[2023-06-08 00:18:29,529] [INFO] DFAST_QC pipeline started.
[2023-06-08 00:18:29,531] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 00:18:29,532] [INFO] DQC Reference Directory: /var/lib/cwl/stg77b89b55-c775-4d39-ad35-26430c1a12bf/dqc_reference
[2023-06-08 00:18:30,724] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 00:18:30,724] [INFO] Task started: Prodigal
[2023-06-08 00:18:30,725] [INFO] Running command: gunzip -c /var/lib/cwl/stg934922cb-e6cf-4fdf-88a7-1e8eb5f05402/GCA_945995625.1_ERR2020030_bin.3_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945995625.1_ERR2020030_bin.3_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945995625.1_ERR2020030_bin.3_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 00:18:32,245] [INFO] Task succeeded: Prodigal
[2023-06-08 00:18:32,245] [INFO] Task started: HMMsearch
[2023-06-08 00:18:32,245] [INFO] Running command: hmmsearch --tblout GCA_945995625.1_ERR2020030_bin.3_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77b89b55-c775-4d39-ad35-26430c1a12bf/dqc_reference/reference_markers.hmm GCA_945995625.1_ERR2020030_bin.3_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 00:18:32,412] [INFO] Task succeeded: HMMsearch
[2023-06-08 00:18:32,413] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg934922cb-e6cf-4fdf-88a7-1e8eb5f05402/GCA_945995625.1_ERR2020030_bin.3_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 00:18:32,431] [INFO] Query marker FASTA was written to GCA_945995625.1_ERR2020030_bin.3_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 00:18:32,432] [INFO] Task started: Blastn
[2023-06-08 00:18:32,432] [INFO] Running command: blastn -query GCA_945995625.1_ERR2020030_bin.3_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg77b89b55-c775-4d39-ad35-26430c1a12bf/dqc_reference/reference_markers.fasta -out GCA_945995625.1_ERR2020030_bin.3_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:18:32,996] [INFO] Task succeeded: Blastn
[2023-06-08 00:18:33,000] [INFO] Selected 27 target genomes.
[2023-06-08 00:18:33,000] [INFO] Target genome list was writen to GCA_945995625.1_ERR2020030_bin.3_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 00:18:33,006] [INFO] Task started: fastANI
[2023-06-08 00:18:33,006] [INFO] Running command: fastANI --query /var/lib/cwl/stg934922cb-e6cf-4fdf-88a7-1e8eb5f05402/GCA_945995625.1_ERR2020030_bin.3_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945995625.1_ERR2020030_bin.3_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945995625.1_ERR2020030_bin.3_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 00:18:44,063] [INFO] Task succeeded: fastANI
[2023-06-08 00:18:44,064] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77b89b55-c775-4d39-ad35-26430c1a12bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 00:18:44,064] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77b89b55-c775-4d39-ad35-26430c1a12bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 00:18:44,066] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 00:18:44,066] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 00:18:44,066] [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 00:18:44,068] [INFO] DFAST Taxonomy check result was written to GCA_945995625.1_ERR2020030_bin.3_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 00:18:44,069] [INFO] ===== Taxonomy check completed =====
[2023-06-08 00:18:44,069] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 00:18:44,069] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77b89b55-c775-4d39-ad35-26430c1a12bf/dqc_reference/checkm_data
[2023-06-08 00:18:44,072] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 00:18:44,087] [INFO] Task started: CheckM
[2023-06-08 00:18:44,088] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945995625.1_ERR2020030_bin.3_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945995625.1_ERR2020030_bin.3_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945995625.1_ERR2020030_bin.3_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 00:18:56,394] [INFO] Task succeeded: CheckM
[2023-06-08 00:18:56,395] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 00:18:56,412] [INFO] ===== Completeness check finished =====
[2023-06-08 00:18:56,412] [INFO] ===== Start GTDB Search =====
[2023-06-08 00:18:56,412] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945995625.1_ERR2020030_bin.3_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 00:18:56,412] [INFO] Task started: Blastn
[2023-06-08 00:18:56,412] [INFO] Running command: blastn -query GCA_945995625.1_ERR2020030_bin.3_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg77b89b55-c775-4d39-ad35-26430c1a12bf/dqc_reference/reference_markers_gtdb.fasta -out GCA_945995625.1_ERR2020030_bin.3_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:18:57,299] [INFO] Task succeeded: Blastn
[2023-06-08 00:18:57,302] [INFO] Selected 14 target genomes.
[2023-06-08 00:18:57,303] [INFO] Target genome list was writen to GCA_945995625.1_ERR2020030_bin.3_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 00:18:57,317] [INFO] Task started: fastANI
[2023-06-08 00:18:57,317] [INFO] Running command: fastANI --query /var/lib/cwl/stg934922cb-e6cf-4fdf-88a7-1e8eb5f05402/GCA_945995625.1_ERR2020030_bin.3_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945995625.1_ERR2020030_bin.3_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945995625.1_ERR2020030_bin.3_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 00:19:00,385] [INFO] Task succeeded: fastANI
[2023-06-08 00:19:00,394] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 00:19:00,395] [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_000438295.1	s__Onthousia sp000438295	96.3269	284	343	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Onthousia	95.0	96.69	96.41	0.79	0.73	4	conclusive
GCA_014846175.1	s__Onthousia sp014846175	88.2757	230	343	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Onthousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900758495.1	s__Onthousia sp900758495	83.7393	243	343	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Onthousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018715925.1	s__Onthousia faecipullorum	78.0404	96	343	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Onthousia	95.0	99.48	99.48	0.89	0.89	2	-
GCA_018711135.1	s__Onthousia faecavium	77.7381	79	343	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Onthousia	95.0	99.89	99.89	0.91	0.91	2	-
GCA_900760545.1	s__Onthousia sp900760545	77.6349	83	343	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Onthousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904420615.1	s__Onthousia sp904420615	77.6073	91	343	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Onthousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018712385.1	s__Onthousia excrementipullorum	77.5088	103	343	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Onthousia	95.0	97.70	95.09	0.85	0.78	4	-
GCA_018716225.1	s__Onthousia faecigallinarum	77.4028	76	343	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Onthousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017460175.1	s__UBA3789 sp017460175	77.3284	51	343	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 00:19:00,396] [INFO] GTDB search result was written to GCA_945995625.1_ERR2020030_bin.3_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 00:19:00,397] [INFO] ===== GTDB Search completed =====
[2023-06-08 00:19:00,399] [INFO] DFAST_QC result json was written to GCA_945995625.1_ERR2020030_bin.3_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 00:19:00,399] [INFO] DFAST_QC completed!
[2023-06-08 00:19:00,399] [INFO] Total running time: 0h0m31s