[2023-03-16 09:57:25,617] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:57:25,618] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:57:25,618] [INFO] DQC Reference Directory: /var/lib/cwl/stg0e6baee0-033b-4584-8bd3-f1854876149d/dqc_reference
[2023-03-16 09:57:26,724] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:57:26,725] [INFO] Task started: Prodigal
[2023-03-16 09:57:26,725] [INFO] Running command: cat /var/lib/cwl/stgf73d640e-1187-4e3b-99f9-50dc5bc2dc25/OceanDNA-a1524.fa | prodigal -d OceanDNA-a1524/cds.fna -a OceanDNA-a1524/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:57:30,157] [INFO] Task succeeded: Prodigal
[2023-03-16 09:57:30,157] [INFO] Task started: HMMsearch
[2023-03-16 09:57:30,157] [INFO] Running command: hmmsearch --tblout OceanDNA-a1524/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0e6baee0-033b-4584-8bd3-f1854876149d/dqc_reference/reference_markers.hmm OceanDNA-a1524/protein.faa > /dev/null
[2023-03-16 09:57:30,294] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:57:30,294] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgf73d640e-1187-4e3b-99f9-50dc5bc2dc25/OceanDNA-a1524.fa]
[2023-03-16 09:57:30,302] [INFO] Query marker FASTA was written to OceanDNA-a1524/markers.fasta
[2023-03-16 09:57:30,303] [INFO] Task started: Blastn
[2023-03-16 09:57:30,303] [INFO] Running command: blastn -query OceanDNA-a1524/markers.fasta -db /var/lib/cwl/stg0e6baee0-033b-4584-8bd3-f1854876149d/dqc_reference/reference_markers.fasta -out OceanDNA-a1524/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:57:30,931] [INFO] Task succeeded: Blastn
[2023-03-16 09:57:30,932] [INFO] Selected 5 target genomes.
[2023-03-16 09:57:30,932] [INFO] Target genome list was writen to OceanDNA-a1524/target_genomes.txt
[2023-03-16 09:57:30,938] [INFO] Task started: fastANI
[2023-03-16 09:57:30,939] [INFO] Running command: fastANI --query /var/lib/cwl/stgf73d640e-1187-4e3b-99f9-50dc5bc2dc25/OceanDNA-a1524.fa --refList OceanDNA-a1524/target_genomes.txt --output OceanDNA-a1524/fastani_result.tsv --threads 1
[2023-03-16 09:57:33,637] [INFO] Task succeeded: fastANI
[2023-03-16 09:57:33,638] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0e6baee0-033b-4584-8bd3-f1854876149d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:57:33,638] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0e6baee0-033b-4584-8bd3-f1854876149d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:57:33,638] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:57:33,638] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 09:57:33,638] [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 09:57:33,638] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1524/tc_result.tsv
[2023-03-16 09:57:33,638] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:57:33,638] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:57:33,639] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0e6baee0-033b-4584-8bd3-f1854876149d/dqc_reference/checkm_data
[2023-03-16 09:57:33,650] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:57:33,653] [INFO] Task started: CheckM
[2023-03-16 09:57:33,653] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1524/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1524/checkm_input OceanDNA-a1524/checkm_result
[2023-03-16 09:57:50,138] [INFO] Task succeeded: CheckM
[2023-03-16 09:57:50,139] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.75%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 09:57:50,140] [INFO] ===== Completeness check finished =====
[2023-03-16 09:57:50,140] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:57:50,141] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1524/markers.fasta)
[2023-03-16 09:57:50,142] [INFO] Task started: Blastn
[2023-03-16 09:57:50,142] [INFO] Running command: blastn -query OceanDNA-a1524/markers.fasta -db /var/lib/cwl/stg0e6baee0-033b-4584-8bd3-f1854876149d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1524/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:57:50,878] [INFO] Task succeeded: Blastn
[2023-03-16 09:57:50,879] [INFO] Selected 9 target genomes.
[2023-03-16 09:57:50,879] [INFO] Target genome list was writen to OceanDNA-a1524/target_genomes_gtdb.txt
[2023-03-16 09:57:50,885] [INFO] Task started: fastANI
[2023-03-16 09:57:50,885] [INFO] Running command: fastANI --query /var/lib/cwl/stgf73d640e-1187-4e3b-99f9-50dc5bc2dc25/OceanDNA-a1524.fa --refList OceanDNA-a1524/target_genomes_gtdb.txt --output OceanDNA-a1524/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:57:53,362] [INFO] Task succeeded: fastANI
[2023-03-16 09:57:53,364] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 09:57:53,365] [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_002506485.1	s__CG-Epi1 sp002506485	91.2645	151	191	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	99.64	99.58	0.87	0.83	4	-
GCA_015658585.1	s__CG-Epi1 sp015658585	90.2072	116	191	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 09:57:53,365] [INFO] GTDB search result was written to OceanDNA-a1524/result_gtdb.tsv
[2023-03-16 09:57:53,365] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:57:53,365] [INFO] DFAST_QC result json was written to OceanDNA-a1524/dqc_result.json
[2023-03-16 09:57:53,365] [INFO] DFAST_QC completed!
[2023-03-16 09:57:53,366] [INFO] Total running time: 0h0m28s