[2023-03-17 07:28:31,320] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:28:31,334] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:28:31,334] [INFO] DQC Reference Directory: /var/lib/cwl/stg46abcec8-a27e-4da5-92e2-b0213e957b6e/dqc_reference
[2023-03-17 07:28:33,083] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:28:33,084] [INFO] Task started: Prodigal
[2023-03-17 07:28:33,084] [INFO] Running command: cat /var/lib/cwl/stgf0e63487-c895-47f7-96a5-b434782b36b5/OceanDNA-a1536.fa | prodigal -d OceanDNA-a1536/cds.fna -a OceanDNA-a1536/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:28:36,933] [INFO] Task succeeded: Prodigal
[2023-03-17 07:28:36,933] [INFO] Task started: HMMsearch
[2023-03-17 07:28:36,933] [INFO] Running command: hmmsearch --tblout OceanDNA-a1536/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46abcec8-a27e-4da5-92e2-b0213e957b6e/dqc_reference/reference_markers.hmm OceanDNA-a1536/protein.faa > /dev/null
[2023-03-17 07:28:37,097] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:28:37,098] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgf0e63487-c895-47f7-96a5-b434782b36b5/OceanDNA-a1536.fa]
[2023-03-17 07:28:37,106] [INFO] Query marker FASTA was written to OceanDNA-a1536/markers.fasta
[2023-03-17 07:28:37,106] [INFO] Task started: Blastn
[2023-03-17 07:28:37,106] [INFO] Running command: blastn -query OceanDNA-a1536/markers.fasta -db /var/lib/cwl/stg46abcec8-a27e-4da5-92e2-b0213e957b6e/dqc_reference/reference_markers.fasta -out OceanDNA-a1536/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:28:38,577] [INFO] Task succeeded: Blastn
[2023-03-17 07:28:38,578] [INFO] Selected 8 target genomes.
[2023-03-17 07:28:38,578] [INFO] Target genome list was writen to OceanDNA-a1536/target_genomes.txt
[2023-03-17 07:28:38,584] [INFO] Task started: fastANI
[2023-03-17 07:28:38,584] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0e63487-c895-47f7-96a5-b434782b36b5/OceanDNA-a1536.fa --refList OceanDNA-a1536/target_genomes.txt --output OceanDNA-a1536/fastani_result.tsv --threads 1
[2023-03-17 07:28:42,380] [INFO] Task succeeded: fastANI
[2023-03-17 07:28:42,380] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46abcec8-a27e-4da5-92e2-b0213e957b6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:28:42,380] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46abcec8-a27e-4da5-92e2-b0213e957b6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:28:42,381] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:28:42,381] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 07:28:42,381] [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
--------------------------------------------------------------------------------
[2023-03-17 07:28:42,381] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1536/tc_result.tsv
[2023-03-17 07:28:42,381] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:28:42,381] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:28:42,381] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46abcec8-a27e-4da5-92e2-b0213e957b6e/dqc_reference/checkm_data
[2023-03-17 07:28:42,384] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:28:42,386] [INFO] Task started: CheckM
[2023-03-17 07:28:42,386] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1536/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1536/checkm_input OceanDNA-a1536/checkm_result
[2023-03-17 07:28:59,119] [INFO] Task succeeded: CheckM
[2023-03-17 07:28:59,119] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.95%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:28:59,121] [INFO] ===== Completeness check finished =====
[2023-03-17 07:28:59,121] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:28:59,121] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1536/markers.fasta)
[2023-03-17 07:28:59,121] [INFO] Task started: Blastn
[2023-03-17 07:28:59,121] [INFO] Running command: blastn -query OceanDNA-a1536/markers.fasta -db /var/lib/cwl/stg46abcec8-a27e-4da5-92e2-b0213e957b6e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1536/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:28:59,821] [INFO] Task succeeded: Blastn
[2023-03-17 07:28:59,822] [INFO] Selected 14 target genomes.
[2023-03-17 07:28:59,822] [INFO] Target genome list was writen to OceanDNA-a1536/target_genomes_gtdb.txt
[2023-03-17 07:29:00,360] [INFO] Task started: fastANI
[2023-03-17 07:29:00,360] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0e63487-c895-47f7-96a5-b434782b36b5/OceanDNA-a1536.fa --refList OceanDNA-a1536/target_genomes_gtdb.txt --output OceanDNA-a1536/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:29:05,545] [INFO] Task succeeded: fastANI
[2023-03-17 07:29:05,548] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 07:29:05,548] [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	78.0995	75	209	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_014240255.1	s__CG-Epi1 sp014240255	77.4974	50	209	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	-
--------------------------------------------------------------------------------
[2023-03-17 07:29:05,548] [INFO] GTDB search result was written to OceanDNA-a1536/result_gtdb.tsv
[2023-03-17 07:29:05,548] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:29:05,554] [INFO] DFAST_QC result json was written to OceanDNA-a1536/dqc_result.json
[2023-03-17 07:29:05,555] [INFO] DFAST_QC completed!
[2023-03-17 07:29:05,555] [INFO] Total running time: 0h0m34s