[2023-07-01 06:19:26,220] [INFO] DFAST_QC pipeline started.
[2023-07-01 06:19:26,222] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 06:19:26,222] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f0e3bca-95ee-4643-bbec-0f56b083c779/dqc_reference
[2023-07-01 06:19:28,121] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 06:19:28,122] [INFO] Task started: Prodigal
[2023-07-01 06:19:28,123] [INFO] Running command: gunzip -c /var/lib/cwl/stge8bf0bf6-9903-492d-9441-e38f1e0ed38e/GCA_903954175.1_freshwater_MAG_---_Loc090721-8-6m_bin-0083_genomic.fna.gz | prodigal -d GCA_903954175.1_freshwater_MAG_---_Loc090721-8-6m_bin-0083_genomic.fna/cds.fna -a GCA_903954175.1_freshwater_MAG_---_Loc090721-8-6m_bin-0083_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 06:19:35,438] [INFO] Task succeeded: Prodigal
[2023-07-01 06:19:35,439] [INFO] Task started: HMMsearch
[2023-07-01 06:19:35,439] [INFO] Running command: hmmsearch --tblout GCA_903954175.1_freshwater_MAG_---_Loc090721-8-6m_bin-0083_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f0e3bca-95ee-4643-bbec-0f56b083c779/dqc_reference/reference_markers.hmm GCA_903954175.1_freshwater_MAG_---_Loc090721-8-6m_bin-0083_genomic.fna/protein.faa > /dev/null
[2023-07-01 06:19:35,631] [INFO] Task succeeded: HMMsearch
[2023-07-01 06:19:35,632] [WARNING] Found 2/6 markers. [/var/lib/cwl/stge8bf0bf6-9903-492d-9441-e38f1e0ed38e/GCA_903954175.1_freshwater_MAG_---_Loc090721-8-6m_bin-0083_genomic.fna.gz]
[2023-07-01 06:19:35,654] [INFO] Query marker FASTA was written to GCA_903954175.1_freshwater_MAG_---_Loc090721-8-6m_bin-0083_genomic.fna/markers.fasta
[2023-07-01 06:19:35,655] [INFO] Task started: Blastn
[2023-07-01 06:19:35,655] [INFO] Running command: blastn -query GCA_903954175.1_freshwater_MAG_---_Loc090721-8-6m_bin-0083_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f0e3bca-95ee-4643-bbec-0f56b083c779/dqc_reference/reference_markers.fasta -out GCA_903954175.1_freshwater_MAG_---_Loc090721-8-6m_bin-0083_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 06:19:38,223] [INFO] Task succeeded: Blastn
[2023-07-01 06:19:38,227] [INFO] Selected 10 target genomes.
[2023-07-01 06:19:38,228] [INFO] Target genome list was writen to GCA_903954175.1_freshwater_MAG_---_Loc090721-8-6m_bin-0083_genomic.fna/target_genomes.txt
[2023-07-01 06:19:38,231] [INFO] Task started: fastANI
[2023-07-01 06:19:38,231] [INFO] Running command: fastANI --query /var/lib/cwl/stge8bf0bf6-9903-492d-9441-e38f1e0ed38e/GCA_903954175.1_freshwater_MAG_---_Loc090721-8-6m_bin-0083_genomic.fna.gz --refList GCA_903954175.1_freshwater_MAG_---_Loc090721-8-6m_bin-0083_genomic.fna/target_genomes.txt --output GCA_903954175.1_freshwater_MAG_---_Loc090721-8-6m_bin-0083_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 06:19:45,151] [INFO] Task succeeded: fastANI
[2023-07-01 06:19:45,151] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f0e3bca-95ee-4643-bbec-0f56b083c779/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 06:19:45,151] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f0e3bca-95ee-4643-bbec-0f56b083c779/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 06:19:45,154] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 06:19:45,154] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-07-01 06:19:45,154] [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
--------------------------------------------------------------------------------
[2023-07-01 06:19:45,156] [INFO] DFAST Taxonomy check result was written to GCA_903954175.1_freshwater_MAG_---_Loc090721-8-6m_bin-0083_genomic.fna/tc_result.tsv
[2023-07-01 06:19:45,157] [INFO] ===== Taxonomy check completed =====
[2023-07-01 06:19:45,157] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 06:19:45,157] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f0e3bca-95ee-4643-bbec-0f56b083c779/dqc_reference/checkm_data
[2023-07-01 06:19:45,160] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 06:19:45,186] [INFO] Task started: CheckM
[2023-07-01 06:19:45,187] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903954175.1_freshwater_MAG_---_Loc090721-8-6m_bin-0083_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903954175.1_freshwater_MAG_---_Loc090721-8-6m_bin-0083_genomic.fna/checkm_input GCA_903954175.1_freshwater_MAG_---_Loc090721-8-6m_bin-0083_genomic.fna/checkm_result
[2023-07-01 06:20:11,587] [INFO] Task succeeded: CheckM
[2023-07-01 06:20:11,588] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.31%
Contamintation: 6.25%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-07-01 06:20:11,610] [INFO] ===== Completeness check finished =====
[2023-07-01 06:20:11,611] [INFO] ===== Start GTDB Search =====
[2023-07-01 06:20:11,611] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903954175.1_freshwater_MAG_---_Loc090721-8-6m_bin-0083_genomic.fna/markers.fasta)
[2023-07-01 06:20:11,611] [INFO] Task started: Blastn
[2023-07-01 06:20:11,612] [INFO] Running command: blastn -query GCA_903954175.1_freshwater_MAG_---_Loc090721-8-6m_bin-0083_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f0e3bca-95ee-4643-bbec-0f56b083c779/dqc_reference/reference_markers_gtdb.fasta -out GCA_903954175.1_freshwater_MAG_---_Loc090721-8-6m_bin-0083_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 06:20:12,250] [INFO] Task succeeded: Blastn
[2023-07-01 06:20:12,255] [INFO] Selected 6 target genomes.
[2023-07-01 06:20:12,255] [INFO] Target genome list was writen to GCA_903954175.1_freshwater_MAG_---_Loc090721-8-6m_bin-0083_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 06:20:12,261] [INFO] Task started: fastANI
[2023-07-01 06:20:12,261] [INFO] Running command: fastANI --query /var/lib/cwl/stge8bf0bf6-9903-492d-9441-e38f1e0ed38e/GCA_903954175.1_freshwater_MAG_---_Loc090721-8-6m_bin-0083_genomic.fna.gz --refList GCA_903954175.1_freshwater_MAG_---_Loc090721-8-6m_bin-0083_genomic.fna/target_genomes_gtdb.txt --output GCA_903954175.1_freshwater_MAG_---_Loc090721-8-6m_bin-0083_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 06:20:14,338] [INFO] Task succeeded: fastANI
[2023-07-01 06:20:14,350] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-07-01 06:20:14,350] [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_004293385.1	s__UBA953 sp004293385	91.1068	124	243	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	89.1125	220	243	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005798925.1	s__UBA953 sp005798925	86.4394	185	243	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903913915.1	s__UBA953 sp903913915	84.7886	203	243	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	99.51	99.16	0.93	0.89	3	-
GCA_009917805.1	s__UBA953 sp009917805	84.6362	159	243	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003569245.1	s__UBA953 sp003569245	81.868	175	243	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 06:20:14,352] [INFO] GTDB search result was written to GCA_903954175.1_freshwater_MAG_---_Loc090721-8-6m_bin-0083_genomic.fna/result_gtdb.tsv
[2023-07-01 06:20:14,353] [INFO] ===== GTDB Search completed =====
[2023-07-01 06:20:14,355] [INFO] DFAST_QC result json was written to GCA_903954175.1_freshwater_MAG_---_Loc090721-8-6m_bin-0083_genomic.fna/dqc_result.json
[2023-07-01 06:20:14,355] [INFO] DFAST_QC completed!
[2023-07-01 06:20:14,355] [INFO] Total running time: 0h0m48s