[2023-06-08 15:53:40,996] [INFO] DFAST_QC pipeline started.
[2023-06-08 15:53:41,000] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 15:53:41,000] [INFO] DQC Reference Directory: /var/lib/cwl/stgb92a4ae0-095f-473e-b4af-7a447ef10b29/dqc_reference
[2023-06-08 15:53:43,605] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 15:53:43,606] [INFO] Task started: Prodigal
[2023-06-08 15:53:43,607] [INFO] Running command: gunzip -c /var/lib/cwl/stgdc0c7dc4-b911-4c9c-a1e3-648322e76eec/GCA_945830845.1_SRR5240737_bin.19_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945830845.1_SRR5240737_bin.19_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945830845.1_SRR5240737_bin.19_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 15:53:49,601] [INFO] Task succeeded: Prodigal
[2023-06-08 15:53:49,602] [INFO] Task started: HMMsearch
[2023-06-08 15:53:49,602] [INFO] Running command: hmmsearch --tblout GCA_945830845.1_SRR5240737_bin.19_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb92a4ae0-095f-473e-b4af-7a447ef10b29/dqc_reference/reference_markers.hmm GCA_945830845.1_SRR5240737_bin.19_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 15:53:49,862] [INFO] Task succeeded: HMMsearch
[2023-06-08 15:53:49,864] [INFO] Found 6/6 markers.
[2023-06-08 15:53:49,892] [INFO] Query marker FASTA was written to GCA_945830845.1_SRR5240737_bin.19_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 15:53:49,892] [INFO] Task started: Blastn
[2023-06-08 15:53:49,892] [INFO] Running command: blastn -query GCA_945830845.1_SRR5240737_bin.19_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb92a4ae0-095f-473e-b4af-7a447ef10b29/dqc_reference/reference_markers.fasta -out GCA_945830845.1_SRR5240737_bin.19_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 15:53:50,628] [INFO] Task succeeded: Blastn
[2023-06-08 15:53:50,633] [INFO] Selected 22 target genomes.
[2023-06-08 15:53:50,633] [INFO] Target genome list was writen to GCA_945830845.1_SRR5240737_bin.19_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 15:53:50,635] [INFO] Task started: fastANI
[2023-06-08 15:53:50,635] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc0c7dc4-b911-4c9c-a1e3-648322e76eec/GCA_945830845.1_SRR5240737_bin.19_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945830845.1_SRR5240737_bin.19_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945830845.1_SRR5240737_bin.19_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 15:53:59,309] [INFO] Task succeeded: fastANI
[2023-06-08 15:53:59,310] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb92a4ae0-095f-473e-b4af-7a447ef10b29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 15:53:59,310] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb92a4ae0-095f-473e-b4af-7a447ef10b29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 15:53:59,328] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 15:53:59,328] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 15:53:59,328] [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
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	79.8866	147	688	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	79.1381	130	688	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	77.9282	69	688	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	77.8442	72	688	95	below_threshold
Intestinimonas butyriciproducens	strain=SRB-521-5-I	GCA_004154955.1	1297617	1297617	type	True	77.558	56	688	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	77.5167	55	688	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	77.4748	53	688	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.4217	119	688	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	77.3475	87	688	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	77.3015	68	688	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	77.2294	81	688	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.095	87	688	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	77.08	88	688	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	77.0603	84	688	95	below_threshold
Feifania hominis	strain=BX7	GCA_014384765.1	2763660	2763660	type	True	76.4035	54	688	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 15:53:59,330] [INFO] DFAST Taxonomy check result was written to GCA_945830845.1_SRR5240737_bin.19_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 15:53:59,330] [INFO] ===== Taxonomy check completed =====
[2023-06-08 15:53:59,330] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 15:53:59,330] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb92a4ae0-095f-473e-b4af-7a447ef10b29/dqc_reference/checkm_data
[2023-06-08 15:53:59,331] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 15:53:59,379] [INFO] Task started: CheckM
[2023-06-08 15:53:59,380] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945830845.1_SRR5240737_bin.19_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945830845.1_SRR5240737_bin.19_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945830845.1_SRR5240737_bin.19_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 15:54:22,687] [INFO] Task succeeded: CheckM
[2023-06-08 15:54:22,689] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-08 15:54:22,712] [INFO] ===== Completeness check finished =====
[2023-06-08 15:54:22,713] [INFO] ===== Start GTDB Search =====
[2023-06-08 15:54:22,713] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945830845.1_SRR5240737_bin.19_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 15:54:22,714] [INFO] Task started: Blastn
[2023-06-08 15:54:22,714] [INFO] Running command: blastn -query GCA_945830845.1_SRR5240737_bin.19_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb92a4ae0-095f-473e-b4af-7a447ef10b29/dqc_reference/reference_markers_gtdb.fasta -out GCA_945830845.1_SRR5240737_bin.19_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 15:54:24,033] [INFO] Task succeeded: Blastn
[2023-06-08 15:54:24,038] [INFO] Selected 10 target genomes.
[2023-06-08 15:54:24,038] [INFO] Target genome list was writen to GCA_945830845.1_SRR5240737_bin.19_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 15:54:24,040] [INFO] Task started: fastANI
[2023-06-08 15:54:24,040] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc0c7dc4-b911-4c9c-a1e3-648322e76eec/GCA_945830845.1_SRR5240737_bin.19_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945830845.1_SRR5240737_bin.19_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945830845.1_SRR5240737_bin.19_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 15:54:28,593] [INFO] Task succeeded: fastANI
[2023-06-08 15:54:28,604] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 15:54:28,605] [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_000765235.1	s__ER4 sp000765235	97.0701	549	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	96.82	96.40	0.83	0.70	19	conclusive
GCA_900552015.1	s__ER4 sp900552015	90.7241	453	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	100.00	100.00	0.99	0.99	2	-
GCA_900550165.1	s__ER4 sp900550165	89.2364	417	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	96.79	96.53	0.85	0.84	4	-
GCA_900763705.1	s__ER4 sp900763705	88.5748	365	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003522105.1	s__ER4 sp003522105	88.2428	430	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	97.35	97.09	0.78	0.74	7	-
GCA_900546295.1	s__ER4 sp900546295	87.6172	415	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	98.01	98.01	0.87	0.87	2	-
GCA_900556145.1	s__ER4 sp900556145	86.9045	274	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002405995.1	s__ER4 sp002405995	85.7817	380	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	99.39	99.39	0.82	0.82	2	-
GCA_900549405.1	s__Lawsonibacter sp900549405	77.5321	83	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	97.96	97.96	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-06-08 15:54:28,607] [INFO] GTDB search result was written to GCA_945830845.1_SRR5240737_bin.19_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 15:54:28,607] [INFO] ===== GTDB Search completed =====
[2023-06-08 15:54:28,611] [INFO] DFAST_QC result json was written to GCA_945830845.1_SRR5240737_bin.19_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 15:54:28,612] [INFO] DFAST_QC completed!
[2023-06-08 15:54:28,612] [INFO] Total running time: 0h0m48s