[2023-06-29 17:08:29,913] [INFO] DFAST_QC pipeline started.
[2023-06-29 17:08:29,915] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 17:08:29,916] [INFO] DQC Reference Directory: /var/lib/cwl/stgc5666060-add9-4313-9326-89ae2ee4ac6e/dqc_reference
[2023-06-29 17:08:33,927] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 17:08:33,928] [INFO] Task started: Prodigal
[2023-06-29 17:08:33,928] [INFO] Running command: gunzip -c /var/lib/cwl/stg98105d35-5344-4317-8a9a-335e0a34e9b5/GCA_932199865.1_0316_E_concoct.009_genomic.fna.gz | prodigal -d GCA_932199865.1_0316_E_concoct.009_genomic.fna/cds.fna -a GCA_932199865.1_0316_E_concoct.009_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 17:08:53,885] [INFO] Task succeeded: Prodigal
[2023-06-29 17:08:53,886] [INFO] Task started: HMMsearch
[2023-06-29 17:08:53,886] [INFO] Running command: hmmsearch --tblout GCA_932199865.1_0316_E_concoct.009_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc5666060-add9-4313-9326-89ae2ee4ac6e/dqc_reference/reference_markers.hmm GCA_932199865.1_0316_E_concoct.009_genomic.fna/protein.faa > /dev/null
[2023-06-29 17:08:54,158] [INFO] Task succeeded: HMMsearch
[2023-06-29 17:08:54,160] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg98105d35-5344-4317-8a9a-335e0a34e9b5/GCA_932199865.1_0316_E_concoct.009_genomic.fna.gz]
[2023-06-29 17:08:54,196] [INFO] Query marker FASTA was written to GCA_932199865.1_0316_E_concoct.009_genomic.fna/markers.fasta
[2023-06-29 17:08:54,197] [INFO] Task started: Blastn
[2023-06-29 17:08:54,197] [INFO] Running command: blastn -query GCA_932199865.1_0316_E_concoct.009_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5666060-add9-4313-9326-89ae2ee4ac6e/dqc_reference/reference_markers.fasta -out GCA_932199865.1_0316_E_concoct.009_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 17:08:54,818] [INFO] Task succeeded: Blastn
[2023-06-29 17:08:54,822] [INFO] Selected 17 target genomes.
[2023-06-29 17:08:54,823] [INFO] Target genome list was writen to GCA_932199865.1_0316_E_concoct.009_genomic.fna/target_genomes.txt
[2023-06-29 17:08:54,835] [INFO] Task started: fastANI
[2023-06-29 17:08:54,835] [INFO] Running command: fastANI --query /var/lib/cwl/stg98105d35-5344-4317-8a9a-335e0a34e9b5/GCA_932199865.1_0316_E_concoct.009_genomic.fna.gz --refList GCA_932199865.1_0316_E_concoct.009_genomic.fna/target_genomes.txt --output GCA_932199865.1_0316_E_concoct.009_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 17:09:03,660] [INFO] Task succeeded: fastANI
[2023-06-29 17:09:03,661] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc5666060-add9-4313-9326-89ae2ee4ac6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 17:09:03,661] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc5666060-add9-4313-9326-89ae2ee4ac6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 17:09:03,667] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 17:09:03,667] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 17:09:03,667] [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	76.2671	53	1199	95	below_threshold
Muribaculum gordoncarteri	strain=TLL-A4	GCA_004803695.1	2530390	2530390	type	True	76.2271	73	1199	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 17:09:03,670] [INFO] DFAST Taxonomy check result was written to GCA_932199865.1_0316_E_concoct.009_genomic.fna/tc_result.tsv
[2023-06-29 17:09:03,670] [INFO] ===== Taxonomy check completed =====
[2023-06-29 17:09:03,671] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 17:09:03,671] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc5666060-add9-4313-9326-89ae2ee4ac6e/dqc_reference/checkm_data
[2023-06-29 17:09:03,672] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 17:09:03,710] [INFO] Task started: CheckM
[2023-06-29 17:09:03,710] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_932199865.1_0316_E_concoct.009_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_932199865.1_0316_E_concoct.009_genomic.fna/checkm_input GCA_932199865.1_0316_E_concoct.009_genomic.fna/checkm_result
[2023-06-29 17:10:02,578] [INFO] Task succeeded: CheckM
[2023-06-29 17:10:02,580] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 17:10:02,599] [INFO] ===== Completeness check finished =====
[2023-06-29 17:10:02,600] [INFO] ===== Start GTDB Search =====
[2023-06-29 17:10:02,600] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_932199865.1_0316_E_concoct.009_genomic.fna/markers.fasta)
[2023-06-29 17:10:02,601] [INFO] Task started: Blastn
[2023-06-29 17:10:02,601] [INFO] Running command: blastn -query GCA_932199865.1_0316_E_concoct.009_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5666060-add9-4313-9326-89ae2ee4ac6e/dqc_reference/reference_markers_gtdb.fasta -out GCA_932199865.1_0316_E_concoct.009_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 17:10:03,351] [INFO] Task succeeded: Blastn
[2023-06-29 17:10:03,356] [INFO] Selected 15 target genomes.
[2023-06-29 17:10:03,356] [INFO] Target genome list was writen to GCA_932199865.1_0316_E_concoct.009_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 17:10:03,364] [INFO] Task started: fastANI
[2023-06-29 17:10:03,364] [INFO] Running command: fastANI --query /var/lib/cwl/stg98105d35-5344-4317-8a9a-335e0a34e9b5/GCA_932199865.1_0316_E_concoct.009_genomic.fna.gz --refList GCA_932199865.1_0316_E_concoct.009_genomic.fna/target_genomes_gtdb.txt --output GCA_932199865.1_0316_E_concoct.009_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 17:10:11,436] [INFO] Task succeeded: fastANI
[2023-06-29 17:10:11,453] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 17:10:11,453] [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_003762615.1	s__CAG-485 sp002493045	99.2613	1124	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	99.48	99.22	0.95	0.91	14	conclusive
GCA_910583795.1	s__CAG-485 sp910583795	78.4695	255	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585275.1	s__CAG-485 sp910585275	78.2175	218	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014801605.1	s__CAG-485 sp014801605	78.1232	136	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009775365.1	s__CAG-485 sp009775365	78.0726	202	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	99.04	99.04	0.86	0.86	2	-
GCA_910588245.1	s__CAG-485 sp910588245	77.7837	219	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	98.72	98.72	0.89	0.89	2	-
GCA_014800895.1	s__CAG-485 sp014800895	77.5948	106	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009775375.1	s__CAG-485 sp009775375	77.5388	192	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	99.86	99.86	0.92	0.92	2	-
GCA_002493515.1	s__CAG-485 sp002493515	77.4311	103	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	97.64	97.64	0.78	0.78	2	-
GCA_014800245.1	s__CAG-485 sp014800245	77.3398	81	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577585.1	s__CAG-485 sp910577585	77.2974	116	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585285.1	s__CAG-485 sp910585285	77.1986	109	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014800515.1	s__CAG-485 sp014800515	77.1726	70	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905209725.1	s__CAG-485 sp900556595	76.9489	90	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	99.46	99.46	0.94	0.94	2	-
GCA_900761855.1	s__CAG-485 sp900761855	76.8256	72	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 17:10:11,457] [INFO] GTDB search result was written to GCA_932199865.1_0316_E_concoct.009_genomic.fna/result_gtdb.tsv
[2023-06-29 17:10:11,457] [INFO] ===== GTDB Search completed =====
[2023-06-29 17:10:11,460] [INFO] DFAST_QC result json was written to GCA_932199865.1_0316_E_concoct.009_genomic.fna/dqc_result.json
[2023-06-29 17:10:11,460] [INFO] DFAST_QC completed!
[2023-06-29 17:10:11,461] [INFO] Total running time: 0h1m42s