[2023-06-08 01:49:09,176] [INFO] DFAST_QC pipeline started.
[2023-06-08 01:49:09,178] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 01:49:09,178] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b3e1aa9-9a43-40e8-ade1-a0c76fa44a50/dqc_reference
[2023-06-08 01:49:10,588] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 01:49:10,588] [INFO] Task started: Prodigal
[2023-06-08 01:49:10,589] [INFO] Running command: gunzip -c /var/lib/cwl/stgf0d6e0d6-d4bf-4aaf-8836-2f96dfb76324/GCA_945830765.1_SRR5240751_bin.30_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945830765.1_SRR5240751_bin.30_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945830765.1_SRR5240751_bin.30_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 01:49:16,854] [INFO] Task succeeded: Prodigal
[2023-06-08 01:49:16,854] [INFO] Task started: HMMsearch
[2023-06-08 01:49:16,854] [INFO] Running command: hmmsearch --tblout GCA_945830765.1_SRR5240751_bin.30_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b3e1aa9-9a43-40e8-ade1-a0c76fa44a50/dqc_reference/reference_markers.hmm GCA_945830765.1_SRR5240751_bin.30_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 01:49:17,143] [INFO] Task succeeded: HMMsearch
[2023-06-08 01:49:17,144] [INFO] Found 6/6 markers.
[2023-06-08 01:49:17,169] [INFO] Query marker FASTA was written to GCA_945830765.1_SRR5240751_bin.30_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 01:49:17,170] [INFO] Task started: Blastn
[2023-06-08 01:49:17,170] [INFO] Running command: blastn -query GCA_945830765.1_SRR5240751_bin.30_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b3e1aa9-9a43-40e8-ade1-a0c76fa44a50/dqc_reference/reference_markers.fasta -out GCA_945830765.1_SRR5240751_bin.30_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 01:49:17,772] [INFO] Task succeeded: Blastn
[2023-06-08 01:49:17,777] [INFO] Selected 21 target genomes.
[2023-06-08 01:49:17,777] [INFO] Target genome list was writen to GCA_945830765.1_SRR5240751_bin.30_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 01:49:17,779] [INFO] Task started: fastANI
[2023-06-08 01:49:17,779] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0d6e0d6-d4bf-4aaf-8836-2f96dfb76324/GCA_945830765.1_SRR5240751_bin.30_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945830765.1_SRR5240751_bin.30_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945830765.1_SRR5240751_bin.30_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 01:49:28,472] [INFO] Task succeeded: fastANI
[2023-06-08 01:49:28,472] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b3e1aa9-9a43-40e8-ade1-a0c76fa44a50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 01:49:28,473] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b3e1aa9-9a43-40e8-ade1-a0c76fa44a50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 01:49:28,479] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 01:49:28,479] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 01:49:28,479] [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
Wujia chipingensis	strain=NSJ-4	GCA_014337155.1	2763670	2763670	type	True	89.4907	638	771	95	below_threshold
Coprococcus eutactus	strain=ATCC 27759	GCA_000154425.1	33043	33043	suspected-type	True	78.6579	72	771	95	below_threshold
Coprococcus eutactus	strain=ATCC 27759	GCA_025149915.1	33043	33043	suspected-type	True	78.6496	72	771	95	below_threshold
Jutongia huaianensis	strain=NSJ-37	GCA_014384985.1	2763668	2763668	type	True	76.6396	65	771	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 01:49:28,481] [INFO] DFAST Taxonomy check result was written to GCA_945830765.1_SRR5240751_bin.30_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 01:49:28,482] [INFO] ===== Taxonomy check completed =====
[2023-06-08 01:49:28,482] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 01:49:28,483] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b3e1aa9-9a43-40e8-ade1-a0c76fa44a50/dqc_reference/checkm_data
[2023-06-08 01:49:28,484] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 01:49:28,516] [INFO] Task started: CheckM
[2023-06-08 01:49:28,516] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945830765.1_SRR5240751_bin.30_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945830765.1_SRR5240751_bin.30_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945830765.1_SRR5240751_bin.30_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 01:49:54,176] [INFO] Task succeeded: CheckM
[2023-06-08 01:49:54,178] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.56%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 01:49:54,205] [INFO] ===== Completeness check finished =====
[2023-06-08 01:49:54,205] [INFO] ===== Start GTDB Search =====
[2023-06-08 01:49:54,206] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945830765.1_SRR5240751_bin.30_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 01:49:54,207] [INFO] Task started: Blastn
[2023-06-08 01:49:54,207] [INFO] Running command: blastn -query GCA_945830765.1_SRR5240751_bin.30_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b3e1aa9-9a43-40e8-ade1-a0c76fa44a50/dqc_reference/reference_markers_gtdb.fasta -out GCA_945830765.1_SRR5240751_bin.30_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 01:49:55,064] [INFO] Task succeeded: Blastn
[2023-06-08 01:49:55,068] [INFO] Selected 7 target genomes.
[2023-06-08 01:49:55,068] [INFO] Target genome list was writen to GCA_945830765.1_SRR5240751_bin.30_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 01:49:55,074] [INFO] Task started: fastANI
[2023-06-08 01:49:55,075] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0d6e0d6-d4bf-4aaf-8836-2f96dfb76324/GCA_945830765.1_SRR5240751_bin.30_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945830765.1_SRR5240751_bin.30_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945830765.1_SRR5240751_bin.30_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 01:49:59,337] [INFO] Task succeeded: fastANI
[2023-06-08 01:49:59,349] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 01:49:59,350] [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_900553925.1	s__CAG-127 sp900553925	96.9003	488	771	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	97.14	96.66	0.89	0.85	4	conclusive
GCF_018918185.1	s__CAG-127 sp900539705	90.3831	631	771	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	97.05	96.96	0.87	0.83	4	-
GCA_014337155.1	s__CAG-127 sp900319515	89.4907	638	771	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	98.02	96.09	0.90	0.85	25	-
GCA_900767585.1	s__CAG-127 sp900767585	89.2424	559	771	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002431865.1	s__CAG-127 sp002431865	86.5105	515	771	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	99.73	99.73	0.84	0.84	3	-
GCA_002404515.1	s__CAG-127 sp002404515	86.4559	483	771	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902780405.1	s__CAG-127 sp902780405	77.2132	67	771	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 01:49:59,352] [INFO] GTDB search result was written to GCA_945830765.1_SRR5240751_bin.30_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 01:49:59,352] [INFO] ===== GTDB Search completed =====
[2023-06-08 01:49:59,355] [INFO] DFAST_QC result json was written to GCA_945830765.1_SRR5240751_bin.30_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 01:49:59,355] [INFO] DFAST_QC completed!
[2023-06-08 01:49:59,355] [INFO] Total running time: 0h0m50s