[2023-06-14 01:25:48,176] [INFO] DFAST_QC pipeline started.
[2023-06-14 01:25:48,196] [INFO] DFAST_QC version: 0.5.7
[2023-06-14 01:25:48,196] [INFO] DQC Reference Directory: /var/lib/cwl/stg36d0d8c3-c8eb-4399-9491-7a50e8152373/dqc_reference
[2023-06-14 01:25:50,362] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-14 01:25:50,362] [INFO] Task started: Prodigal
[2023-06-14 01:25:50,363] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf7b64ba-8088-437a-84bd-f24e2246c335/GCA_947036705.1_ERR8099106_bin.15_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947036705.1_ERR8099106_bin.15_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947036705.1_ERR8099106_bin.15_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-14 01:26:04,025] [INFO] Task succeeded: Prodigal
[2023-06-14 01:26:04,026] [INFO] Task started: HMMsearch
[2023-06-14 01:26:04,026] [INFO] Running command: hmmsearch --tblout GCA_947036705.1_ERR8099106_bin.15_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36d0d8c3-c8eb-4399-9491-7a50e8152373/dqc_reference/reference_markers.hmm GCA_947036705.1_ERR8099106_bin.15_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-14 01:26:04,214] [INFO] Task succeeded: HMMsearch
[2023-06-14 01:26:04,215] [INFO] Found 6/6 markers.
[2023-06-14 01:26:04,239] [INFO] Query marker FASTA was written to GCA_947036705.1_ERR8099106_bin.15_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-14 01:26:04,239] [INFO] Task started: Blastn
[2023-06-14 01:26:04,239] [INFO] Running command: blastn -query GCA_947036705.1_ERR8099106_bin.15_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg36d0d8c3-c8eb-4399-9491-7a50e8152373/dqc_reference/reference_markers.fasta -out GCA_947036705.1_ERR8099106_bin.15_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:26:04,806] [INFO] Task succeeded: Blastn
[2023-06-14 01:26:04,810] [INFO] Selected 15 target genomes.
[2023-06-14 01:26:04,810] [INFO] Target genome list was writen to GCA_947036705.1_ERR8099106_bin.15_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-14 01:26:04,811] [INFO] Task started: fastANI
[2023-06-14 01:26:04,811] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf7b64ba-8088-437a-84bd-f24e2246c335/GCA_947036705.1_ERR8099106_bin.15_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947036705.1_ERR8099106_bin.15_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947036705.1_ERR8099106_bin.15_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-14 01:26:14,556] [INFO] Task succeeded: fastANI
[2023-06-14 01:26:14,557] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36d0d8c3-c8eb-4399-9491-7a50e8152373/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-14 01:26:14,557] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36d0d8c3-c8eb-4399-9491-7a50e8152373/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-14 01:26:14,564] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2023-06-14 01:26:14,564] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-14 01:26:14,564] [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
Duncaniella dubosii	strain=H5	GCA_004803915.1	2518971	2518971	type	True	99.1523	855	895	95	conclusive
Duncaniella muris	strain=DSM 103720	GCA_003024805.1	2094150	2094150	type	True	79.5255	315	895	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_016696845.1	1796646	1796646	type	True	78.5639	106	895	95	below_threshold
Duncaniella freteri	strain=TLL-A3	GCA_004766125.1	2530391	2530391	type	True	77.8396	149	895	95	below_threshold
Paramuribaculum intestinale	strain=DSM 100749	GCA_003024925.1	2094151	2094151	type	True	77.7741	87	895	95	below_threshold
Muribaculum gordoncarteri	strain=TLL-A4	GCA_004803695.1	2530390	2530390	type	True	77.5709	99	895	95	below_threshold
Heminiphilus faecis	strain=AM35	GCA_008728965.1	2601703	2601703	type	True	76.7911	82	895	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-14 01:26:14,566] [INFO] DFAST Taxonomy check result was written to GCA_947036705.1_ERR8099106_bin.15_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-14 01:26:14,567] [INFO] ===== Taxonomy check completed =====
[2023-06-14 01:26:14,567] [INFO] ===== Start completeness check using CheckM =====
[2023-06-14 01:26:14,567] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36d0d8c3-c8eb-4399-9491-7a50e8152373/dqc_reference/checkm_data
[2023-06-14 01:26:14,568] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-14 01:26:14,595] [INFO] Task started: CheckM
[2023-06-14 01:26:14,595] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947036705.1_ERR8099106_bin.15_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947036705.1_ERR8099106_bin.15_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947036705.1_ERR8099106_bin.15_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-14 01:26:57,238] [INFO] Task succeeded: CheckM
[2023-06-14 01:26:57,240] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-14 01:26:57,254] [INFO] ===== Completeness check finished =====
[2023-06-14 01:26:57,254] [INFO] ===== Start GTDB Search =====
[2023-06-14 01:26:57,254] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947036705.1_ERR8099106_bin.15_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-14 01:26:57,254] [INFO] Task started: Blastn
[2023-06-14 01:26:57,254] [INFO] Running command: blastn -query GCA_947036705.1_ERR8099106_bin.15_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg36d0d8c3-c8eb-4399-9491-7a50e8152373/dqc_reference/reference_markers_gtdb.fasta -out GCA_947036705.1_ERR8099106_bin.15_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:26:58,092] [INFO] Task succeeded: Blastn
[2023-06-14 01:26:58,095] [INFO] Selected 8 target genomes.
[2023-06-14 01:26:58,095] [INFO] Target genome list was writen to GCA_947036705.1_ERR8099106_bin.15_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-14 01:26:58,096] [INFO] Task started: fastANI
[2023-06-14 01:26:58,096] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf7b64ba-8088-437a-84bd-f24e2246c335/GCA_947036705.1_ERR8099106_bin.15_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947036705.1_ERR8099106_bin.15_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947036705.1_ERR8099106_bin.15_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-14 01:27:02,892] [INFO] Task succeeded: fastANI
[2023-06-14 01:27:02,902] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-14 01:27:02,902] [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_004803915.1	s__Duncaniella dubosii	99.1264	856	895	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	98.46	96.11	0.91	0.80	8	conclusive
GCA_910578445.1	s__Duncaniella sp910578445	87.4029	779	895	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577345.1	s__Duncaniella sp910577345	80.2292	471	895	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014802345.1	s__Duncaniella sp014802345	80.0416	364	895	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	98.04	97.99	0.90	0.88	3	-
GCA_014801945.1	s__Duncaniella sp014801945	79.5816	326	895	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	97.85	97.85	0.77	0.77	2	-
GCF_003024805.1	s__Duncaniella muris	79.5413	314	895	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	98.34	97.90	0.87	0.80	17	-
GCA_910586665.1	s__Duncaniella sp910586665	79.3682	366	895	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544535.1	s__Duncaniella sp900544535	79.1507	286	895	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-14 01:27:02,905] [INFO] GTDB search result was written to GCA_947036705.1_ERR8099106_bin.15_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-14 01:27:02,905] [INFO] ===== GTDB Search completed =====
[2023-06-14 01:27:02,908] [INFO] DFAST_QC result json was written to GCA_947036705.1_ERR8099106_bin.15_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-14 01:27:02,908] [INFO] DFAST_QC completed!
[2023-06-14 01:27:02,908] [INFO] Total running time: 0h1m15s