[2023-06-13 21:59:06,315] [INFO] DFAST_QC pipeline started.
[2023-06-13 21:59:06,318] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 21:59:06,318] [INFO] DQC Reference Directory: /var/lib/cwl/stgf804ed21-6ed7-4af5-b523-2e45351f4c76/dqc_reference
[2023-06-13 21:59:07,634] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 21:59:07,635] [INFO] Task started: Prodigal
[2023-06-13 21:59:07,635] [INFO] Running command: gunzip -c /var/lib/cwl/stga676f8e9-39f8-424d-8ff1-73709d4d1732/GCA_947073765.1_SRR12464007_bin.3_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947073765.1_SRR12464007_bin.3_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947073765.1_SRR12464007_bin.3_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 21:59:14,127] [INFO] Task succeeded: Prodigal
[2023-06-13 21:59:14,128] [INFO] Task started: HMMsearch
[2023-06-13 21:59:14,128] [INFO] Running command: hmmsearch --tblout GCA_947073765.1_SRR12464007_bin.3_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf804ed21-6ed7-4af5-b523-2e45351f4c76/dqc_reference/reference_markers.hmm GCA_947073765.1_SRR12464007_bin.3_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 21:59:14,374] [INFO] Task succeeded: HMMsearch
[2023-06-13 21:59:14,376] [INFO] Found 6/6 markers.
[2023-06-13 21:59:14,402] [INFO] Query marker FASTA was written to GCA_947073765.1_SRR12464007_bin.3_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-13 21:59:14,403] [INFO] Task started: Blastn
[2023-06-13 21:59:14,403] [INFO] Running command: blastn -query GCA_947073765.1_SRR12464007_bin.3_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf804ed21-6ed7-4af5-b523-2e45351f4c76/dqc_reference/reference_markers.fasta -out GCA_947073765.1_SRR12464007_bin.3_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 21:59:15,064] [INFO] Task succeeded: Blastn
[2023-06-13 21:59:15,068] [INFO] Selected 14 target genomes.
[2023-06-13 21:59:15,069] [INFO] Target genome list was writen to GCA_947073765.1_SRR12464007_bin.3_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-13 21:59:15,070] [INFO] Task started: fastANI
[2023-06-13 21:59:15,070] [INFO] Running command: fastANI --query /var/lib/cwl/stga676f8e9-39f8-424d-8ff1-73709d4d1732/GCA_947073765.1_SRR12464007_bin.3_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947073765.1_SRR12464007_bin.3_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947073765.1_SRR12464007_bin.3_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 21:59:21,304] [INFO] Task succeeded: fastANI
[2023-06-13 21:59:21,305] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf804ed21-6ed7-4af5-b523-2e45351f4c76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 21:59:21,306] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf804ed21-6ed7-4af5-b523-2e45351f4c76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 21:59:21,322] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 21:59:21,323] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 21:59:21,323] [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	79.2956	280	742	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	78.3304	192	742	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	78.3099	181	742	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.7847	119	742	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_008121455.1	2211183	2211183	type	True	77.7664	82	742	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.7604	157	742	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_003425665.1	2211183	2211183	type	True	77.7263	83	742	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	77.7116	132	742	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.4658	98	742	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	77.2956	80	742	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	77.16	86	742	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 21:59:21,325] [INFO] DFAST Taxonomy check result was written to GCA_947073765.1_SRR12464007_bin.3_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-13 21:59:21,326] [INFO] ===== Taxonomy check completed =====
[2023-06-13 21:59:21,326] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 21:59:21,326] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf804ed21-6ed7-4af5-b523-2e45351f4c76/dqc_reference/checkm_data
[2023-06-13 21:59:21,327] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 21:59:21,353] [INFO] Task started: CheckM
[2023-06-13 21:59:21,354] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947073765.1_SRR12464007_bin.3_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947073765.1_SRR12464007_bin.3_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947073765.1_SRR12464007_bin.3_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-13 21:59:45,970] [INFO] Task succeeded: CheckM
[2023-06-13 21:59:45,972] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.44%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 21:59:46,000] [INFO] ===== Completeness check finished =====
[2023-06-13 21:59:46,001] [INFO] ===== Start GTDB Search =====
[2023-06-13 21:59:46,001] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947073765.1_SRR12464007_bin.3_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-13 21:59:46,002] [INFO] Task started: Blastn
[2023-06-13 21:59:46,002] [INFO] Running command: blastn -query GCA_947073765.1_SRR12464007_bin.3_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf804ed21-6ed7-4af5-b523-2e45351f4c76/dqc_reference/reference_markers_gtdb.fasta -out GCA_947073765.1_SRR12464007_bin.3_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 21:59:47,190] [INFO] Task succeeded: Blastn
[2023-06-13 21:59:47,195] [INFO] Selected 11 target genomes.
[2023-06-13 21:59:47,195] [INFO] Target genome list was writen to GCA_947073765.1_SRR12464007_bin.3_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 21:59:47,196] [INFO] Task started: fastANI
[2023-06-13 21:59:47,196] [INFO] Running command: fastANI --query /var/lib/cwl/stga676f8e9-39f8-424d-8ff1-73709d4d1732/GCA_947073765.1_SRR12464007_bin.3_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947073765.1_SRR12464007_bin.3_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947073765.1_SRR12464007_bin.3_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 21:59:54,239] [INFO] Task succeeded: fastANI
[2023-06-13 21:59:54,249] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 21:59:54,249] [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_910585815.1	s__Lawsonibacter sp910585815	83.7562	499	742	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	82.9183	423	742	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	82.8426	447	742	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_910589085.1	s__Lawsonibacter sp910589085	82.8384	431	742	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	82.7243	442	742	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_910575265.1	s__Lawsonibacter sp910575265	82.5735	468	742	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	82.4663	472	742	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	82.3161	463	742	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_009917615.1	s__Lawsonibacter sp009917615	82.1862	490	742	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_009911645.1	s__Lawsonibacter sp009911645	81.8404	435	742	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	81.657	445	742	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 21:59:54,251] [INFO] GTDB search result was written to GCA_947073765.1_SRR12464007_bin.3_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 21:59:54,252] [INFO] ===== GTDB Search completed =====
[2023-06-13 21:59:54,255] [INFO] DFAST_QC result json was written to GCA_947073765.1_SRR12464007_bin.3_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-13 21:59:54,256] [INFO] DFAST_QC completed!
[2023-06-13 21:59:54,256] [INFO] Total running time: 0h0m48s