[2023-06-30 11:12:24,852] [INFO] DFAST_QC pipeline started.
[2023-06-30 11:12:24,855] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 11:12:24,855] [INFO] DQC Reference Directory: /var/lib/cwl/stg964f58ac-fb33-4395-aa0f-2bdaf12371ed/dqc_reference
[2023-06-30 11:12:26,113] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 11:12:26,114] [INFO] Task started: Prodigal
[2023-06-30 11:12:26,114] [INFO] Running command: gunzip -c /var/lib/cwl/stged9bd64f-6694-46aa-9430-068f301bf1f4/GCA_903933405.1_freshwater_MAG_---_Loc090721-4m_bin-0804_genomic.fna.gz | prodigal -d GCA_903933405.1_freshwater_MAG_---_Loc090721-4m_bin-0804_genomic.fna/cds.fna -a GCA_903933405.1_freshwater_MAG_---_Loc090721-4m_bin-0804_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 11:12:33,924] [INFO] Task succeeded: Prodigal
[2023-06-30 11:12:33,925] [INFO] Task started: HMMsearch
[2023-06-30 11:12:33,925] [INFO] Running command: hmmsearch --tblout GCA_903933405.1_freshwater_MAG_---_Loc090721-4m_bin-0804_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg964f58ac-fb33-4395-aa0f-2bdaf12371ed/dqc_reference/reference_markers.hmm GCA_903933405.1_freshwater_MAG_---_Loc090721-4m_bin-0804_genomic.fna/protein.faa > /dev/null
[2023-06-30 11:12:34,108] [INFO] Task succeeded: HMMsearch
[2023-06-30 11:12:34,110] [WARNING] Found 3/6 markers. [/var/lib/cwl/stged9bd64f-6694-46aa-9430-068f301bf1f4/GCA_903933405.1_freshwater_MAG_---_Loc090721-4m_bin-0804_genomic.fna.gz]
[2023-06-30 11:12:34,147] [INFO] Query marker FASTA was written to GCA_903933405.1_freshwater_MAG_---_Loc090721-4m_bin-0804_genomic.fna/markers.fasta
[2023-06-30 11:12:34,148] [INFO] Task started: Blastn
[2023-06-30 11:12:34,148] [INFO] Running command: blastn -query GCA_903933405.1_freshwater_MAG_---_Loc090721-4m_bin-0804_genomic.fna/markers.fasta -db /var/lib/cwl/stg964f58ac-fb33-4395-aa0f-2bdaf12371ed/dqc_reference/reference_markers.fasta -out GCA_903933405.1_freshwater_MAG_---_Loc090721-4m_bin-0804_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 11:12:34,756] [INFO] Task succeeded: Blastn
[2023-06-30 11:12:34,760] [INFO] Selected 15 target genomes.
[2023-06-30 11:12:34,760] [INFO] Target genome list was writen to GCA_903933405.1_freshwater_MAG_---_Loc090721-4m_bin-0804_genomic.fna/target_genomes.txt
[2023-06-30 11:12:34,763] [INFO] Task started: fastANI
[2023-06-30 11:12:34,764] [INFO] Running command: fastANI --query /var/lib/cwl/stged9bd64f-6694-46aa-9430-068f301bf1f4/GCA_903933405.1_freshwater_MAG_---_Loc090721-4m_bin-0804_genomic.fna.gz --refList GCA_903933405.1_freshwater_MAG_---_Loc090721-4m_bin-0804_genomic.fna/target_genomes.txt --output GCA_903933405.1_freshwater_MAG_---_Loc090721-4m_bin-0804_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 11:12:45,841] [INFO] Task succeeded: fastANI
[2023-06-30 11:12:45,842] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg964f58ac-fb33-4395-aa0f-2bdaf12371ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 11:12:45,842] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg964f58ac-fb33-4395-aa0f-2bdaf12371ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 11:12:45,844] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 11:12:45,844] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 11:12:45,844] [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 11:12:45,846] [INFO] DFAST Taxonomy check result was written to GCA_903933405.1_freshwater_MAG_---_Loc090721-4m_bin-0804_genomic.fna/tc_result.tsv
[2023-06-30 11:12:45,847] [INFO] ===== Taxonomy check completed =====
[2023-06-30 11:12:45,847] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 11:12:45,847] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg964f58ac-fb33-4395-aa0f-2bdaf12371ed/dqc_reference/checkm_data
[2023-06-30 11:12:45,850] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 11:12:45,873] [INFO] Task started: CheckM
[2023-06-30 11:12:45,874] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903933405.1_freshwater_MAG_---_Loc090721-4m_bin-0804_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903933405.1_freshwater_MAG_---_Loc090721-4m_bin-0804_genomic.fna/checkm_input GCA_903933405.1_freshwater_MAG_---_Loc090721-4m_bin-0804_genomic.fna/checkm_result
[2023-06-30 11:13:12,073] [INFO] Task succeeded: CheckM
[2023-06-30 11:13:12,074] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.54%
Contamintation: 4.63%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 11:13:12,097] [INFO] ===== Completeness check finished =====
[2023-06-30 11:13:12,098] [INFO] ===== Start GTDB Search =====
[2023-06-30 11:13:12,098] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903933405.1_freshwater_MAG_---_Loc090721-4m_bin-0804_genomic.fna/markers.fasta)
[2023-06-30 11:13:12,098] [INFO] Task started: Blastn
[2023-06-30 11:13:12,099] [INFO] Running command: blastn -query GCA_903933405.1_freshwater_MAG_---_Loc090721-4m_bin-0804_genomic.fna/markers.fasta -db /var/lib/cwl/stg964f58ac-fb33-4395-aa0f-2bdaf12371ed/dqc_reference/reference_markers_gtdb.fasta -out GCA_903933405.1_freshwater_MAG_---_Loc090721-4m_bin-0804_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 11:13:12,931] [INFO] Task succeeded: Blastn
[2023-06-30 11:13:12,936] [INFO] Selected 9 target genomes.
[2023-06-30 11:13:12,936] [INFO] Target genome list was writen to GCA_903933405.1_freshwater_MAG_---_Loc090721-4m_bin-0804_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 11:13:12,941] [INFO] Task started: fastANI
[2023-06-30 11:13:12,941] [INFO] Running command: fastANI --query /var/lib/cwl/stged9bd64f-6694-46aa-9430-068f301bf1f4/GCA_903933405.1_freshwater_MAG_---_Loc090721-4m_bin-0804_genomic.fna.gz --refList GCA_903933405.1_freshwater_MAG_---_Loc090721-4m_bin-0804_genomic.fna/target_genomes_gtdb.txt --output GCA_903933405.1_freshwater_MAG_---_Loc090721-4m_bin-0804_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 11:13:15,742] [INFO] Task succeeded: fastANI
[2023-06-30 11:13:15,750] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 11:13:15,751] [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_903882335.1	s__UBA953 sp903882335	97.2308	169	186	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	98.91	98.33	0.83	0.81	7	conclusive
GCA_003569245.1	s__UBA953 sp003569245	94.635	179	186	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014193315.1	s__UBA953 sp003569405	84.5947	163	186	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	97.72	96.62	0.94	0.91	4	-
GCA_004293385.1	s__UBA953 sp004293385	83.4015	70	186	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871725.1	s__UBA953 sp016871725	83.0121	135	186	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009924535.1	s__UBA953 sp009924535	81.8724	101	186	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009917805.1	s__UBA953 sp009917805	81.7085	103	186	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903853185.1	s__UBA953 sp903853185	81.5878	83	186	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	98.54	98.54	0.77	0.77	2	-
GCA_003569165.1	s__UBA953 sp003569165	81.3351	116	186	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 11:13:15,753] [INFO] GTDB search result was written to GCA_903933405.1_freshwater_MAG_---_Loc090721-4m_bin-0804_genomic.fna/result_gtdb.tsv
[2023-06-30 11:13:15,754] [INFO] ===== GTDB Search completed =====
[2023-06-30 11:13:15,758] [INFO] DFAST_QC result json was written to GCA_903933405.1_freshwater_MAG_---_Loc090721-4m_bin-0804_genomic.fna/dqc_result.json
[2023-06-30 11:13:15,759] [INFO] DFAST_QC completed!
[2023-06-30 11:13:15,759] [INFO] Total running time: 0h0m51s