[2023-06-14 01:48:06,613] [INFO] DFAST_QC pipeline started.
[2023-06-14 01:48:06,615] [INFO] DFAST_QC version: 0.5.7
[2023-06-14 01:48:06,615] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4f15bbc-9a75-4e2a-8870-56a4a5c275fb/dqc_reference
[2023-06-14 01:48:07,938] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-14 01:48:07,938] [INFO] Task started: Prodigal
[2023-06-14 01:48:07,939] [INFO] Running command: gunzip -c /var/lib/cwl/stg41f66a92-feff-4543-9e23-a3dd21e0833e/GCA_947039835.1_ERR5647221_bin.3_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947039835.1_ERR5647221_bin.3_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947039835.1_ERR5647221_bin.3_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-14 01:48:13,641] [INFO] Task succeeded: Prodigal
[2023-06-14 01:48:13,642] [INFO] Task started: HMMsearch
[2023-06-14 01:48:13,642] [INFO] Running command: hmmsearch --tblout GCA_947039835.1_ERR5647221_bin.3_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4f15bbc-9a75-4e2a-8870-56a4a5c275fb/dqc_reference/reference_markers.hmm GCA_947039835.1_ERR5647221_bin.3_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-14 01:48:13,898] [INFO] Task succeeded: HMMsearch
[2023-06-14 01:48:13,900] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg41f66a92-feff-4543-9e23-a3dd21e0833e/GCA_947039835.1_ERR5647221_bin.3_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-14 01:48:13,975] [INFO] Query marker FASTA was written to GCA_947039835.1_ERR5647221_bin.3_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-14 01:48:13,975] [INFO] Task started: Blastn
[2023-06-14 01:48:13,976] [INFO] Running command: blastn -query GCA_947039835.1_ERR5647221_bin.3_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4f15bbc-9a75-4e2a-8870-56a4a5c275fb/dqc_reference/reference_markers.fasta -out GCA_947039835.1_ERR5647221_bin.3_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:48:14,622] [INFO] Task succeeded: Blastn
[2023-06-14 01:48:14,626] [INFO] Selected 18 target genomes.
[2023-06-14 01:48:14,627] [INFO] Target genome list was writen to GCA_947039835.1_ERR5647221_bin.3_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-14 01:48:14,632] [INFO] Task started: fastANI
[2023-06-14 01:48:14,632] [INFO] Running command: fastANI --query /var/lib/cwl/stg41f66a92-feff-4543-9e23-a3dd21e0833e/GCA_947039835.1_ERR5647221_bin.3_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947039835.1_ERR5647221_bin.3_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947039835.1_ERR5647221_bin.3_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-14 01:48:24,202] [INFO] Task succeeded: fastANI
[2023-06-14 01:48:24,203] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4f15bbc-9a75-4e2a-8870-56a4a5c275fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-14 01:48:24,203] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4f15bbc-9a75-4e2a-8870-56a4a5c275fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-14 01:48:24,205] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-14 01:48:24,205] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-14 01:48:24,206] [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
--------------------------------------------------------------------------------
[2023-06-14 01:48:24,208] [INFO] DFAST Taxonomy check result was written to GCA_947039835.1_ERR5647221_bin.3_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-14 01:48:24,208] [INFO] ===== Taxonomy check completed =====
[2023-06-14 01:48:24,208] [INFO] ===== Start completeness check using CheckM =====
[2023-06-14 01:48:24,209] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4f15bbc-9a75-4e2a-8870-56a4a5c275fb/dqc_reference/checkm_data
[2023-06-14 01:48:24,213] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-14 01:48:24,248] [INFO] Task started: CheckM
[2023-06-14 01:48:24,248] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947039835.1_ERR5647221_bin.3_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947039835.1_ERR5647221_bin.3_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947039835.1_ERR5647221_bin.3_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-14 01:48:48,373] [INFO] Task succeeded: CheckM
[2023-06-14 01:48:48,375] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.26%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-14 01:48:48,397] [INFO] ===== Completeness check finished =====
[2023-06-14 01:48:48,397] [INFO] ===== Start GTDB Search =====
[2023-06-14 01:48:48,398] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947039835.1_ERR5647221_bin.3_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-14 01:48:48,398] [INFO] Task started: Blastn
[2023-06-14 01:48:48,398] [INFO] Running command: blastn -query GCA_947039835.1_ERR5647221_bin.3_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4f15bbc-9a75-4e2a-8870-56a4a5c275fb/dqc_reference/reference_markers_gtdb.fasta -out GCA_947039835.1_ERR5647221_bin.3_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:48:49,233] [INFO] Task succeeded: Blastn
[2023-06-14 01:48:49,238] [INFO] Selected 6 target genomes.
[2023-06-14 01:48:49,238] [INFO] Target genome list was writen to GCA_947039835.1_ERR5647221_bin.3_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-14 01:48:49,242] [INFO] Task started: fastANI
[2023-06-14 01:48:49,242] [INFO] Running command: fastANI --query /var/lib/cwl/stg41f66a92-feff-4543-9e23-a3dd21e0833e/GCA_947039835.1_ERR5647221_bin.3_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947039835.1_ERR5647221_bin.3_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947039835.1_ERR5647221_bin.3_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-14 01:48:53,880] [INFO] Task succeeded: fastANI
[2023-06-14 01:48:53,886] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-14 01:48:53,887] [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_910577225.1	s__Eubacterium_J sp910577225	99.5721	629	682	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_J	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000364225.1	s__Eubacterium_J plexicaudatum	80.5165	369	682	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_J	95.0	99.29	99.29	0.93	0.93	2	-
GCA_910584595.1	s__Eubacterium_J sp910584595	80.1021	351	682	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_J	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584345.1	s__Eubacterium_J sp910584345	80.0604	331	682	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_J	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586225.1	s__Eubacterium_J sp910586225	79.1212	290	682	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_J	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910574915.1	s__Eubacterium_J sp910574915	78.8477	292	682	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_J	95.0	99.60	98.88	0.96	0.92	4	-
--------------------------------------------------------------------------------
[2023-06-14 01:48:53,889] [INFO] GTDB search result was written to GCA_947039835.1_ERR5647221_bin.3_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-14 01:48:53,890] [INFO] ===== GTDB Search completed =====
[2023-06-14 01:48:53,892] [INFO] DFAST_QC result json was written to GCA_947039835.1_ERR5647221_bin.3_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-14 01:48:53,893] [INFO] DFAST_QC completed!
[2023-06-14 01:48:53,893] [INFO] Total running time: 0h0m47s