[2023-03-16 04:39:48,760] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:39:48,760] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:39:48,760] [INFO] DQC Reference Directory: /var/lib/cwl/stgd141f000-772e-4a36-9039-1f4667082dd1/dqc_reference
[2023-03-16 04:39:49,840] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:39:49,840] [INFO] Task started: Prodigal
[2023-03-16 04:39:49,841] [INFO] Running command: cat /var/lib/cwl/stg9163ad1d-7d33-46b4-b216-2565ea4f67c3/OceanDNA-b3082.fa | prodigal -d OceanDNA-b3082/cds.fna -a OceanDNA-b3082/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:39:54,008] [INFO] Task succeeded: Prodigal
[2023-03-16 04:39:54,008] [INFO] Task started: HMMsearch
[2023-03-16 04:39:54,008] [INFO] Running command: hmmsearch --tblout OceanDNA-b3082/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd141f000-772e-4a36-9039-1f4667082dd1/dqc_reference/reference_markers.hmm OceanDNA-b3082/protein.faa > /dev/null
[2023-03-16 04:39:54,159] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:39:54,160] [INFO] Found 6/6 markers.
[2023-03-16 04:39:54,168] [INFO] Query marker FASTA was written to OceanDNA-b3082/markers.fasta
[2023-03-16 04:39:54,170] [INFO] Task started: Blastn
[2023-03-16 04:39:54,170] [INFO] Running command: blastn -query OceanDNA-b3082/markers.fasta -db /var/lib/cwl/stgd141f000-772e-4a36-9039-1f4667082dd1/dqc_reference/reference_markers.fasta -out OceanDNA-b3082/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:39:54,721] [INFO] Task succeeded: Blastn
[2023-03-16 04:39:54,721] [INFO] Selected 25 target genomes.
[2023-03-16 04:39:54,722] [INFO] Target genome list was writen to OceanDNA-b3082/target_genomes.txt
[2023-03-16 04:39:54,733] [INFO] Task started: fastANI
[2023-03-16 04:39:54,733] [INFO] Running command: fastANI --query /var/lib/cwl/stg9163ad1d-7d33-46b4-b216-2565ea4f67c3/OceanDNA-b3082.fa --refList OceanDNA-b3082/target_genomes.txt --output OceanDNA-b3082/fastani_result.tsv --threads 1
[2023-03-16 04:40:07,913] [INFO] Task succeeded: fastANI
[2023-03-16 04:40:07,913] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd141f000-772e-4a36-9039-1f4667082dd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:40:07,913] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd141f000-772e-4a36-9039-1f4667082dd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:40:07,914] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:40:07,914] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 04:40:07,914] [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
--------------------------------------------------------------------------------
[2023-03-16 04:40:07,914] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3082/tc_result.tsv
[2023-03-16 04:40:07,914] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:40:07,914] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:40:07,914] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd141f000-772e-4a36-9039-1f4667082dd1/dqc_reference/checkm_data
[2023-03-16 04:40:07,917] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:40:07,980] [INFO] Task started: CheckM
[2023-03-16 04:40:07,980] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3082/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3082/checkm_input OceanDNA-b3082/checkm_result
[2023-03-16 04:40:24,807] [INFO] Task succeeded: CheckM
[2023-03-16 04:40:24,808] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.74%
Contamintation: 1.04%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-16 04:40:24,809] [INFO] ===== Completeness check finished =====
[2023-03-16 04:40:24,810] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:40:24,810] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3082/markers.fasta)
[2023-03-16 04:40:24,810] [INFO] Task started: Blastn
[2023-03-16 04:40:24,810] [INFO] Running command: blastn -query OceanDNA-b3082/markers.fasta -db /var/lib/cwl/stgd141f000-772e-4a36-9039-1f4667082dd1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3082/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:40:25,513] [INFO] Task succeeded: Blastn
[2023-03-16 04:40:25,513] [INFO] Selected 21 target genomes.
[2023-03-16 04:40:25,513] [INFO] Target genome list was writen to OceanDNA-b3082/target_genomes_gtdb.txt
[2023-03-16 04:40:25,536] [INFO] Task started: fastANI
[2023-03-16 04:40:25,536] [INFO] Running command: fastANI --query /var/lib/cwl/stg9163ad1d-7d33-46b4-b216-2565ea4f67c3/OceanDNA-b3082.fa --refList OceanDNA-b3082/target_genomes_gtdb.txt --output OceanDNA-b3082/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:40:29,587] [INFO] Task succeeded: fastANI
[2023-03-16 04:40:29,590] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 04:40:29,590] [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_017858325.1	s__Planktophila sp017858325	98.6329	184	196	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_009702965.1	s__Planktophila sp009702965	81.9745	115	196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009703165.1	s__Planktophila sp009703165	78.7659	64	196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:40:29,590] [INFO] GTDB search result was written to OceanDNA-b3082/result_gtdb.tsv
[2023-03-16 04:40:29,590] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:40:29,591] [INFO] DFAST_QC result json was written to OceanDNA-b3082/dqc_result.json
[2023-03-16 04:40:29,591] [INFO] DFAST_QC completed!
[2023-03-16 04:40:29,591] [INFO] Total running time: 0h0m41s