[2023-03-19 04:11:06,930] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:11:06,930] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:11:06,930] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb69275f-7a40-42af-8dd5-93f60da6ea8f/dqc_reference
[2023-03-19 04:11:08,645] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:11:08,645] [INFO] Task started: Prodigal
[2023-03-19 04:11:08,645] [INFO] Running command: cat /var/lib/cwl/stg6c726d9e-575a-480e-ac5e-d9d6415895f2/OceanDNA-b3096.fa | prodigal -d OceanDNA-b3096/cds.fna -a OceanDNA-b3096/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:11:14,461] [INFO] Task succeeded: Prodigal
[2023-03-19 04:11:14,462] [INFO] Task started: HMMsearch
[2023-03-19 04:11:14,462] [INFO] Running command: hmmsearch --tblout OceanDNA-b3096/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb69275f-7a40-42af-8dd5-93f60da6ea8f/dqc_reference/reference_markers.hmm OceanDNA-b3096/protein.faa > /dev/null
[2023-03-19 04:11:14,621] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:11:14,622] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg6c726d9e-575a-480e-ac5e-d9d6415895f2/OceanDNA-b3096.fa]
[2023-03-19 04:11:14,630] [INFO] Query marker FASTA was written to OceanDNA-b3096/markers.fasta
[2023-03-19 04:11:14,630] [INFO] Task started: Blastn
[2023-03-19 04:11:14,630] [INFO] Running command: blastn -query OceanDNA-b3096/markers.fasta -db /var/lib/cwl/stgbb69275f-7a40-42af-8dd5-93f60da6ea8f/dqc_reference/reference_markers.fasta -out OceanDNA-b3096/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:11:15,140] [INFO] Task succeeded: Blastn
[2023-03-19 04:11:15,141] [INFO] Selected 15 target genomes.
[2023-03-19 04:11:15,141] [INFO] Target genome list was writen to OceanDNA-b3096/target_genomes.txt
[2023-03-19 04:11:15,155] [INFO] Task started: fastANI
[2023-03-19 04:11:15,155] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c726d9e-575a-480e-ac5e-d9d6415895f2/OceanDNA-b3096.fa --refList OceanDNA-b3096/target_genomes.txt --output OceanDNA-b3096/fastani_result.tsv --threads 1
[2023-03-19 04:11:20,755] [INFO] Task succeeded: fastANI
[2023-03-19 04:11:20,756] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb69275f-7a40-42af-8dd5-93f60da6ea8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:11:20,756] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb69275f-7a40-42af-8dd5-93f60da6ea8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:11:20,756] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:11:20,756] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 04:11:20,756] [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
--------------------------------------------------------------------------------
[2023-03-19 04:11:20,757] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3096/tc_result.tsv
[2023-03-19 04:11:20,757] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:11:20,757] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:11:20,757] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb69275f-7a40-42af-8dd5-93f60da6ea8f/dqc_reference/checkm_data
[2023-03-19 04:11:20,760] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:11:20,762] [INFO] Task started: CheckM
[2023-03-19 04:11:20,763] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3096/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3096/checkm_input OceanDNA-b3096/checkm_result
[2023-03-19 04:11:41,333] [INFO] Task succeeded: CheckM
[2023-03-19 04:11:41,334] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.76%
Contamintation: 4.17%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-19 04:11:41,335] [INFO] ===== Completeness check finished =====
[2023-03-19 04:11:41,336] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:11:41,336] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3096/markers.fasta)
[2023-03-19 04:11:41,336] [INFO] Task started: Blastn
[2023-03-19 04:11:41,336] [INFO] Running command: blastn -query OceanDNA-b3096/markers.fasta -db /var/lib/cwl/stgbb69275f-7a40-42af-8dd5-93f60da6ea8f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3096/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:11:42,079] [INFO] Task succeeded: Blastn
[2023-03-19 04:11:42,080] [INFO] Selected 6 target genomes.
[2023-03-19 04:11:42,080] [INFO] Target genome list was writen to OceanDNA-b3096/target_genomes_gtdb.txt
[2023-03-19 04:11:42,163] [INFO] Task started: fastANI
[2023-03-19 04:11:42,163] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c726d9e-575a-480e-ac5e-d9d6415895f2/OceanDNA-b3096.fa --refList OceanDNA-b3096/target_genomes_gtdb.txt --output OceanDNA-b3096/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:11:43,778] [INFO] Task succeeded: fastANI
[2023-03-19 04:11:43,782] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 04:11:43,783] [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_010024385.1	s__Planktophila sp010024385	99.3436	297	339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.43	99.35	0.91	0.87	13	conclusive
GCA_005789205.1	s__Planktophila sp005789205	93.9775	224	339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002288185.1	s__Planktophila vernalis	91.3254	302	339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002284895.1	s__Planktophila sp002284895	88.9534	301	339	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	87.4465	266	339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	96.66	96.52	0.78	0.69	3	-
GCA_003569265.1	s__Planktophila sp003569265	85.97	164	339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.55	99.55	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-03-19 04:11:43,783] [INFO] GTDB search result was written to OceanDNA-b3096/result_gtdb.tsv
[2023-03-19 04:11:43,783] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:11:43,784] [INFO] DFAST_QC result json was written to OceanDNA-b3096/dqc_result.json
[2023-03-19 04:11:43,784] [INFO] DFAST_QC completed!
[2023-03-19 04:11:43,784] [INFO] Total running time: 0h0m37s