[2023-06-28 12:00:45,531] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:00:45,537] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:00:45,537] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f507e23-b1db-495f-afb4-f48a9831770b/dqc_reference
[2023-06-28 12:00:46,812] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:00:46,813] [INFO] Task started: Prodigal
[2023-06-28 12:00:46,813] [INFO] Running command: gunzip -c /var/lib/cwl/stg298b391a-542b-461c-bcaa-fad1e15b9a55/GCA_948437705.1_SRR17794273_bin.34_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_948437705.1_SRR17794273_bin.34_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_948437705.1_SRR17794273_bin.34_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:00:56,312] [INFO] Task succeeded: Prodigal
[2023-06-28 12:00:56,313] [INFO] Task started: HMMsearch
[2023-06-28 12:00:56,313] [INFO] Running command: hmmsearch --tblout GCA_948437705.1_SRR17794273_bin.34_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f507e23-b1db-495f-afb4-f48a9831770b/dqc_reference/reference_markers.hmm GCA_948437705.1_SRR17794273_bin.34_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:00:56,583] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:00:56,584] [INFO] Found 6/6 markers.
[2023-06-28 12:00:56,617] [INFO] Query marker FASTA was written to GCA_948437705.1_SRR17794273_bin.34_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-28 12:00:56,617] [INFO] Task started: Blastn
[2023-06-28 12:00:56,617] [INFO] Running command: blastn -query GCA_948437705.1_SRR17794273_bin.34_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f507e23-b1db-495f-afb4-f48a9831770b/dqc_reference/reference_markers.fasta -out GCA_948437705.1_SRR17794273_bin.34_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:00:57,344] [INFO] Task succeeded: Blastn
[2023-06-28 12:00:57,348] [INFO] Selected 18 target genomes.
[2023-06-28 12:00:57,348] [INFO] Target genome list was writen to GCA_948437705.1_SRR17794273_bin.34_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-28 12:00:57,352] [INFO] Task started: fastANI
[2023-06-28 12:00:57,352] [INFO] Running command: fastANI --query /var/lib/cwl/stg298b391a-542b-461c-bcaa-fad1e15b9a55/GCA_948437705.1_SRR17794273_bin.34_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948437705.1_SRR17794273_bin.34_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_948437705.1_SRR17794273_bin.34_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:01:07,214] [INFO] Task succeeded: fastANI
[2023-06-28 12:01:07,215] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f507e23-b1db-495f-afb4-f48a9831770b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:01:07,215] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f507e23-b1db-495f-afb4-f48a9831770b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:01:07,227] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:01:07,227] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 12:01:07,227] [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
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	79.0703	230	1036	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	78.9541	254	1036	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	78.6299	197	1036	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	78.225	185	1036	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	78.0666	147	1036	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	77.614	169	1036	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	77.4223	88	1036	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	77.1921	86	1036	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_003425665.1	2211183	2211183	type	True	77.1786	90	1036	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_008121455.1	2211183	2211183	type	True	77.1786	90	1036	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.1773	122	1036	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	76.5581	91	1036	95	below_threshold
Subdoligranulum variabile	strain=DSM 15176	GCA_025152575.1	214851	214851	type	True	76.522	69	1036	95	below_threshold
Xylophilus rhododendri	strain=KACC 21265	GCA_009906855.1	2697032	2697032	type	True	75.038	50	1036	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 12:01:07,229] [INFO] DFAST Taxonomy check result was written to GCA_948437705.1_SRR17794273_bin.34_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-28 12:01:07,230] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:01:07,230] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:01:07,230] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f507e23-b1db-495f-afb4-f48a9831770b/dqc_reference/checkm_data
[2023-06-28 12:01:07,231] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:01:07,265] [INFO] Task started: CheckM
[2023-06-28 12:01:07,265] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_948437705.1_SRR17794273_bin.34_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_948437705.1_SRR17794273_bin.34_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_948437705.1_SRR17794273_bin.34_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-28 12:01:39,475] [INFO] Task succeeded: CheckM
[2023-06-28 12:01:39,477] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 96.99%
Contamintation: 4.17%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-28 12:01:39,505] [INFO] ===== Completeness check finished =====
[2023-06-28 12:01:39,506] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:01:39,506] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_948437705.1_SRR17794273_bin.34_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-28 12:01:39,507] [INFO] Task started: Blastn
[2023-06-28 12:01:39,507] [INFO] Running command: blastn -query GCA_948437705.1_SRR17794273_bin.34_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f507e23-b1db-495f-afb4-f48a9831770b/dqc_reference/reference_markers_gtdb.fasta -out GCA_948437705.1_SRR17794273_bin.34_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:01:40,759] [INFO] Task succeeded: Blastn
[2023-06-28 12:01:40,763] [INFO] Selected 14 target genomes.
[2023-06-28 12:01:40,764] [INFO] Target genome list was writen to GCA_948437705.1_SRR17794273_bin.34_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:01:40,775] [INFO] Task started: fastANI
[2023-06-28 12:01:40,776] [INFO] Running command: fastANI --query /var/lib/cwl/stg298b391a-542b-461c-bcaa-fad1e15b9a55/GCA_948437705.1_SRR17794273_bin.34_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948437705.1_SRR17794273_bin.34_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_948437705.1_SRR17794273_bin.34_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:01:50,601] [INFO] Task succeeded: fastANI
[2023-06-28 12:01:50,618] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 12:01:50,618] [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_910587205.1	s__Enterenecus sp910587205	99.3548	705	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910587285.1	s__Enterenecus sp910587285	85.0175	564	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585265.1	s__Enterenecus sp910585265	84.6601	542	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004560375.1	s__Enterenecus sp004560375	84.3397	446	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588105.1	s__Enterenecus sp910588105	84.2047	503	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584285.1	s__Enterenecus sp910584285	84.1741	492	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910575695.1	s__Enterenecus sp910575695	83.9674	575	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585155.1	s__Enterenecus sp910585155	83.9404	463	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584835.1	s__Enterenecus sp910584835	83.8546	457	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588495.1	s__Enterenecus sp910588495	83.5543	457	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577525.1	s__Enterenecus sp910577525	83.4738	477	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588135.1	s__Enterenecus sp910588135	83.2079	458	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579595.1	s__Enterenecus sp910579595	82.9934	450	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014799485.1	s__Enterenecus sp014799485	82.9458	265	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 12:01:50,620] [INFO] GTDB search result was written to GCA_948437705.1_SRR17794273_bin.34_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 12:01:50,621] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:01:50,625] [INFO] DFAST_QC result json was written to GCA_948437705.1_SRR17794273_bin.34_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-28 12:01:50,625] [INFO] DFAST_QC completed!
[2023-06-28 12:01:50,625] [INFO] Total running time: 0h1m5s