[2023-06-08 10:57:36,907] [INFO] DFAST_QC pipeline started.
[2023-06-08 10:57:36,910] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 10:57:36,911] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f7aa6c3-f2a6-45cc-9697-a03372d346d0/dqc_reference
[2023-06-08 10:57:38,151] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 10:57:38,152] [INFO] Task started: Prodigal
[2023-06-08 10:57:38,152] [INFO] Running command: gunzip -c /var/lib/cwl/stg1f3d72bb-730c-4eb1-b83a-464d2f11f657/GCA_945971235.1_SRR15725432_bin.7_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945971235.1_SRR15725432_bin.7_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945971235.1_SRR15725432_bin.7_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 10:57:40,391] [INFO] Task succeeded: Prodigal
[2023-06-08 10:57:40,392] [INFO] Task started: HMMsearch
[2023-06-08 10:57:40,392] [INFO] Running command: hmmsearch --tblout GCA_945971235.1_SRR15725432_bin.7_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f7aa6c3-f2a6-45cc-9697-a03372d346d0/dqc_reference/reference_markers.hmm GCA_945971235.1_SRR15725432_bin.7_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 10:57:40,597] [INFO] Task succeeded: HMMsearch
[2023-06-08 10:57:40,598] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1f3d72bb-730c-4eb1-b83a-464d2f11f657/GCA_945971235.1_SRR15725432_bin.7_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 10:57:40,613] [INFO] Query marker FASTA was written to GCA_945971235.1_SRR15725432_bin.7_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 10:57:40,614] [INFO] Task started: Blastn
[2023-06-08 10:57:40,614] [INFO] Running command: blastn -query GCA_945971235.1_SRR15725432_bin.7_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f7aa6c3-f2a6-45cc-9697-a03372d346d0/dqc_reference/reference_markers.fasta -out GCA_945971235.1_SRR15725432_bin.7_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 10:57:41,216] [INFO] Task succeeded: Blastn
[2023-06-08 10:57:41,220] [INFO] Selected 13 target genomes.
[2023-06-08 10:57:41,220] [INFO] Target genome list was writen to GCA_945971235.1_SRR15725432_bin.7_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 10:57:41,223] [INFO] Task started: fastANI
[2023-06-08 10:57:41,223] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f3d72bb-730c-4eb1-b83a-464d2f11f657/GCA_945971235.1_SRR15725432_bin.7_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945971235.1_SRR15725432_bin.7_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945971235.1_SRR15725432_bin.7_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 10:57:46,555] [INFO] Task succeeded: fastANI
[2023-06-08 10:57:46,556] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f7aa6c3-f2a6-45cc-9697-a03372d346d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 10:57:46,556] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f7aa6c3-f2a6-45cc-9697-a03372d346d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 10:57:46,562] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2023-06-08 10:57:46,562] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-08 10:57:46,563] [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 porcinum	strain=ATCC BAA-908	GCA_900167145.1	261392	261392	type	True	97.2458	271	282	95	conclusive
--------------------------------------------------------------------------------
[2023-06-08 10:57:46,565] [INFO] DFAST Taxonomy check result was written to GCA_945971235.1_SRR15725432_bin.7_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 10:57:46,566] [INFO] ===== Taxonomy check completed =====
[2023-06-08 10:57:46,566] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 10:57:46,567] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f7aa6c3-f2a6-45cc-9697-a03372d346d0/dqc_reference/checkm_data
[2023-06-08 10:57:46,568] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 10:57:46,583] [INFO] Task started: CheckM
[2023-06-08 10:57:46,583] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945971235.1_SRR15725432_bin.7_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945971235.1_SRR15725432_bin.7_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945971235.1_SRR15725432_bin.7_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 10:58:01,416] [INFO] Task succeeded: CheckM
[2023-06-08 10:58:01,418] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.87%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 10:58:01,440] [INFO] ===== Completeness check finished =====
[2023-06-08 10:58:01,440] [INFO] ===== Start GTDB Search =====
[2023-06-08 10:58:01,441] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945971235.1_SRR15725432_bin.7_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 10:58:01,441] [INFO] Task started: Blastn
[2023-06-08 10:58:01,441] [INFO] Running command: blastn -query GCA_945971235.1_SRR15725432_bin.7_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f7aa6c3-f2a6-45cc-9697-a03372d346d0/dqc_reference/reference_markers_gtdb.fasta -out GCA_945971235.1_SRR15725432_bin.7_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 10:58:02,407] [INFO] Task succeeded: Blastn
[2023-06-08 10:58:02,411] [INFO] Selected 21 target genomes.
[2023-06-08 10:58:02,411] [INFO] Target genome list was writen to GCA_945971235.1_SRR15725432_bin.7_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 10:58:02,416] [INFO] Task started: fastANI
[2023-06-08 10:58:02,416] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f3d72bb-730c-4eb1-b83a-464d2f11f657/GCA_945971235.1_SRR15725432_bin.7_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945971235.1_SRR15725432_bin.7_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945971235.1_SRR15725432_bin.7_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 10:58:10,734] [INFO] Task succeeded: fastANI
[2023-06-08 10:58:10,750] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 10:58:10,751] [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_900167145.1	s__Treponema_D porcinum	97.2458	271	282	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.53	96.24	0.92	0.88	5	conclusive
GCA_017381365.1	s__Treponema_D sp017381365	78.0982	56	282	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.14	97.14	0.75	0.75	2	-
GCA_002478955.1	s__Treponema_D sp002478955	77.7473	67	282	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.79	97.79	0.82	0.82	2	-
GCA_900541945.1	s__Treponema_D sp900541945	77.7186	85	282	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.94	97.90	0.88	0.87	3	-
GCA_017392945.1	s__Treponema_D sp017392945	77.536	53	282	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900317625.1	s__Treponema_D sp900317625	77.3755	59	282	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	99.21	99.03	0.90	0.87	4	-
GCA_017470605.1	s__Treponema_D sp017470605	77.3338	50	282	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319625.1	s__Treponema_D sp900319625	76.9315	50	282	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.09	97.03	0.92	0.88	5	-
--------------------------------------------------------------------------------
[2023-06-08 10:58:10,753] [INFO] GTDB search result was written to GCA_945971235.1_SRR15725432_bin.7_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 10:58:10,754] [INFO] ===== GTDB Search completed =====
[2023-06-08 10:58:10,758] [INFO] DFAST_QC result json was written to GCA_945971235.1_SRR15725432_bin.7_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 10:58:10,758] [INFO] DFAST_QC completed!
[2023-06-08 10:58:10,759] [INFO] Total running time: 0h0m34s