[2023-07-01 04:06:01,474] [INFO] DFAST_QC pipeline started.
[2023-07-01 04:06:01,478] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 04:06:01,479] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c4d8023-d0a6-4492-b672-6ed76f30b09e/dqc_reference
[2023-07-01 04:06:02,713] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 04:06:02,714] [INFO] Task started: Prodigal
[2023-07-01 04:06:02,714] [INFO] Running command: gunzip -c /var/lib/cwl/stg29b57a68-ff9f-44a7-aa58-e81df9681f74/GCA_903874305.1_freshwater_MAG_---_Erken-D11_bin-0113_genomic.fna.gz | prodigal -d GCA_903874305.1_freshwater_MAG_---_Erken-D11_bin-0113_genomic.fna/cds.fna -a GCA_903874305.1_freshwater_MAG_---_Erken-D11_bin-0113_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 04:06:03,990] [INFO] Task succeeded: Prodigal
[2023-07-01 04:06:03,990] [INFO] Task started: HMMsearch
[2023-07-01 04:06:03,991] [INFO] Running command: hmmsearch --tblout GCA_903874305.1_freshwater_MAG_---_Erken-D11_bin-0113_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c4d8023-d0a6-4492-b672-6ed76f30b09e/dqc_reference/reference_markers.hmm GCA_903874305.1_freshwater_MAG_---_Erken-D11_bin-0113_genomic.fna/protein.faa > /dev/null
[2023-07-01 04:06:04,140] [INFO] Task succeeded: HMMsearch
[2023-07-01 04:06:04,143] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg29b57a68-ff9f-44a7-aa58-e81df9681f74/GCA_903874305.1_freshwater_MAG_---_Erken-D11_bin-0113_genomic.fna.gz]
[2023-07-01 04:06:04,183] [INFO] Query marker FASTA was written to GCA_903874305.1_freshwater_MAG_---_Erken-D11_bin-0113_genomic.fna/markers.fasta
[2023-07-01 04:06:04,183] [INFO] Task started: Blastn
[2023-07-01 04:06:04,184] [INFO] Running command: blastn -query GCA_903874305.1_freshwater_MAG_---_Erken-D11_bin-0113_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c4d8023-d0a6-4492-b672-6ed76f30b09e/dqc_reference/reference_markers.fasta -out GCA_903874305.1_freshwater_MAG_---_Erken-D11_bin-0113_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 04:06:05,888] [INFO] Task succeeded: Blastn
[2023-07-01 04:06:05,891] [INFO] Selected 10 target genomes.
[2023-07-01 04:06:05,891] [INFO] Target genome list was writen to GCA_903874305.1_freshwater_MAG_---_Erken-D11_bin-0113_genomic.fna/target_genomes.txt
[2023-07-01 04:06:05,894] [INFO] Task started: fastANI
[2023-07-01 04:06:05,894] [INFO] Running command: fastANI --query /var/lib/cwl/stg29b57a68-ff9f-44a7-aa58-e81df9681f74/GCA_903874305.1_freshwater_MAG_---_Erken-D11_bin-0113_genomic.fna.gz --refList GCA_903874305.1_freshwater_MAG_---_Erken-D11_bin-0113_genomic.fna/target_genomes.txt --output GCA_903874305.1_freshwater_MAG_---_Erken-D11_bin-0113_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 04:06:08,770] [INFO] Task succeeded: fastANI
[2023-07-01 04:06:08,771] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c4d8023-d0a6-4492-b672-6ed76f30b09e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 04:06:08,771] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c4d8023-d0a6-4492-b672-6ed76f30b09e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 04:06:08,773] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 04:06:08,773] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-07-01 04:06:08,773] [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 04:06:08,774] [INFO] DFAST Taxonomy check result was written to GCA_903874305.1_freshwater_MAG_---_Erken-D11_bin-0113_genomic.fna/tc_result.tsv
[2023-07-01 04:06:08,775] [INFO] ===== Taxonomy check completed =====
[2023-07-01 04:06:08,775] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 04:06:08,775] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c4d8023-d0a6-4492-b672-6ed76f30b09e/dqc_reference/checkm_data
[2023-07-01 04:06:08,778] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 04:06:08,788] [INFO] Task started: CheckM
[2023-07-01 04:06:08,788] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903874305.1_freshwater_MAG_---_Erken-D11_bin-0113_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903874305.1_freshwater_MAG_---_Erken-D11_bin-0113_genomic.fna/checkm_input GCA_903874305.1_freshwater_MAG_---_Erken-D11_bin-0113_genomic.fna/checkm_result
[2023-07-01 04:06:20,959] [INFO] Task succeeded: CheckM
[2023-07-01 04:06:20,960] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 42.71%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 04:06:20,975] [INFO] ===== Completeness check finished =====
[2023-07-01 04:06:20,975] [INFO] ===== Start GTDB Search =====
[2023-07-01 04:06:20,975] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903874305.1_freshwater_MAG_---_Erken-D11_bin-0113_genomic.fna/markers.fasta)
[2023-07-01 04:06:20,975] [INFO] Task started: Blastn
[2023-07-01 04:06:20,976] [INFO] Running command: blastn -query GCA_903874305.1_freshwater_MAG_---_Erken-D11_bin-0113_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c4d8023-d0a6-4492-b672-6ed76f30b09e/dqc_reference/reference_markers_gtdb.fasta -out GCA_903874305.1_freshwater_MAG_---_Erken-D11_bin-0113_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 04:06:21,493] [INFO] Task succeeded: Blastn
[2023-07-01 04:06:21,497] [INFO] Selected 5 target genomes.
[2023-07-01 04:06:21,497] [INFO] Target genome list was writen to GCA_903874305.1_freshwater_MAG_---_Erken-D11_bin-0113_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 04:06:21,498] [INFO] Task started: fastANI
[2023-07-01 04:06:21,498] [INFO] Running command: fastANI --query /var/lib/cwl/stg29b57a68-ff9f-44a7-aa58-e81df9681f74/GCA_903874305.1_freshwater_MAG_---_Erken-D11_bin-0113_genomic.fna.gz --refList GCA_903874305.1_freshwater_MAG_---_Erken-D11_bin-0113_genomic.fna/target_genomes_gtdb.txt --output GCA_903874305.1_freshwater_MAG_---_Erken-D11_bin-0113_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 04:06:22,434] [INFO] Task succeeded: fastANI
[2023-07-01 04:06:22,440] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 04:06:22,440] [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
GCF_002288185.1	s__Planktophila vernalis	96.5852	62	63	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_010024385.1	s__Planktophila sp010024385	90.4862	63	63	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.43	99.35	0.91	0.87	13	-
GCA_002284895.1	s__Planktophila sp002284895	89.8137	61	63	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000378885.1	s__Planktophila sp000378885	88.1513	57	63	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	96.66	96.52	0.78	0.69	3	-
--------------------------------------------------------------------------------
[2023-07-01 04:06:22,442] [INFO] GTDB search result was written to GCA_903874305.1_freshwater_MAG_---_Erken-D11_bin-0113_genomic.fna/result_gtdb.tsv
[2023-07-01 04:06:22,442] [INFO] ===== GTDB Search completed =====
[2023-07-01 04:06:22,445] [INFO] DFAST_QC result json was written to GCA_903874305.1_freshwater_MAG_---_Erken-D11_bin-0113_genomic.fna/dqc_result.json
[2023-07-01 04:06:22,445] [INFO] DFAST_QC completed!
[2023-07-01 04:06:22,445] [INFO] Total running time: 0h0m21s