[2023-06-08 17:47:40,362] [INFO] DFAST_QC pipeline started.
[2023-06-08 17:47:40,374] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 17:47:40,375] [INFO] DQC Reference Directory: /var/lib/cwl/stgc6584b76-c257-4143-85f0-c114c1da7382/dqc_reference
[2023-06-08 17:47:41,552] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 17:47:41,553] [INFO] Task started: Prodigal
[2023-06-08 17:47:41,553] [INFO] Running command: gunzip -c /var/lib/cwl/stg801bd8cd-dac0-4eaf-af6a-83f0bd327168/GCA_945637665.1_SRR14474050_bin.37_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945637665.1_SRR14474050_bin.37_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945637665.1_SRR14474050_bin.37_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 17:47:43,888] [INFO] Task succeeded: Prodigal
[2023-06-08 17:47:43,889] [INFO] Task started: HMMsearch
[2023-06-08 17:47:43,889] [INFO] Running command: hmmsearch --tblout GCA_945637665.1_SRR14474050_bin.37_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc6584b76-c257-4143-85f0-c114c1da7382/dqc_reference/reference_markers.hmm GCA_945637665.1_SRR14474050_bin.37_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 17:47:44,101] [INFO] Task succeeded: HMMsearch
[2023-06-08 17:47:44,102] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg801bd8cd-dac0-4eaf-af6a-83f0bd327168/GCA_945637665.1_SRR14474050_bin.37_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 17:47:44,119] [INFO] Query marker FASTA was written to GCA_945637665.1_SRR14474050_bin.37_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 17:47:44,120] [INFO] Task started: Blastn
[2023-06-08 17:47:44,120] [INFO] Running command: blastn -query GCA_945637665.1_SRR14474050_bin.37_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6584b76-c257-4143-85f0-c114c1da7382/dqc_reference/reference_markers.fasta -out GCA_945637665.1_SRR14474050_bin.37_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:47:44,703] [INFO] Task succeeded: Blastn
[2023-06-08 17:47:44,707] [INFO] Selected 18 target genomes.
[2023-06-08 17:47:44,707] [INFO] Target genome list was writen to GCA_945637665.1_SRR14474050_bin.37_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 17:47:44,713] [INFO] Task started: fastANI
[2023-06-08 17:47:44,713] [INFO] Running command: fastANI --query /var/lib/cwl/stg801bd8cd-dac0-4eaf-af6a-83f0bd327168/GCA_945637665.1_SRR14474050_bin.37_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945637665.1_SRR14474050_bin.37_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945637665.1_SRR14474050_bin.37_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 17:47:55,437] [INFO] Task succeeded: fastANI
[2023-06-08 17:47:55,437] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc6584b76-c257-4143-85f0-c114c1da7382/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 17:47:55,438] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc6584b76-c257-4143-85f0-c114c1da7382/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 17:47:55,440] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 17:47:55,440] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 17:47:55,441] [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 17:47:55,445] [INFO] DFAST Taxonomy check result was written to GCA_945637665.1_SRR14474050_bin.37_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 17:47:55,446] [INFO] ===== Taxonomy check completed =====
[2023-06-08 17:47:55,446] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 17:47:55,447] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc6584b76-c257-4143-85f0-c114c1da7382/dqc_reference/checkm_data
[2023-06-08 17:47:55,451] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 17:47:55,472] [INFO] Task started: CheckM
[2023-06-08 17:47:55,473] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945637665.1_SRR14474050_bin.37_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945637665.1_SRR14474050_bin.37_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945637665.1_SRR14474050_bin.37_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 17:48:10,204] [INFO] Task succeeded: CheckM
[2023-06-08 17:48:10,206] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.43%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 17:48:10,225] [INFO] ===== Completeness check finished =====
[2023-06-08 17:48:10,225] [INFO] ===== Start GTDB Search =====
[2023-06-08 17:48:10,226] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945637665.1_SRR14474050_bin.37_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 17:48:10,226] [INFO] Task started: Blastn
[2023-06-08 17:48:10,226] [INFO] Running command: blastn -query GCA_945637665.1_SRR14474050_bin.37_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6584b76-c257-4143-85f0-c114c1da7382/dqc_reference/reference_markers_gtdb.fasta -out GCA_945637665.1_SRR14474050_bin.37_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:48:11,084] [INFO] Task succeeded: Blastn
[2023-06-08 17:48:11,089] [INFO] Selected 16 target genomes.
[2023-06-08 17:48:11,089] [INFO] Target genome list was writen to GCA_945637665.1_SRR14474050_bin.37_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 17:48:11,099] [INFO] Task started: fastANI
[2023-06-08 17:48:11,099] [INFO] Running command: fastANI --query /var/lib/cwl/stg801bd8cd-dac0-4eaf-af6a-83f0bd327168/GCA_945637665.1_SRR14474050_bin.37_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945637665.1_SRR14474050_bin.37_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945637665.1_SRR14474050_bin.37_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 17:48:16,878] [INFO] Task succeeded: fastANI
[2023-06-08 17:48:16,891] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 17:48:16,891] [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_016297165.1	s__Ruminiclostridium_E sp016297165	98.5033	296	356	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminiclostridium_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900768675.1	s__Ruminiclostridium_E sp900768675	79.1509	167	356	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminiclostridium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017624025.1	s__Ruminiclostridium_E sp017624025	78.6646	89	356	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminiclostridium_E	95.0	98.27	98.27	0.69	0.69	2	-
GCA_017625405.1	s__Ruminiclostridium_E sp017625405	78.4434	100	356	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminiclostridium_E	95.0	95.49	95.49	0.77	0.77	2	-
GCA_017472865.1	s__Ruminiclostridium_E sp017472865	78.2557	105	356	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminiclostridium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900556525.1	s__Ruminiclostridium_E sp900556525	77.1135	55	356	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminiclostridium_E	95.0	99.37	99.37	0.80	0.80	2	-
GCA_002363155.1	s__Ruminiclostridium_E sp002363155	76.4168	56	356	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminiclostridium_E	95.0	99.55	99.55	0.76	0.76	2	-
GCA_017408635.1	s__Ruminiclostridium_E sp017408635	76.3196	50	356	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminiclostridium_E	95.0	95.60	95.60	0.80	0.80	2	-
--------------------------------------------------------------------------------
[2023-06-08 17:48:16,894] [INFO] GTDB search result was written to GCA_945637665.1_SRR14474050_bin.37_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 17:48:16,894] [INFO] ===== GTDB Search completed =====
[2023-06-08 17:48:16,898] [INFO] DFAST_QC result json was written to GCA_945637665.1_SRR14474050_bin.37_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 17:48:16,898] [INFO] DFAST_QC completed!
[2023-06-08 17:48:16,898] [INFO] Total running time: 0h0m37s