[2023-06-08 12:18:51,338] [INFO] DFAST_QC pipeline started.
[2023-06-08 12:18:51,342] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 12:18:51,342] [INFO] DQC Reference Directory: /var/lib/cwl/stg0aed99ce-54e7-4223-9c69-b2b0c9be5a31/dqc_reference
[2023-06-08 12:18:52,699] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 12:18:52,700] [INFO] Task started: Prodigal
[2023-06-08 12:18:52,700] [INFO] Running command: gunzip -c /var/lib/cwl/stg453fedf0-8fde-4de7-90b6-c2ca56797337/GCA_947385345.1_ERR6760080_bin.87_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947385345.1_ERR6760080_bin.87_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947385345.1_ERR6760080_bin.87_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 12:18:59,206] [INFO] Task succeeded: Prodigal
[2023-06-08 12:18:59,206] [INFO] Task started: HMMsearch
[2023-06-08 12:18:59,207] [INFO] Running command: hmmsearch --tblout GCA_947385345.1_ERR6760080_bin.87_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0aed99ce-54e7-4223-9c69-b2b0c9be5a31/dqc_reference/reference_markers.hmm GCA_947385345.1_ERR6760080_bin.87_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 12:18:59,449] [INFO] Task succeeded: HMMsearch
[2023-06-08 12:18:59,450] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg453fedf0-8fde-4de7-90b6-c2ca56797337/GCA_947385345.1_ERR6760080_bin.87_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-08 12:18:59,487] [INFO] Query marker FASTA was written to GCA_947385345.1_ERR6760080_bin.87_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 12:18:59,488] [INFO] Task started: Blastn
[2023-06-08 12:18:59,488] [INFO] Running command: blastn -query GCA_947385345.1_ERR6760080_bin.87_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg0aed99ce-54e7-4223-9c69-b2b0c9be5a31/dqc_reference/reference_markers.fasta -out GCA_947385345.1_ERR6760080_bin.87_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:19:00,210] [INFO] Task succeeded: Blastn
[2023-06-08 12:19:00,215] [INFO] Selected 12 target genomes.
[2023-06-08 12:19:00,215] [INFO] Target genome list was writen to GCA_947385345.1_ERR6760080_bin.87_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 12:19:00,217] [INFO] Task started: fastANI
[2023-06-08 12:19:00,217] [INFO] Running command: fastANI --query /var/lib/cwl/stg453fedf0-8fde-4de7-90b6-c2ca56797337/GCA_947385345.1_ERR6760080_bin.87_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947385345.1_ERR6760080_bin.87_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947385345.1_ERR6760080_bin.87_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 12:19:07,788] [INFO] Task succeeded: fastANI
[2023-06-08 12:19:07,789] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0aed99ce-54e7-4223-9c69-b2b0c9be5a31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 12:19:07,789] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0aed99ce-54e7-4223-9c69-b2b0c9be5a31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 12:19:07,799] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 12:19:07,799] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 12:19:07,800] [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
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	80.3339	372	777	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	78.8872	231	777	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	78.5947	222	777	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	77.8875	177	777	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	77.8383	139	777	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	77.6833	198	777	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	77.6791	185	777	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	77.578	191	777	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	77.576	131	777	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	77.0255	121	777	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	76.6859	84	777	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 12:19:07,802] [INFO] DFAST Taxonomy check result was written to GCA_947385345.1_ERR6760080_bin.87_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 12:19:07,802] [INFO] ===== Taxonomy check completed =====
[2023-06-08 12:19:07,802] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 12:19:07,803] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0aed99ce-54e7-4223-9c69-b2b0c9be5a31/dqc_reference/checkm_data
[2023-06-08 12:19:07,804] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 12:19:07,832] [INFO] Task started: CheckM
[2023-06-08 12:19:07,832] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947385345.1_ERR6760080_bin.87_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947385345.1_ERR6760080_bin.87_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947385345.1_ERR6760080_bin.87_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 12:19:31,207] [INFO] Task succeeded: CheckM
[2023-06-08 12:19:31,208] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.07%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-08 12:19:31,226] [INFO] ===== Completeness check finished =====
[2023-06-08 12:19:31,227] [INFO] ===== Start GTDB Search =====
[2023-06-08 12:19:31,227] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947385345.1_ERR6760080_bin.87_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 12:19:31,227] [INFO] Task started: Blastn
[2023-06-08 12:19:31,227] [INFO] Running command: blastn -query GCA_947385345.1_ERR6760080_bin.87_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg0aed99ce-54e7-4223-9c69-b2b0c9be5a31/dqc_reference/reference_markers_gtdb.fasta -out GCA_947385345.1_ERR6760080_bin.87_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:19:32,385] [INFO] Task succeeded: Blastn
[2023-06-08 12:19:32,389] [INFO] Selected 13 target genomes.
[2023-06-08 12:19:32,389] [INFO] Target genome list was writen to GCA_947385345.1_ERR6760080_bin.87_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 12:19:32,390] [INFO] Task started: fastANI
[2023-06-08 12:19:32,391] [INFO] Running command: fastANI --query /var/lib/cwl/stg453fedf0-8fde-4de7-90b6-c2ca56797337/GCA_947385345.1_ERR6760080_bin.87_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947385345.1_ERR6760080_bin.87_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947385345.1_ERR6760080_bin.87_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 12:19:40,944] [INFO] Task succeeded: fastANI
[2023-06-08 12:19:40,955] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 12:19:40,955] [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_910574635.1	s__Dysosmobacter sp009774015	97.3067	672	777	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	96.89	96.54	0.80	0.71	5	conclusive
GCA_009773995.1	s__Dysosmobacter sp009773995	90.912	504	777	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	99.84	99.84	0.82	0.82	2	-
GCA_910587705.1	s__Dysosmobacter sp910587705	90.2416	594	777	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910583785.1	s__Dysosmobacter sp910583785	90.1323	588	777	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579435.1	s__Dysosmobacter sp910579435	89.8379	543	777	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587875.1	s__Dysosmobacter sp910587875	89.2623	531	777	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910583695.1	s__Dysosmobacter sp910583695	89.023	550	777	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910576865.1	s__Dysosmobacter sp910576865	88.8352	522	777	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588175.1	s__Dysosmobacter sp910588175	88.6231	493	777	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587525.1	s__Dysosmobacter sp910587525	80.8252	345	777	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548505.1	s__Dysosmobacter sp900548505	79.7481	264	777	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577405.1	s__Dysosmobacter sp910577405	78.6347	273	777	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904419835.1	s__Pseudoflavonifractor sp904419835	78.2113	157	777	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Pseudoflavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 12:19:40,957] [INFO] GTDB search result was written to GCA_947385345.1_ERR6760080_bin.87_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 12:19:40,958] [INFO] ===== GTDB Search completed =====
[2023-06-08 12:19:40,961] [INFO] DFAST_QC result json was written to GCA_947385345.1_ERR6760080_bin.87_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 12:19:40,961] [INFO] DFAST_QC completed!
[2023-06-08 12:19:40,962] [INFO] Total running time: 0h0m50s