[2023-06-13 09:11:58,494] [INFO] DFAST_QC pipeline started.
[2023-06-13 09:11:58,500] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 09:11:58,500] [INFO] DQC Reference Directory: /var/lib/cwl/stgfdf3e1b3-b762-4e60-a172-1a3feaf2f309/dqc_reference
[2023-06-13 09:11:59,844] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 09:11:59,844] [INFO] Task started: Prodigal
[2023-06-13 09:11:59,845] [INFO] Running command: gunzip -c /var/lib/cwl/stge9312beb-a56d-4502-836e-9a7bcfc6a25a/GCA_938048305.1_ERR321580_bin.101_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938048305.1_ERR321580_bin.101_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938048305.1_ERR321580_bin.101_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 09:12:16,327] [INFO] Task succeeded: Prodigal
[2023-06-13 09:12:16,328] [INFO] Task started: HMMsearch
[2023-06-13 09:12:16,328] [INFO] Running command: hmmsearch --tblout GCA_938048305.1_ERR321580_bin.101_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfdf3e1b3-b762-4e60-a172-1a3feaf2f309/dqc_reference/reference_markers.hmm GCA_938048305.1_ERR321580_bin.101_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 09:12:16,713] [INFO] Task succeeded: HMMsearch
[2023-06-13 09:12:16,714] [INFO] Found 6/6 markers.
[2023-06-13 09:12:16,778] [INFO] Query marker FASTA was written to GCA_938048305.1_ERR321580_bin.101_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 09:12:16,778] [INFO] Task started: Blastn
[2023-06-13 09:12:16,778] [INFO] Running command: blastn -query GCA_938048305.1_ERR321580_bin.101_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgfdf3e1b3-b762-4e60-a172-1a3feaf2f309/dqc_reference/reference_markers.fasta -out GCA_938048305.1_ERR321580_bin.101_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 09:12:17,760] [INFO] Task succeeded: Blastn
[2023-06-13 09:12:17,764] [INFO] Selected 24 target genomes.
[2023-06-13 09:12:17,765] [INFO] Target genome list was writen to GCA_938048305.1_ERR321580_bin.101_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 09:12:17,774] [INFO] Task started: fastANI
[2023-06-13 09:12:17,775] [INFO] Running command: fastANI --query /var/lib/cwl/stge9312beb-a56d-4502-836e-9a7bcfc6a25a/GCA_938048305.1_ERR321580_bin.101_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938048305.1_ERR321580_bin.101_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938048305.1_ERR321580_bin.101_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 09:12:32,088] [INFO] Task succeeded: fastANI
[2023-06-13 09:12:32,089] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfdf3e1b3-b762-4e60-a172-1a3feaf2f309/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 09:12:32,089] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfdf3e1b3-b762-4e60-a172-1a3feaf2f309/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 09:12:32,099] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 09:12:32,099] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 09:12:32,099] [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
Muribaculum gordoncarteri	strain=TLL-A4	GCA_004803695.1	2530390	2530390	type	True	78.7313	153	926	95	below_threshold
Duncaniella muris	strain=DSM 103720	GCA_003024805.1	2094150	2094150	type	True	78.0035	147	926	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_001688845.2	1796646	1796646	type	True	77.5878	131	926	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_002201515.1	1796646	1796646	type	True	77.5382	133	926	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_016696845.1	1796646	1796646	type	True	77.5229	134	926	95	below_threshold
Duncaniella freteri	strain=TLL-A3	GCA_004766125.1	2530391	2530391	type	True	77.4121	99	926	95	below_threshold
Duncaniella dubosii	strain=H5	GCA_004803915.1	2518971	2518971	type	True	77.3511	98	926	95	below_threshold
Paramuribaculum intestinale	strain=DSM 100749	GCA_003024925.1	2094151	2094151	type	True	77.3446	120	926	95	below_threshold
Heminiphilus faecis	strain=AM35	GCA_008728965.1	2601703	2601703	type	True	77.1554	94	926	95	below_threshold
Barnesiella viscericola	strain=C46, DSM 18177	GCA_000512915.1	397865	397865	type	True	76.5235	78	926	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 09:12:32,104] [INFO] DFAST Taxonomy check result was written to GCA_938048305.1_ERR321580_bin.101_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 09:12:32,105] [INFO] ===== Taxonomy check completed =====
[2023-06-13 09:12:32,105] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 09:12:32,106] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfdf3e1b3-b762-4e60-a172-1a3feaf2f309/dqc_reference/checkm_data
[2023-06-13 09:12:32,108] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 09:12:32,147] [INFO] Task started: CheckM
[2023-06-13 09:12:32,147] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938048305.1_ERR321580_bin.101_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938048305.1_ERR321580_bin.101_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938048305.1_ERR321580_bin.101_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 09:13:20,030] [INFO] Task succeeded: CheckM
[2023-06-13 09:13:20,032] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 09:13:20,057] [INFO] ===== Completeness check finished =====
[2023-06-13 09:13:20,057] [INFO] ===== Start GTDB Search =====
[2023-06-13 09:13:20,057] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938048305.1_ERR321580_bin.101_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 09:13:20,058] [INFO] Task started: Blastn
[2023-06-13 09:13:20,058] [INFO] Running command: blastn -query GCA_938048305.1_ERR321580_bin.101_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgfdf3e1b3-b762-4e60-a172-1a3feaf2f309/dqc_reference/reference_markers_gtdb.fasta -out GCA_938048305.1_ERR321580_bin.101_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 09:13:20,956] [INFO] Task succeeded: Blastn
[2023-06-13 09:13:20,961] [INFO] Selected 12 target genomes.
[2023-06-13 09:13:20,961] [INFO] Target genome list was writen to GCA_938048305.1_ERR321580_bin.101_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 09:13:20,966] [INFO] Task started: fastANI
[2023-06-13 09:13:20,967] [INFO] Running command: fastANI --query /var/lib/cwl/stge9312beb-a56d-4502-836e-9a7bcfc6a25a/GCA_938048305.1_ERR321580_bin.101_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938048305.1_ERR321580_bin.101_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938048305.1_ERR321580_bin.101_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 09:13:27,586] [INFO] Task succeeded: fastANI
[2023-06-13 09:13:27,601] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 09:13:27,601] [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_905210435.1	s__UBA7173 sp905210435	100.0	852	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001915385.1	s__UBA7173 sp001915385	93.2114	616	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	96.67	96.43	0.78	0.73	4	-
GCA_004102805.1	s__UBA7173 sp004102805	81.6463	565	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	98.86	98.86	0.92	0.89	3	-
GCA_014801075.1	s__UBA7173 sp014801075	81.1073	464	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	97.74	97.55	0.90	0.88	4	-
GCA_017536215.1	s__UBA7173 sp017536215	78.3981	121	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545955.1	s__UBA7173 sp900545955	77.8162	130	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	97.61	97.55	0.88	0.85	4	-
GCA_910586665.1	s__Duncaniella sp910586665	77.6008	119	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910576785.1	s__Duncaniella sp910576785	77.1936	125	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584825.1	s__Duncaniella sp910584825	77.1124	148	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579105.1	s__UBA7173 sp910579105	77.1072	100	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550395.1	s__CAG-873 sp900550395	77.0121	99	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	97.34	95.74	0.88	0.82	4	-
GCA_016302215.1	s__CAG-873 sp016302215	76.6061	73	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 09:13:27,604] [INFO] GTDB search result was written to GCA_938048305.1_ERR321580_bin.101_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 09:13:27,604] [INFO] ===== GTDB Search completed =====
[2023-06-13 09:13:27,607] [INFO] DFAST_QC result json was written to GCA_938048305.1_ERR321580_bin.101_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 09:13:27,608] [INFO] DFAST_QC completed!
[2023-06-13 09:13:27,608] [INFO] Total running time: 0h1m29s