[2023-06-08 04:30:48,469] [INFO] DFAST_QC pipeline started.
[2023-06-08 04:30:48,472] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 04:30:48,473] [INFO] DQC Reference Directory: /var/lib/cwl/stge83f62b6-2596-426a-91e5-726b1c4636ea/dqc_reference
[2023-06-08 04:30:51,109] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 04:30:51,111] [INFO] Task started: Prodigal
[2023-06-08 04:30:51,111] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a97c955-a508-4031-8455-b45ece53ad3b/GCA_945939205.1_SRR11489781_bin.12_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945939205.1_SRR11489781_bin.12_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945939205.1_SRR11489781_bin.12_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 04:30:54,373] [INFO] Task succeeded: Prodigal
[2023-06-08 04:30:54,374] [INFO] Task started: HMMsearch
[2023-06-08 04:30:54,374] [INFO] Running command: hmmsearch --tblout GCA_945939205.1_SRR11489781_bin.12_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge83f62b6-2596-426a-91e5-726b1c4636ea/dqc_reference/reference_markers.hmm GCA_945939205.1_SRR11489781_bin.12_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 04:30:54,613] [INFO] Task succeeded: HMMsearch
[2023-06-08 04:30:54,614] [INFO] Found 6/6 markers.
[2023-06-08 04:30:54,638] [INFO] Query marker FASTA was written to GCA_945939205.1_SRR11489781_bin.12_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 04:30:54,638] [INFO] Task started: Blastn
[2023-06-08 04:30:54,638] [INFO] Running command: blastn -query GCA_945939205.1_SRR11489781_bin.12_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stge83f62b6-2596-426a-91e5-726b1c4636ea/dqc_reference/reference_markers.fasta -out GCA_945939205.1_SRR11489781_bin.12_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 04:30:56,915] [INFO] Task succeeded: Blastn
[2023-06-08 04:30:56,919] [INFO] Selected 14 target genomes.
[2023-06-08 04:30:56,920] [INFO] Target genome list was writen to GCA_945939205.1_SRR11489781_bin.12_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 04:30:56,952] [INFO] Task started: fastANI
[2023-06-08 04:30:56,952] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a97c955-a508-4031-8455-b45ece53ad3b/GCA_945939205.1_SRR11489781_bin.12_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945939205.1_SRR11489781_bin.12_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945939205.1_SRR11489781_bin.12_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 04:31:03,710] [INFO] Task succeeded: fastANI
[2023-06-08 04:31:03,711] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge83f62b6-2596-426a-91e5-726b1c4636ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 04:31:03,711] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge83f62b6-2596-426a-91e5-726b1c4636ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 04:31:03,718] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 04:31:03,718] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 04:31:03,718] [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	78.2462	119	580	95	below_threshold
Treponema berlinense	strain=ATCC BAA-909	GCA_900167025.1	225004	225004	type	True	76.7274	77	580	95	below_threshold
Treponema succinifaciens	strain=DSM 2489	GCA_000195275.1	167	167	type	True	76.4965	56	580	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 04:31:03,721] [INFO] DFAST Taxonomy check result was written to GCA_945939205.1_SRR11489781_bin.12_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 04:31:03,721] [INFO] ===== Taxonomy check completed =====
[2023-06-08 04:31:03,722] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 04:31:03,722] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge83f62b6-2596-426a-91e5-726b1c4636ea/dqc_reference/checkm_data
[2023-06-08 04:31:03,723] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 04:31:03,755] [INFO] Task started: CheckM
[2023-06-08 04:31:03,756] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945939205.1_SRR11489781_bin.12_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945939205.1_SRR11489781_bin.12_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945939205.1_SRR11489781_bin.12_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 04:31:21,685] [INFO] Task succeeded: CheckM
[2023-06-08 04:31:21,686] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 04:31:21,703] [INFO] ===== Completeness check finished =====
[2023-06-08 04:31:21,704] [INFO] ===== Start GTDB Search =====
[2023-06-08 04:31:21,704] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945939205.1_SRR11489781_bin.12_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 04:31:21,704] [INFO] Task started: Blastn
[2023-06-08 04:31:21,705] [INFO] Running command: blastn -query GCA_945939205.1_SRR11489781_bin.12_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stge83f62b6-2596-426a-91e5-726b1c4636ea/dqc_reference/reference_markers_gtdb.fasta -out GCA_945939205.1_SRR11489781_bin.12_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 04:31:22,691] [INFO] Task succeeded: Blastn
[2023-06-08 04:31:22,696] [INFO] Selected 18 target genomes.
[2023-06-08 04:31:22,697] [INFO] Target genome list was writen to GCA_945939205.1_SRR11489781_bin.12_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 04:31:22,705] [INFO] Task started: fastANI
[2023-06-08 04:31:22,705] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a97c955-a508-4031-8455-b45ece53ad3b/GCA_945939205.1_SRR11489781_bin.12_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945939205.1_SRR11489781_bin.12_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945939205.1_SRR11489781_bin.12_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 04:31:30,610] [INFO] Task succeeded: fastANI
[2023-06-08 04:31:30,626] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 04:31:30,627] [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
GCA_016293005.1	s__Treponema_D sp016293005	98.0874	493	580	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.04	98.04	0.88	0.88	2	conclusive
GCA_900769325.1	s__Treponema_D sp900769325	91.8732	524	580	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_900167145.1	s__Treponema_D porcinum	78.2529	117	580	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.53	96.24	0.92	0.88	5	-
GCA_900317625.1	s__Treponema_D sp900317625	77.1366	115	580	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_900769975.1	s__Treponema_D sp900769975	77.0786	94	580	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_016287815.1	s__Treponema_D sp016287815	76.8953	79	580	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_016297805.1	s__Treponema_D sp016297805	76.841	58	580	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_017521105.1	s__Treponema_D sp017521105	76.8227	59	580	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	96.98	96.98	0.70	0.70	2	-
GCA_002478955.1	s__Treponema_D sp002478955	76.7723	108	580	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.79	97.79	0.82	0.82	2	-
GCF_900167025.1	s__Treponema_D berlinense	76.7274	77	580	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.85	98.81	0.93	0.90	4	-
GCF_000421345.1	s__Treponema_D bryantii_B	76.5626	51	580	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_015061465.1	s__Treponema_D bryantii_D	76.5292	76	580	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	96.46	96.39	0.85	0.81	3	-
GCA_002477955.1	s__Treponema_D sp002477955	76.5029	60	580	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	99.57	99.37	0.91	0.86	7	-
GCA_016297415.1	s__Treponema_D sp016297415	76.1826	50	580	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_902789325.1	s__Treponema_D sp902789325	76.1468	57	580	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 04:31:30,630] [INFO] GTDB search result was written to GCA_945939205.1_SRR11489781_bin.12_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 04:31:30,631] [INFO] ===== GTDB Search completed =====
[2023-06-08 04:31:30,637] [INFO] DFAST_QC result json was written to GCA_945939205.1_SRR11489781_bin.12_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 04:31:30,637] [INFO] DFAST_QC completed!
[2023-06-08 04:31:30,638] [INFO] Total running time: 0h0m42s