[2023-06-30 06:43:24,578] [INFO] DFAST_QC pipeline started.
[2023-06-30 06:43:24,580] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 06:43:24,580] [INFO] DQC Reference Directory: /var/lib/cwl/stg81f7d01f-fe9a-46af-a156-3d514183e106/dqc_reference
[2023-06-30 06:43:25,773] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 06:43:25,774] [INFO] Task started: Prodigal
[2023-06-30 06:43:25,774] [INFO] Running command: gunzip -c /var/lib/cwl/stg40d4288f-8905-4286-a354-f56a80e7e441/GCA_903940335.1_freshwater_MAG_---_Loc090907-1m_bin-040_genomic.fna.gz | prodigal -d GCA_903940335.1_freshwater_MAG_---_Loc090907-1m_bin-040_genomic.fna/cds.fna -a GCA_903940335.1_freshwater_MAG_---_Loc090907-1m_bin-040_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 06:43:31,414] [INFO] Task succeeded: Prodigal
[2023-06-30 06:43:31,415] [INFO] Task started: HMMsearch
[2023-06-30 06:43:31,415] [INFO] Running command: hmmsearch --tblout GCA_903940335.1_freshwater_MAG_---_Loc090907-1m_bin-040_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81f7d01f-fe9a-46af-a156-3d514183e106/dqc_reference/reference_markers.hmm GCA_903940335.1_freshwater_MAG_---_Loc090907-1m_bin-040_genomic.fna/protein.faa > /dev/null
[2023-06-30 06:43:31,636] [INFO] Task succeeded: HMMsearch
[2023-06-30 06:43:31,637] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg40d4288f-8905-4286-a354-f56a80e7e441/GCA_903940335.1_freshwater_MAG_---_Loc090907-1m_bin-040_genomic.fna.gz]
[2023-06-30 06:43:31,657] [INFO] Query marker FASTA was written to GCA_903940335.1_freshwater_MAG_---_Loc090907-1m_bin-040_genomic.fna/markers.fasta
[2023-06-30 06:43:31,658] [INFO] Task started: Blastn
[2023-06-30 06:43:31,658] [INFO] Running command: blastn -query GCA_903940335.1_freshwater_MAG_---_Loc090907-1m_bin-040_genomic.fna/markers.fasta -db /var/lib/cwl/stg81f7d01f-fe9a-46af-a156-3d514183e106/dqc_reference/reference_markers.fasta -out GCA_903940335.1_freshwater_MAG_---_Loc090907-1m_bin-040_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 06:43:32,225] [INFO] Task succeeded: Blastn
[2023-06-30 06:43:32,230] [INFO] Selected 22 target genomes.
[2023-06-30 06:43:32,230] [INFO] Target genome list was writen to GCA_903940335.1_freshwater_MAG_---_Loc090907-1m_bin-040_genomic.fna/target_genomes.txt
[2023-06-30 06:43:32,232] [INFO] Task started: fastANI
[2023-06-30 06:43:32,232] [INFO] Running command: fastANI --query /var/lib/cwl/stg40d4288f-8905-4286-a354-f56a80e7e441/GCA_903940335.1_freshwater_MAG_---_Loc090907-1m_bin-040_genomic.fna.gz --refList GCA_903940335.1_freshwater_MAG_---_Loc090907-1m_bin-040_genomic.fna/target_genomes.txt --output GCA_903940335.1_freshwater_MAG_---_Loc090907-1m_bin-040_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 06:43:41,152] [INFO] Task succeeded: fastANI
[2023-06-30 06:43:41,152] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81f7d01f-fe9a-46af-a156-3d514183e106/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 06:43:41,153] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81f7d01f-fe9a-46af-a156-3d514183e106/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 06:43:41,155] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 06:43:41,155] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 06:43:41,156] [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
--------------------------------------------------------------------------------
[2023-06-30 06:43:41,158] [INFO] DFAST Taxonomy check result was written to GCA_903940335.1_freshwater_MAG_---_Loc090907-1m_bin-040_genomic.fna/tc_result.tsv
[2023-06-30 06:43:41,159] [INFO] ===== Taxonomy check completed =====
[2023-06-30 06:43:41,159] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 06:43:41,159] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81f7d01f-fe9a-46af-a156-3d514183e106/dqc_reference/checkm_data
[2023-06-30 06:43:41,163] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 06:43:41,186] [INFO] Task started: CheckM
[2023-06-30 06:43:41,186] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903940335.1_freshwater_MAG_---_Loc090907-1m_bin-040_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903940335.1_freshwater_MAG_---_Loc090907-1m_bin-040_genomic.fna/checkm_input GCA_903940335.1_freshwater_MAG_---_Loc090907-1m_bin-040_genomic.fna/checkm_result
[2023-06-30 06:44:04,540] [INFO] Task succeeded: CheckM
[2023-06-30 06:44:04,542] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 06:44:04,561] [INFO] ===== Completeness check finished =====
[2023-06-30 06:44:04,562] [INFO] ===== Start GTDB Search =====
[2023-06-30 06:44:04,562] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903940335.1_freshwater_MAG_---_Loc090907-1m_bin-040_genomic.fna/markers.fasta)
[2023-06-30 06:44:04,562] [INFO] Task started: Blastn
[2023-06-30 06:44:04,563] [INFO] Running command: blastn -query GCA_903940335.1_freshwater_MAG_---_Loc090907-1m_bin-040_genomic.fna/markers.fasta -db /var/lib/cwl/stg81f7d01f-fe9a-46af-a156-3d514183e106/dqc_reference/reference_markers_gtdb.fasta -out GCA_903940335.1_freshwater_MAG_---_Loc090907-1m_bin-040_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 06:44:05,398] [INFO] Task succeeded: Blastn
[2023-06-30 06:44:05,403] [INFO] Selected 9 target genomes.
[2023-06-30 06:44:05,403] [INFO] Target genome list was writen to GCA_903940335.1_freshwater_MAG_---_Loc090907-1m_bin-040_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 06:44:05,406] [INFO] Task started: fastANI
[2023-06-30 06:44:05,406] [INFO] Running command: fastANI --query /var/lib/cwl/stg40d4288f-8905-4286-a354-f56a80e7e441/GCA_903940335.1_freshwater_MAG_---_Loc090907-1m_bin-040_genomic.fna.gz --refList GCA_903940335.1_freshwater_MAG_---_Loc090907-1m_bin-040_genomic.fna/target_genomes_gtdb.txt --output GCA_903940335.1_freshwater_MAG_---_Loc090907-1m_bin-040_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 06:44:08,235] [INFO] Task succeeded: fastANI
[2023-06-30 06:44:08,248] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 06:44:08,248] [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_903937405.1	s__UBA2645 sp903937405	99.7372	439	450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__UBA1997;g__UBA2645	95.0	99.33	98.10	0.93	0.79	16	conclusive
GCA_903879805.1	s__UBA2645 sp903879805	79.2218	217	450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__UBA1997;g__UBA2645	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017999675.1	s__UBA2645 sp017999675	78.9265	190	450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__UBA1997;g__UBA2645	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903898475.1	s__UBA2645 sp903898475	78.6914	184	450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__UBA1997;g__UBA2645	95.0	99.93	99.93	0.95	0.95	2	-
GCA_002359655.1	s__UBA2645 sp002359655	78.1521	171	450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__UBA1997;g__UBA2645	95.0	99.96	99.93	0.97	0.95	3	-
GCA_018969185.1	s__UBA2645 sp018969185	77.7121	140	450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__UBA1997;g__UBA2645	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903959715.1	s__SYAR01 sp903959715	76.7353	79	450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__UBA1997;g__SYAR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016882165.1	s__UBA2645 sp016882165	76.6416	90	450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__UBA1997;g__UBA2645	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 06:44:08,250] [INFO] GTDB search result was written to GCA_903940335.1_freshwater_MAG_---_Loc090907-1m_bin-040_genomic.fna/result_gtdb.tsv
[2023-06-30 06:44:08,251] [INFO] ===== GTDB Search completed =====
[2023-06-30 06:44:08,253] [INFO] DFAST_QC result json was written to GCA_903940335.1_freshwater_MAG_---_Loc090907-1m_bin-040_genomic.fna/dqc_result.json
[2023-06-30 06:44:08,254] [INFO] DFAST_QC completed!
[2023-06-30 06:44:08,254] [INFO] Total running time: 0h0m44s