[2023-06-08 00:55:02,067] [INFO] DFAST_QC pipeline started.
[2023-06-08 00:55:02,071] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 00:55:02,072] [INFO] DQC Reference Directory: /var/lib/cwl/stg69703f92-8ebc-4aaa-a933-d2bbc6ab1740/dqc_reference
[2023-06-08 00:55:03,424] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 00:55:03,425] [INFO] Task started: Prodigal
[2023-06-08 00:55:03,425] [INFO] Running command: gunzip -c /var/lib/cwl/stg28620c51-cd42-47f6-a4bc-9a0a3229b54d/GCA_947573305.1_SRR15730544_bin.47_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947573305.1_SRR15730544_bin.47_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947573305.1_SRR15730544_bin.47_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 00:55:15,928] [INFO] Task succeeded: Prodigal
[2023-06-08 00:55:15,929] [INFO] Task started: HMMsearch
[2023-06-08 00:55:15,929] [INFO] Running command: hmmsearch --tblout GCA_947573305.1_SRR15730544_bin.47_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69703f92-8ebc-4aaa-a933-d2bbc6ab1740/dqc_reference/reference_markers.hmm GCA_947573305.1_SRR15730544_bin.47_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 00:55:16,181] [INFO] Task succeeded: HMMsearch
[2023-06-08 00:55:16,182] [INFO] Found 6/6 markers.
[2023-06-08 00:55:16,211] [INFO] Query marker FASTA was written to GCA_947573305.1_SRR15730544_bin.47_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 00:55:16,211] [INFO] Task started: Blastn
[2023-06-08 00:55:16,212] [INFO] Running command: blastn -query GCA_947573305.1_SRR15730544_bin.47_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg69703f92-8ebc-4aaa-a933-d2bbc6ab1740/dqc_reference/reference_markers.fasta -out GCA_947573305.1_SRR15730544_bin.47_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:55:16,830] [INFO] Task succeeded: Blastn
[2023-06-08 00:55:16,834] [INFO] Selected 17 target genomes.
[2023-06-08 00:55:16,834] [INFO] Target genome list was writen to GCA_947573305.1_SRR15730544_bin.47_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 00:55:16,837] [INFO] Task started: fastANI
[2023-06-08 00:55:16,837] [INFO] Running command: fastANI --query /var/lib/cwl/stg28620c51-cd42-47f6-a4bc-9a0a3229b54d/GCA_947573305.1_SRR15730544_bin.47_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947573305.1_SRR15730544_bin.47_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947573305.1_SRR15730544_bin.47_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 00:55:24,965] [INFO] Task succeeded: fastANI
[2023-06-08 00:55:24,966] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69703f92-8ebc-4aaa-a933-d2bbc6ab1740/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 00:55:24,966] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69703f92-8ebc-4aaa-a933-d2bbc6ab1740/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 00:55:24,982] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2023-06-08 00:55:24,982] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-08 00:55:24,982] [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 muris	strain=DSM 103720	GCA_003024805.1	2094150	2094150	type	True	98.7561	739	770	95	conclusive
Duncaniella dubosii	strain=H5	GCA_004803915.1	2518971	2518971	type	True	78.5797	289	770	95	below_threshold
Duncaniella freteri	strain=TLL-A3	GCA_004766125.1	2530391	2530391	type	True	77.1423	127	770	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_016696845.1	1796646	1796646	type	True	76.7867	90	770	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_001688845.2	1796646	1796646	type	True	76.7348	92	770	95	below_threshold
Muribaculum gordoncarteri	strain=TLL-A4	GCA_004803695.1	2530390	2530390	type	True	76.5477	93	770	95	below_threshold
Paramuribaculum intestinale	strain=DSM 100749	GCA_003024925.1	2094151	2094151	type	True	76.5292	89	770	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 00:55:24,984] [INFO] DFAST Taxonomy check result was written to GCA_947573305.1_SRR15730544_bin.47_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 00:55:24,985] [INFO] ===== Taxonomy check completed =====
[2023-06-08 00:55:24,985] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 00:55:24,986] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69703f92-8ebc-4aaa-a933-d2bbc6ab1740/dqc_reference/checkm_data
[2023-06-08 00:55:24,987] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 00:55:25,023] [INFO] Task started: CheckM
[2023-06-08 00:55:25,024] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947573305.1_SRR15730544_bin.47_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947573305.1_SRR15730544_bin.47_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947573305.1_SRR15730544_bin.47_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 00:56:05,255] [INFO] Task succeeded: CheckM
[2023-06-08 00:56:05,257] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.76%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 00:56:05,278] [INFO] ===== Completeness check finished =====
[2023-06-08 00:56:05,278] [INFO] ===== Start GTDB Search =====
[2023-06-08 00:56:05,279] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947573305.1_SRR15730544_bin.47_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 00:56:05,279] [INFO] Task started: Blastn
[2023-06-08 00:56:05,279] [INFO] Running command: blastn -query GCA_947573305.1_SRR15730544_bin.47_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg69703f92-8ebc-4aaa-a933-d2bbc6ab1740/dqc_reference/reference_markers_gtdb.fasta -out GCA_947573305.1_SRR15730544_bin.47_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:56:06,160] [INFO] Task succeeded: Blastn
[2023-06-08 00:56:06,165] [INFO] Selected 11 target genomes.
[2023-06-08 00:56:06,165] [INFO] Target genome list was writen to GCA_947573305.1_SRR15730544_bin.47_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 00:56:06,168] [INFO] Task started: fastANI
[2023-06-08 00:56:06,168] [INFO] Running command: fastANI --query /var/lib/cwl/stg28620c51-cd42-47f6-a4bc-9a0a3229b54d/GCA_947573305.1_SRR15730544_bin.47_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947573305.1_SRR15730544_bin.47_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947573305.1_SRR15730544_bin.47_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 00:56:12,885] [INFO] Task succeeded: fastANI
[2023-06-08 00:56:12,905] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 00:56:12,906] [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_003024805.1	s__Duncaniella muris	98.7561	739	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	98.34	97.90	0.87	0.80	17	conclusive
GCA_900544535.1	s__Duncaniella sp900544535	82.1029	548	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_910586665.1	s__Duncaniella sp910586665	79.1919	323	770	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	79.0912	364	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578445.1	s__Duncaniella sp910578445	78.6863	303	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004803915.1	s__Duncaniella dubosii	78.5929	288	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	98.46	96.11	0.91	0.80	8	-
GCA_014801945.1	s__Duncaniella sp014801945	78.4046	214	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	97.85	97.85	0.77	0.77	2	-
GCA_910584825.1	s__Duncaniella sp910584825	78.1978	228	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577255.1	s__Duncaniella sp910577255	78.1763	233	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587185.1	s__Paramuribaculum sp910587185	76.8616	75	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	96.59	96.53	0.88	0.86	5	-
GCA_014802435.1	s__UBA3263 sp014802435	76.33	53	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA3263	95.0	97.99	97.67	0.88	0.83	9	-
--------------------------------------------------------------------------------
[2023-06-08 00:56:12,908] [INFO] GTDB search result was written to GCA_947573305.1_SRR15730544_bin.47_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 00:56:12,909] [INFO] ===== GTDB Search completed =====
[2023-06-08 00:56:12,912] [INFO] DFAST_QC result json was written to GCA_947573305.1_SRR15730544_bin.47_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 00:56:12,912] [INFO] DFAST_QC completed!
[2023-06-08 00:56:12,912] [INFO] Total running time: 0h1m11s