[2023-06-08 03:42:42,830] [INFO] DFAST_QC pipeline started.
[2023-06-08 03:42:42,838] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 03:42:42,838] [INFO] DQC Reference Directory: /var/lib/cwl/stg1bc1c3be-8596-46c3-867d-fb207a33eb0b/dqc_reference
[2023-06-08 03:42:44,852] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 03:42:44,855] [INFO] Task started: Prodigal
[2023-06-08 03:42:44,855] [INFO] Running command: gunzip -c /var/lib/cwl/stgf1d4c124-6b6b-41f1-bec3-31d889ef770b/GCA_945937835.1_SRR11489789_bin.10_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945937835.1_SRR11489789_bin.10_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945937835.1_SRR11489789_bin.10_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 03:42:48,351] [INFO] Task succeeded: Prodigal
[2023-06-08 03:42:48,351] [INFO] Task started: HMMsearch
[2023-06-08 03:42:48,351] [INFO] Running command: hmmsearch --tblout GCA_945937835.1_SRR11489789_bin.10_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1bc1c3be-8596-46c3-867d-fb207a33eb0b/dqc_reference/reference_markers.hmm GCA_945937835.1_SRR11489789_bin.10_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 03:42:48,615] [INFO] Task succeeded: HMMsearch
[2023-06-08 03:42:48,616] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf1d4c124-6b6b-41f1-bec3-31d889ef770b/GCA_945937835.1_SRR11489789_bin.10_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 03:42:48,638] [INFO] Query marker FASTA was written to GCA_945937835.1_SRR11489789_bin.10_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 03:42:48,638] [INFO] Task started: Blastn
[2023-06-08 03:42:48,638] [INFO] Running command: blastn -query GCA_945937835.1_SRR11489789_bin.10_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg1bc1c3be-8596-46c3-867d-fb207a33eb0b/dqc_reference/reference_markers.fasta -out GCA_945937835.1_SRR11489789_bin.10_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:42:49,313] [INFO] Task succeeded: Blastn
[2023-06-08 03:42:49,317] [INFO] Selected 24 target genomes.
[2023-06-08 03:42:49,318] [INFO] Target genome list was writen to GCA_945937835.1_SRR11489789_bin.10_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 03:42:49,325] [INFO] Task started: fastANI
[2023-06-08 03:42:49,325] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1d4c124-6b6b-41f1-bec3-31d889ef770b/GCA_945937835.1_SRR11489789_bin.10_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945937835.1_SRR11489789_bin.10_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945937835.1_SRR11489789_bin.10_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 03:43:07,208] [INFO] Task succeeded: fastANI
[2023-06-08 03:43:07,208] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1bc1c3be-8596-46c3-867d-fb207a33eb0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 03:43:07,208] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1bc1c3be-8596-46c3-867d-fb207a33eb0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 03:43:07,210] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 03:43:07,211] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 03:43:07,211] [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
--------------------------------------------------------------------------------
[2023-06-08 03:43:07,213] [INFO] DFAST Taxonomy check result was written to GCA_945937835.1_SRR11489789_bin.10_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 03:43:07,214] [INFO] ===== Taxonomy check completed =====
[2023-06-08 03:43:07,214] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 03:43:07,215] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1bc1c3be-8596-46c3-867d-fb207a33eb0b/dqc_reference/checkm_data
[2023-06-08 03:43:07,218] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 03:43:07,240] [INFO] Task started: CheckM
[2023-06-08 03:43:07,240] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945937835.1_SRR11489789_bin.10_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945937835.1_SRR11489789_bin.10_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945937835.1_SRR11489789_bin.10_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 03:43:26,129] [INFO] Task succeeded: CheckM
[2023-06-08 03:43:26,131] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.63%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 03:43:26,155] [INFO] ===== Completeness check finished =====
[2023-06-08 03:43:26,156] [INFO] ===== Start GTDB Search =====
[2023-06-08 03:43:26,156] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945937835.1_SRR11489789_bin.10_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 03:43:26,157] [INFO] Task started: Blastn
[2023-06-08 03:43:26,157] [INFO] Running command: blastn -query GCA_945937835.1_SRR11489789_bin.10_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg1bc1c3be-8596-46c3-867d-fb207a33eb0b/dqc_reference/reference_markers_gtdb.fasta -out GCA_945937835.1_SRR11489789_bin.10_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:43:27,101] [INFO] Task succeeded: Blastn
[2023-06-08 03:43:27,106] [INFO] Selected 7 target genomes.
[2023-06-08 03:43:27,107] [INFO] Target genome list was writen to GCA_945937835.1_SRR11489789_bin.10_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 03:43:27,111] [INFO] Task started: fastANI
[2023-06-08 03:43:27,111] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1d4c124-6b6b-41f1-bec3-31d889ef770b/GCA_945937835.1_SRR11489789_bin.10_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945937835.1_SRR11489789_bin.10_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945937835.1_SRR11489789_bin.10_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 03:43:29,459] [INFO] Task succeeded: fastANI
[2023-06-08 03:43:29,467] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 03:43:29,468] [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_900549225.1	s__CAG-475 sp900549225	98.9742	310	355	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-917;g__CAG-475	95.0	99.88	99.88	0.96	0.96	2	conclusive
GCA_002449145.1	s__CAG-475 sp002449145	83.7695	282	355	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-917;g__CAG-475	95.0	98.71	98.37	0.92	0.89	8	-
GCA_900550855.1	s__CAG-475 sp900550855	83.709	235	355	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-917;g__CAG-475	95.0	100.00	100.00	0.97	0.97	2	-
GCA_900547975.1	s__CAG-475 sp900547975	83.671	268	355	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-917;g__CAG-475	95.0	98.01	97.92	0.89	0.88	3	-
GCA_000434435.1	s__CAG-475 sp000434435	82.3602	261	355	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-917;g__CAG-475	95.0	97.86	97.61	0.93	0.92	5	-
GCA_900763875.1	s__CAG-475 sp900763875	81.7188	244	355	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-917;g__CAG-475	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002297185.1	s__CAG-475 sp002297185	79.7871	172	355	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-917;g__CAG-475	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 03:43:29,470] [INFO] GTDB search result was written to GCA_945937835.1_SRR11489789_bin.10_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 03:43:29,471] [INFO] ===== GTDB Search completed =====
[2023-06-08 03:43:29,474] [INFO] DFAST_QC result json was written to GCA_945937835.1_SRR11489789_bin.10_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 03:43:29,474] [INFO] DFAST_QC completed!
[2023-06-08 03:43:29,474] [INFO] Total running time: 0h0m47s