malt_ATCC_51939_V1_genomic.fna.gz | prodigal -d GCF_000413055.1_Trep_malt_ATCC_51939_V1_genomic.fna/cds.fna -a GCF_000413055.1_Trep_malt_ATCC_51939_V1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:59:57,931] [INFO] Task succeeded: Prodigal
[2024-01-25 18:59:57,932] [INFO] Task started: HMMsearch
[2024-01-25 18:59:57,932] [INFO] Running command: hmmsearch --tblout GCF_000413055.1_Trep_malt_ATCC_51939_V1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f5293eb-a0d4-4566-86c1-d617820690b3/dqc_reference/reference_markers.hmm GCF_000413055.1_Trep_malt_ATCC_51939_V1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:59:58,110] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:59:58,111] [INFO] Found 6/6 markers.
[2024-01-25 18:59:58,132] [INFO] Query marker FASTA was written to GCF_000413055.1_Trep_malt_ATCC_51939_V1_genomic.fna/markers.fasta
[2024-01-25 18:59:58,133] [INFO] Task started: Blastn
[2024-01-25 18:59:58,133] [INFO] Running command: blastn -query GCF_000413055.1_Trep_malt_ATCC_51939_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f5293eb-a0d4-4566-86c1-d617820690b3/dqc_reference/reference_markers.fasta -out GCF_000413055.1_Trep_malt_ATCC_51939_V1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:58,664] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:58,668] [INFO] Selected 19 target genomes.
[2024-01-25 18:59:58,668] [INFO] Target genome list was writen to GCF_000413055.1_Trep_malt_ATCC_51939_V1_genomic.fna/target_genomes.txt
[2024-01-25 18:59:58,688] [INFO] Task started: fastANI
[2024-01-25 18:59:58,689] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5eff735-5a14-4805-8391-724675c3a7b0/GCF_000413055.1_Trep_malt_ATCC_51939_V1_genomic.fna.gz --refList GCF_000413055.1_Trep_malt_ATCC_51939_V1_genomic.fna/target_genomes.txt --output GCF_000413055.1_Trep_malt_ATCC_51939_V1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:00:10,985] [INFO] Task succeeded: fastANI
[2024-01-25 19:00:10,985] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f5293eb-a0d4-4566-86c1-d617820690b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:00:10,985] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f5293eb-a0d4-4566-86c1-d617820690b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:00:10,990] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:00:10,990] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:00:10,990] [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
Treponema maltophilum	strain=ATCC 51939	GCA_000413055.1	51160	51160	type	True	100.0	842	843	95	conclusive
Treponema denticola	strain=ATCC 35405	GCA_000008185.1	158	158	type	True	80.4323	52	843	95	below_threshold
Treponema brennaborense	strain=DSM 12168	GCA_000212415.1	81028	81028	type	True	77.3625	76	843	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:00:10,992] [INFO] DFAST Taxonomy check result was written to GCF_000413055.1_Trep_malt_ATCC_51939_V1_genomic.fna/tc_result.tsv
[2024-01-25 19:00:10,993] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:00:10,993] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:00:10,993] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f5293eb-a0d4-4566-86c1-d617820690b3/dqc_reference/checkm_data
[2024-01-25 19:00:10,994] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:00:11,021] [INFO] Task started: CheckM
[2024-01-25 19:00:11,021] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000413055.1_Trep_malt_ATCC_51939_V1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000413055.1_Trep_malt_ATCC_51939_V1_genomic.fna/checkm_input GCF_000413055.1_Trep_malt_ATCC_51939_V1_genomic.fna/checkm_result
[2024-01-25 19:00:33,008] [INFO] Task succeeded: CheckM
[2024-01-25 19:00:33,009] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:00:33,028] [INFO] ===== Completeness check finished =====
[2024-01-25 19:00:33,028] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:00:33,029] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000413055.1_Trep_malt_ATCC_51939_V1_genomic.fna/markers.fasta)
[2024-01-25 19:00:33,029] [INFO] Task started: Blastn
[2024-01-25 19:00:33,029] [INFO] Running command: blastn -query GCF_000413055.1_Trep_malt_ATCC_51939_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f5293eb-a0d4-4566-86c1-d617820690b3/dqc_reference/reference_markers_gtdb.fasta -out GCF_000413055.1_Trep_malt_ATCC_51939_V1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:00:33,804] [INFO] Task succeeded: Blastn
[2024-01-25 19:00:33,807] [INFO] Selected 15 target genomes.
[2024-01-25 19:00:33,807] [INFO] Target genome list was writen to GCF_000413055.1_Trep_malt_ATCC_51939_V1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:00:33,846] [INFO] Task started: fastANI
[2024-01-25 19:00:33,846] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5eff735-5a14-4805-8391-724675c3a7b0/GCF_000413055.1_Trep_malt_ATCC_51939_V1_genomic.fna.gz --refList GCF_000413055.1_Trep_malt_ATCC_51939_V1_genomic.fna/target_genomes_gtdb.txt --output GCF_000413055.1_Trep_malt_ATCC_51939_V1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:00:41,023] [INFO] Task succeeded: fastANI
[2024-01-25 19:00:41,028] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:00:41,028] [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_000413055.1	s__Treponema_C maltophilum	100.0	843	843	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905372025.1	s__Treponema_C sp905372025	93.2663	689	843	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902983995.1	s__Treponema_D buccale	81.211	142	843	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000468055.1	s__Treponema_C lecithinolyticum	80.5085	296	843	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_C	95.0	98.36	98.36	0.98	0.98	2	-
GCF_000468115.1	s__Treponema_D socranskii	79.9323	131	843	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	99.97	99.97	0.95	0.95	2	-
GCF_000212415.1	s__Treponema_F brennaborense	77.1482	75	843	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_F	95.0	99.21	99.21	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:00:41,030] [INFO] GTDB search result was written to GCF_000413055.1_Trep_malt_ATCC_51939_V1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:00:41,030] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:00:41,032] [INFO] DFAST_QC result json was written to GCF_000413055.1_Trep_malt_ATCC_51939_V1_genomic.fna/dqc_result.json
[2024-01-25 19:00:41,032] [INFO] DFAST_QC completed!
[2024-01-25 19:00:41,032] [INFO] Total running time: 0h0m50s