[2023-06-08 03:14:38,866] [INFO] DFAST_QC pipeline started.
[2023-06-08 03:14:38,883] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 03:14:38,883] [INFO] DQC Reference Directory: /var/lib/cwl/stg5414ac89-ea35-4d52-bc93-1a3111a470bb/dqc_reference
[2023-06-08 03:14:40,195] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 03:14:40,196] [INFO] Task started: Prodigal
[2023-06-08 03:14:40,196] [INFO] Running command: gunzip -c /var/lib/cwl/stgfee8b946-5a4f-41ef-a6a2-756bc751b0d4/GCA_945495355.1_SRR7188235_bin.27_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945495355.1_SRR7188235_bin.27_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945495355.1_SRR7188235_bin.27_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 03:14:43,590] [INFO] Task succeeded: Prodigal
[2023-06-08 03:14:43,591] [INFO] Task started: HMMsearch
[2023-06-08 03:14:43,591] [INFO] Running command: hmmsearch --tblout GCA_945495355.1_SRR7188235_bin.27_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5414ac89-ea35-4d52-bc93-1a3111a470bb/dqc_reference/reference_markers.hmm GCA_945495355.1_SRR7188235_bin.27_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 03:14:43,864] [INFO] Task succeeded: HMMsearch
[2023-06-08 03:14:43,865] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfee8b946-5a4f-41ef-a6a2-756bc751b0d4/GCA_945495355.1_SRR7188235_bin.27_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 03:14:43,900] [INFO] Query marker FASTA was written to GCA_945495355.1_SRR7188235_bin.27_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 03:14:43,901] [INFO] Task started: Blastn
[2023-06-08 03:14:43,901] [INFO] Running command: blastn -query GCA_945495355.1_SRR7188235_bin.27_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg5414ac89-ea35-4d52-bc93-1a3111a470bb/dqc_reference/reference_markers.fasta -out GCA_945495355.1_SRR7188235_bin.27_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:14:44,523] [INFO] Task succeeded: Blastn
[2023-06-08 03:14:44,527] [INFO] Selected 15 target genomes.
[2023-06-08 03:14:44,527] [INFO] Target genome list was writen to GCA_945495355.1_SRR7188235_bin.27_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 03:14:44,528] [INFO] Task started: fastANI
[2023-06-08 03:14:44,528] [INFO] Running command: fastANI --query /var/lib/cwl/stgfee8b946-5a4f-41ef-a6a2-756bc751b0d4/GCA_945495355.1_SRR7188235_bin.27_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945495355.1_SRR7188235_bin.27_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945495355.1_SRR7188235_bin.27_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 03:14:50,845] [INFO] Task succeeded: fastANI
[2023-06-08 03:14:50,846] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5414ac89-ea35-4d52-bc93-1a3111a470bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 03:14:50,846] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5414ac89-ea35-4d52-bc93-1a3111a470bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 03:14:50,860] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2023-06-08 03:14:50,861] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-08 03:14:50,861] [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
Catenibacterium mitsuokai	strain=DSM 15897	GCA_025148785.1	100886	100886	suspected-type	True	96.6657	466	577	95	conclusive
Kandleria vitulina	strain=DSM 20405	GCA_001436965.1	1630	1630	type	True	77.9994	100	577	95	below_threshold
Kandleria vitulina	strain=DSM 20405	GCA_000702065.1	1630	1630	type	True	77.9935	101	577	95	below_threshold
Sharpea azabuensis	strain=DSM 18934	GCA_000702165.1	322505	322505	type	True	77.5022	98	577	95	below_threshold
Coprobacillus cateniformis	strain=RCA1-24	GCA_009767585.1	100884	100884	type	True	76.7448	52	577	95	below_threshold
Longibaculum muris	strain=DSM 29487	GCA_004343035.1	1796628	1796628	type	True	76.7222	95	577	95	below_threshold
Longibaculum muris	strain=DSM 29487	GCA_024622235.1	1796628	1796628	type	True	76.6342	97	577	95	below_threshold
Erysipelatoclostridium ramosum		GCA_900660185.1	1547	1547	type	True	76.5989	55	577	95	below_threshold
Eggerthia catenaformis	strain=DSM 20559	GCA_000422605.1	31973	31973	type	True	76.3938	67	577	95	below_threshold
Eggerthia catenaformis	strain=OT 569	GCA_000340375.1	31973	31973	type	True	76.3042	63	577	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 03:14:50,863] [INFO] DFAST Taxonomy check result was written to GCA_945495355.1_SRR7188235_bin.27_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 03:14:50,863] [INFO] ===== Taxonomy check completed =====
[2023-06-08 03:14:50,863] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 03:14:50,864] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5414ac89-ea35-4d52-bc93-1a3111a470bb/dqc_reference/checkm_data
[2023-06-08 03:14:50,865] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 03:14:50,889] [INFO] Task started: CheckM
[2023-06-08 03:14:50,889] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945495355.1_SRR7188235_bin.27_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945495355.1_SRR7188235_bin.27_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945495355.1_SRR7188235_bin.27_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 03:15:09,682] [INFO] Task succeeded: CheckM
[2023-06-08 03:15:09,683] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.29%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 03:15:09,707] [INFO] ===== Completeness check finished =====
[2023-06-08 03:15:09,707] [INFO] ===== Start GTDB Search =====
[2023-06-08 03:15:09,708] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945495355.1_SRR7188235_bin.27_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 03:15:09,708] [INFO] Task started: Blastn
[2023-06-08 03:15:09,708] [INFO] Running command: blastn -query GCA_945495355.1_SRR7188235_bin.27_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg5414ac89-ea35-4d52-bc93-1a3111a470bb/dqc_reference/reference_markers_gtdb.fasta -out GCA_945495355.1_SRR7188235_bin.27_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:15:10,729] [INFO] Task succeeded: Blastn
[2023-06-08 03:15:10,733] [INFO] Selected 7 target genomes.
[2023-06-08 03:15:10,734] [INFO] Target genome list was writen to GCA_945495355.1_SRR7188235_bin.27_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 03:15:10,738] [INFO] Task started: fastANI
[2023-06-08 03:15:10,739] [INFO] Running command: fastANI --query /var/lib/cwl/stgfee8b946-5a4f-41ef-a6a2-756bc751b0d4/GCA_945495355.1_SRR7188235_bin.27_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945495355.1_SRR7188235_bin.27_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945495355.1_SRR7188235_bin.27_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 03:15:13,905] [INFO] Task succeeded: fastANI
[2023-06-08 03:15:13,917] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 03:15:13,917] [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_000173795.1	s__Catenibacterium mitsuokai	96.6792	451	577	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium	95.0	97.03	96.27	0.82	0.73	7	conclusive
GCA_900540665.1	s__Catenibacterium sp900540665	94.0145	425	577	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium	95.0	99.03	99.03	0.84	0.84	2	-
GCF_004168205.1	s__Catenibacterium sp000437715	93.8254	412	577	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium	95.0	96.65	95.64	0.81	0.75	29	-
GCA_900764565.1	s__Catenibacterium sp900764565	93.3033	390	577	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540685.1	s__Catenibacterium sp900540685	92.5346	408	577	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium	95.0	99.87	99.87	0.90	0.90	2	-
GCA_900764725.1	s__Catenibacterium sp900764725	91.2967	389	577	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 03:15:13,919] [INFO] GTDB search result was written to GCA_945495355.1_SRR7188235_bin.27_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 03:15:13,920] [INFO] ===== GTDB Search completed =====
[2023-06-08 03:15:13,922] [INFO] DFAST_QC result json was written to GCA_945495355.1_SRR7188235_bin.27_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 03:15:13,923] [INFO] DFAST_QC completed!
[2023-06-08 03:15:13,923] [INFO] Total running time: 0h0m35s