[2023-03-16 04:39:48,175] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:39:48,175] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:39:48,175] [INFO] DQC Reference Directory: /var/lib/cwl/stge1a1f6ea-1cd7-4b8d-9a10-2824c217aeb8/dqc_reference
[2023-03-16 04:39:49,275] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:39:49,275] [INFO] Task started: Prodigal
[2023-03-16 04:39:49,275] [INFO] Running command: cat /var/lib/cwl/stg5ae1f69a-5bb9-419d-a5b4-078e73157093/OceanDNA-b46897.fa | prodigal -d OceanDNA-b46897/cds.fna -a OceanDNA-b46897/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:40:01,302] [INFO] Task succeeded: Prodigal
[2023-03-16 04:40:01,303] [INFO] Task started: HMMsearch
[2023-03-16 04:40:01,303] [INFO] Running command: hmmsearch --tblout OceanDNA-b46897/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1a1f6ea-1cd7-4b8d-9a10-2824c217aeb8/dqc_reference/reference_markers.hmm OceanDNA-b46897/protein.faa > /dev/null
[2023-03-16 04:40:01,511] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:40:01,512] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg5ae1f69a-5bb9-419d-a5b4-078e73157093/OceanDNA-b46897.fa]
[2023-03-16 04:40:01,528] [INFO] Query marker FASTA was written to OceanDNA-b46897/markers.fasta
[2023-03-16 04:40:01,529] [INFO] Task started: Blastn
[2023-03-16 04:40:01,529] [INFO] Running command: blastn -query OceanDNA-b46897/markers.fasta -db /var/lib/cwl/stge1a1f6ea-1cd7-4b8d-9a10-2824c217aeb8/dqc_reference/reference_markers.fasta -out OceanDNA-b46897/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:40:01,975] [INFO] Task succeeded: Blastn
[2023-03-16 04:40:01,975] [INFO] Selected 10 target genomes.
[2023-03-16 04:40:01,976] [INFO] Target genome list was writen to OceanDNA-b46897/target_genomes.txt
[2023-03-16 04:40:01,981] [INFO] Task started: fastANI
[2023-03-16 04:40:01,981] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ae1f69a-5bb9-419d-a5b4-078e73157093/OceanDNA-b46897.fa --refList OceanDNA-b46897/target_genomes.txt --output OceanDNA-b46897/fastani_result.tsv --threads 1
[2023-03-16 04:40:08,663] [INFO] Task succeeded: fastANI
[2023-03-16 04:40:08,663] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1a1f6ea-1cd7-4b8d-9a10-2824c217aeb8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:40:08,664] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1a1f6ea-1cd7-4b8d-9a10-2824c217aeb8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:40:08,664] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:40:08,664] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 04:40:08,664] [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 04:40:08,664] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46897/tc_result.tsv
[2023-03-16 04:40:08,664] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:40:08,664] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:40:08,664] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1a1f6ea-1cd7-4b8d-9a10-2824c217aeb8/dqc_reference/checkm_data
[2023-03-16 04:40:08,667] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:40:08,670] [INFO] Task started: CheckM
[2023-03-16 04:40:08,671] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46897/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46897/checkm_input OceanDNA-b46897/checkm_result
[2023-03-16 04:40:44,513] [INFO] Task succeeded: CheckM
[2023-03-16 04:40:44,513] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.40%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:40:44,516] [INFO] ===== Completeness check finished =====
[2023-03-16 04:40:44,516] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:40:44,516] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46897/markers.fasta)
[2023-03-16 04:40:44,516] [INFO] Task started: Blastn
[2023-03-16 04:40:44,516] [INFO] Running command: blastn -query OceanDNA-b46897/markers.fasta -db /var/lib/cwl/stge1a1f6ea-1cd7-4b8d-9a10-2824c217aeb8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46897/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:40:44,954] [INFO] Task succeeded: Blastn
[2023-03-16 04:40:44,954] [INFO] Selected 12 target genomes.
[2023-03-16 04:40:44,954] [INFO] Target genome list was writen to OceanDNA-b46897/target_genomes_gtdb.txt
[2023-03-16 04:40:44,992] [INFO] Task started: fastANI
[2023-03-16 04:40:44,992] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ae1f69a-5bb9-419d-a5b4-078e73157093/OceanDNA-b46897.fa --refList OceanDNA-b46897/target_genomes_gtdb.txt --output OceanDNA-b46897/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:40:51,100] [INFO] Task succeeded: fastANI
[2023-03-16 04:40:51,102] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:40:51,102] [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_013041925.1	s__UBA985 sp013041925	77.4312	61	260	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA985	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-16 04:40:51,103] [INFO] GTDB search result was written to OceanDNA-b46897/result_gtdb.tsv
[2023-03-16 04:40:51,103] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:40:51,103] [INFO] DFAST_QC result json was written to OceanDNA-b46897/dqc_result.json
[2023-03-16 04:40:51,103] [INFO] DFAST_QC completed!
[2023-03-16 04:40:51,103] [INFO] Total running time: 0h1m3s