[2023-06-28 18:09:33,993] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:09:33,996] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:09:33,996] [INFO] DQC Reference Directory: /var/lib/cwl/stgb142a018-365e-4267-8d74-bf03d46f81d4/dqc_reference
[2023-06-28 18:09:36,606] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:09:36,607] [INFO] Task started: Prodigal
[2023-06-28 18:09:36,608] [INFO] Running command: gunzip -c /var/lib/cwl/stg0f3817ca-d6d0-4a29-b009-b1d241b3c9d8/GCA_913041925.1_ERR598946_bin.134_MetaBAT_v2.12.1_MAG_genomic.fna.gz | prodigal -d GCA_913041925.1_ERR598946_bin.134_MetaBAT_v2.12.1_MAG_genomic.fna/cds.fna -a GCA_913041925.1_ERR598946_bin.134_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:09:43,281] [INFO] Task succeeded: Prodigal
[2023-06-28 18:09:43,282] [INFO] Task started: HMMsearch
[2023-06-28 18:09:43,282] [INFO] Running command: hmmsearch --tblout GCA_913041925.1_ERR598946_bin.134_MetaBAT_v2.12.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb142a018-365e-4267-8d74-bf03d46f81d4/dqc_reference/reference_markers.hmm GCA_913041925.1_ERR598946_bin.134_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:09:43,538] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:09:43,539] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0f3817ca-d6d0-4a29-b009-b1d241b3c9d8/GCA_913041925.1_ERR598946_bin.134_MetaBAT_v2.12.1_MAG_genomic.fna.gz]
[2023-06-28 18:09:43,571] [INFO] Query marker FASTA was written to GCA_913041925.1_ERR598946_bin.134_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta
[2023-06-28 18:09:43,571] [INFO] Task started: Blastn
[2023-06-28 18:09:43,572] [INFO] Running command: blastn -query GCA_913041925.1_ERR598946_bin.134_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb142a018-365e-4267-8d74-bf03d46f81d4/dqc_reference/reference_markers.fasta -out GCA_913041925.1_ERR598946_bin.134_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:09:44,252] [INFO] Task succeeded: Blastn
[2023-06-28 18:09:44,257] [INFO] Selected 27 target genomes.
[2023-06-28 18:09:44,257] [INFO] Target genome list was writen to GCA_913041925.1_ERR598946_bin.134_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt
[2023-06-28 18:09:44,274] [INFO] Task started: fastANI
[2023-06-28 18:09:44,274] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f3817ca-d6d0-4a29-b009-b1d241b3c9d8/GCA_913041925.1_ERR598946_bin.134_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913041925.1_ERR598946_bin.134_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt --output GCA_913041925.1_ERR598946_bin.134_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:10:02,338] [INFO] Task succeeded: fastANI
[2023-06-28 18:10:02,338] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb142a018-365e-4267-8d74-bf03d46f81d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:10:02,338] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb142a018-365e-4267-8d74-bf03d46f81d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:10:02,340] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:10:02,340] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 18:10:02,340] [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
--------------------------------------------------------------------------------
[2023-06-28 18:10:02,342] [INFO] DFAST Taxonomy check result was written to GCA_913041925.1_ERR598946_bin.134_MetaBAT_v2.12.1_MAG_genomic.fna/tc_result.tsv
[2023-06-28 18:10:02,343] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:10:02,343] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:10:02,343] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb142a018-365e-4267-8d74-bf03d46f81d4/dqc_reference/checkm_data
[2023-06-28 18:10:02,345] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:10:02,376] [INFO] Task started: CheckM
[2023-06-28 18:10:02,376] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913041925.1_ERR598946_bin.134_MetaBAT_v2.12.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913041925.1_ERR598946_bin.134_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_input GCA_913041925.1_ERR598946_bin.134_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_result
[2023-06-28 18:10:28,371] [INFO] Task succeeded: CheckM
[2023-06-28 18:10:28,372] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 18:10:28,398] [INFO] ===== Completeness check finished =====
[2023-06-28 18:10:28,398] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:10:28,399] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913041925.1_ERR598946_bin.134_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta)
[2023-06-28 18:10:28,399] [INFO] Task started: Blastn
[2023-06-28 18:10:28,399] [INFO] Running command: blastn -query GCA_913041925.1_ERR598946_bin.134_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb142a018-365e-4267-8d74-bf03d46f81d4/dqc_reference/reference_markers_gtdb.fasta -out GCA_913041925.1_ERR598946_bin.134_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:10:29,501] [INFO] Task succeeded: Blastn
[2023-06-28 18:10:29,506] [INFO] Selected 27 target genomes.
[2023-06-28 18:10:29,506] [INFO] Target genome list was writen to GCA_913041925.1_ERR598946_bin.134_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:10:29,531] [INFO] Task started: fastANI
[2023-06-28 18:10:29,531] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f3817ca-d6d0-4a29-b009-b1d241b3c9d8/GCA_913041925.1_ERR598946_bin.134_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913041925.1_ERR598946_bin.134_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_913041925.1_ERR598946_bin.134_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:10:43,827] [INFO] Task succeeded: fastANI
[2023-06-28 18:10:43,839] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 18:10:43,840] [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_002726415.1	s__GCA-2726415 sp002726415	99.4197	511	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__GCA-2726415	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018698075.1	s__GCA-2726415 sp018698075	80.3401	168	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__GCA-2726415	95.0	99.40	99.29	0.88	0.80	16	-
GCA_014239255.1	s__GCA-2726415 sp014239255	79.2175	178	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__GCA-2726415	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239575.1	s__GCA-2726415 sp014239575	78.8831	158	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__GCA-2726415	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002171735.1	s__UBA868 sp002171735	77.4227	63	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	98.83	98.60	0.84	0.82	3	-
GCA_016845525.1	s__UBA868 sp016845525	77.399	65	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 18:10:43,842] [INFO] GTDB search result was written to GCA_913041925.1_ERR598946_bin.134_MetaBAT_v2.12.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 18:10:43,843] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:10:43,846] [INFO] DFAST_QC result json was written to GCA_913041925.1_ERR598946_bin.134_MetaBAT_v2.12.1_MAG_genomic.fna/dqc_result.json
[2023-06-28 18:10:43,846] [INFO] DFAST_QC completed!
[2023-06-28 18:10:43,846] [INFO] Total running time: 0h1m10s