[2023-06-07 23:37:45,376] [INFO] DFAST_QC pipeline started.
[2023-06-07 23:37:45,389] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 23:37:45,389] [INFO] DQC Reference Directory: /var/lib/cwl/stg72a39830-4cde-4b13-a0be-c8ffb2703606/dqc_reference
[2023-06-07 23:37:48,130] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 23:37:48,131] [INFO] Task started: Prodigal
[2023-06-07 23:37:48,131] [INFO] Running command: gunzip -c /var/lib/cwl/stgeba12efd-0055-40d4-92cb-c66aefabc1fa/GCA_947074655.1_SRR13169512_bin.7_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947074655.1_SRR13169512_bin.7_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947074655.1_SRR13169512_bin.7_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 23:37:53,889] [INFO] Task succeeded: Prodigal
[2023-06-07 23:37:53,890] [INFO] Task started: HMMsearch
[2023-06-07 23:37:53,890] [INFO] Running command: hmmsearch --tblout GCA_947074655.1_SRR13169512_bin.7_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg72a39830-4cde-4b13-a0be-c8ffb2703606/dqc_reference/reference_markers.hmm GCA_947074655.1_SRR13169512_bin.7_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-07 23:37:54,124] [INFO] Task succeeded: HMMsearch
[2023-06-07 23:37:54,126] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgeba12efd-0055-40d4-92cb-c66aefabc1fa/GCA_947074655.1_SRR13169512_bin.7_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-07 23:37:54,151] [INFO] Query marker FASTA was written to GCA_947074655.1_SRR13169512_bin.7_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-07 23:37:54,152] [INFO] Task started: Blastn
[2023-06-07 23:37:54,152] [INFO] Running command: blastn -query GCA_947074655.1_SRR13169512_bin.7_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg72a39830-4cde-4b13-a0be-c8ffb2703606/dqc_reference/reference_markers.fasta -out GCA_947074655.1_SRR13169512_bin.7_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 23:37:54,774] [INFO] Task succeeded: Blastn
[2023-06-07 23:37:54,777] [INFO] Selected 14 target genomes.
[2023-06-07 23:37:54,777] [INFO] Target genome list was writen to GCA_947074655.1_SRR13169512_bin.7_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-07 23:37:54,778] [INFO] Task started: fastANI
[2023-06-07 23:37:54,778] [INFO] Running command: fastANI --query /var/lib/cwl/stgeba12efd-0055-40d4-92cb-c66aefabc1fa/GCA_947074655.1_SRR13169512_bin.7_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947074655.1_SRR13169512_bin.7_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947074655.1_SRR13169512_bin.7_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 23:38:01,153] [INFO] Task succeeded: fastANI
[2023-06-07 23:38:01,153] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg72a39830-4cde-4b13-a0be-c8ffb2703606/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 23:38:01,154] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg72a39830-4cde-4b13-a0be-c8ffb2703606/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 23:38:01,168] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 23:38:01,169] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 23:38:01,169] [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
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	80.0196	266	657	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	78.7595	162	657	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	78.7066	203	657	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	78.6497	191	657	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	77.5457	130	657	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	77.5353	122	657	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.4419	125	657	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_003425665.1	2211183	2211183	type	True	77.4349	96	657	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.3508	100	657	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	77.2984	64	657	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	76.9195	84	657	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	76.8883	73	657	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 23:38:01,171] [INFO] DFAST Taxonomy check result was written to GCA_947074655.1_SRR13169512_bin.7_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-07 23:38:01,172] [INFO] ===== Taxonomy check completed =====
[2023-06-07 23:38:01,172] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 23:38:01,172] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg72a39830-4cde-4b13-a0be-c8ffb2703606/dqc_reference/checkm_data
[2023-06-07 23:38:01,174] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 23:38:01,208] [INFO] Task started: CheckM
[2023-06-07 23:38:01,208] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947074655.1_SRR13169512_bin.7_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947074655.1_SRR13169512_bin.7_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947074655.1_SRR13169512_bin.7_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-07 23:38:24,922] [INFO] Task succeeded: CheckM
[2023-06-07 23:38:24,923] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.14%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 23:38:24,939] [INFO] ===== Completeness check finished =====
[2023-06-07 23:38:24,940] [INFO] ===== Start GTDB Search =====
[2023-06-07 23:38:24,940] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947074655.1_SRR13169512_bin.7_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-07 23:38:24,941] [INFO] Task started: Blastn
[2023-06-07 23:38:24,941] [INFO] Running command: blastn -query GCA_947074655.1_SRR13169512_bin.7_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg72a39830-4cde-4b13-a0be-c8ffb2703606/dqc_reference/reference_markers_gtdb.fasta -out GCA_947074655.1_SRR13169512_bin.7_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 23:38:25,985] [INFO] Task succeeded: Blastn
[2023-06-07 23:38:25,989] [INFO] Selected 8 target genomes.
[2023-06-07 23:38:25,989] [INFO] Target genome list was writen to GCA_947074655.1_SRR13169512_bin.7_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 23:38:25,990] [INFO] Task started: fastANI
[2023-06-07 23:38:25,991] [INFO] Running command: fastANI --query /var/lib/cwl/stgeba12efd-0055-40d4-92cb-c66aefabc1fa/GCA_947074655.1_SRR13169512_bin.7_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947074655.1_SRR13169512_bin.7_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947074655.1_SRR13169512_bin.7_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 23:38:30,987] [INFO] Task succeeded: fastANI
[2023-06-07 23:38:31,002] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 23:38:31,002] [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_910589085.1	s__Lawsonibacter sp910589085	98.4185	524	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910585815.1	s__Lawsonibacter sp910585815	86.296	436	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009911595.1	s__Lawsonibacter sp009911595	85.8021	394	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578735.1	s__Lawsonibacter sp910578735	85.0575	389	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588635.1	s__Lawsonibacter sp910588635	84.4129	387	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584605.1	s__Lawsonibacter sp910584605	84.3467	380	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000492175.1	s__Lawsonibacter sp000492175	84.3388	422	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003612335.1	s__Lawsonibacter sp003612335	84.1873	406	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 23:38:31,003] [INFO] GTDB search result was written to GCA_947074655.1_SRR13169512_bin.7_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-07 23:38:31,004] [INFO] ===== GTDB Search completed =====
[2023-06-07 23:38:31,007] [INFO] DFAST_QC result json was written to GCA_947074655.1_SRR13169512_bin.7_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-07 23:38:31,007] [INFO] DFAST_QC completed!
[2023-06-07 23:38:31,007] [INFO] Total running time: 0h0m46s