[2023-03-17 09:59:00,947] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:59:00,950] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:59:00,950] [INFO] DQC Reference Directory: /var/lib/cwl/stgd9d13421-546c-49a3-9b19-411be3b2e255/dqc_reference
[2023-03-17 09:59:02,045] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:59:02,045] [INFO] Task started: Prodigal
[2023-03-17 09:59:02,045] [INFO] Running command: cat /var/lib/cwl/stg26115e9f-8c46-4816-9faf-69b33c66e8bd/OceanDNA-b5279.fa | prodigal -d OceanDNA-b5279/cds.fna -a OceanDNA-b5279/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:59:14,936] [INFO] Task succeeded: Prodigal
[2023-03-17 09:59:14,936] [INFO] Task started: HMMsearch
[2023-03-17 09:59:14,936] [INFO] Running command: hmmsearch --tblout OceanDNA-b5279/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd9d13421-546c-49a3-9b19-411be3b2e255/dqc_reference/reference_markers.hmm OceanDNA-b5279/protein.faa > /dev/null
[2023-03-17 09:59:15,122] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:59:15,123] [INFO] Found 6/6 markers.
[2023-03-17 09:59:15,159] [INFO] Query marker FASTA was written to OceanDNA-b5279/markers.fasta
[2023-03-17 09:59:15,160] [INFO] Task started: Blastn
[2023-03-17 09:59:15,160] [INFO] Running command: blastn -query OceanDNA-b5279/markers.fasta -db /var/lib/cwl/stgd9d13421-546c-49a3-9b19-411be3b2e255/dqc_reference/reference_markers.fasta -out OceanDNA-b5279/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:59:15,735] [INFO] Task succeeded: Blastn
[2023-03-17 09:59:15,743] [INFO] Selected 26 target genomes.
[2023-03-17 09:59:15,744] [INFO] Target genome list was writen to OceanDNA-b5279/target_genomes.txt
[2023-03-17 09:59:15,940] [INFO] Task started: fastANI
[2023-03-17 09:59:15,940] [INFO] Running command: fastANI --query /var/lib/cwl/stg26115e9f-8c46-4816-9faf-69b33c66e8bd/OceanDNA-b5279.fa --refList OceanDNA-b5279/target_genomes.txt --output OceanDNA-b5279/fastani_result.tsv --threads 1
[2023-03-17 09:59:30,856] [INFO] Task succeeded: fastANI
[2023-03-17 09:59:30,856] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd9d13421-546c-49a3-9b19-411be3b2e255/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:59:30,856] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd9d13421-546c-49a3-9b19-411be3b2e255/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:59:30,856] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:59:30,856] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 09:59:30,857] [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 09:59:30,860] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5279/tc_result.tsv
[2023-03-17 09:59:30,867] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:59:30,867] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:59:30,867] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd9d13421-546c-49a3-9b19-411be3b2e255/dqc_reference/checkm_data
[2023-03-17 09:59:30,869] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:59:30,945] [INFO] Task started: CheckM
[2023-03-17 09:59:30,945] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5279/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5279/checkm_input OceanDNA-b5279/checkm_result
[2023-03-17 10:00:08,651] [INFO] Task succeeded: CheckM
[2023-03-17 10:00:08,651] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.57%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 10:00:08,780] [INFO] ===== Completeness check finished =====
[2023-03-17 10:00:08,780] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:00:08,780] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5279/markers.fasta)
[2023-03-17 10:00:08,781] [INFO] Task started: Blastn
[2023-03-17 10:00:08,781] [INFO] Running command: blastn -query OceanDNA-b5279/markers.fasta -db /var/lib/cwl/stgd9d13421-546c-49a3-9b19-411be3b2e255/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5279/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:00:09,704] [INFO] Task succeeded: Blastn
[2023-03-17 10:00:09,712] [INFO] Selected 23 target genomes.
[2023-03-17 10:00:09,712] [INFO] Target genome list was writen to OceanDNA-b5279/target_genomes_gtdb.txt
[2023-03-17 10:00:10,079] [INFO] Task started: fastANI
[2023-03-17 10:00:10,079] [INFO] Running command: fastANI --query /var/lib/cwl/stg26115e9f-8c46-4816-9faf-69b33c66e8bd/OceanDNA-b5279.fa --refList OceanDNA-b5279/target_genomes_gtdb.txt --output OceanDNA-b5279/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:00:21,662] [INFO] Task succeeded: fastANI
[2023-03-17 10:00:21,664] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 10:00:21,664] [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_006226555.1	s__SZUA-381 sp006226555	76.2038	51	537	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__SZUA-381	95.0	98.73	98.73	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-03-17 10:00:21,667] [INFO] GTDB search result was written to OceanDNA-b5279/result_gtdb.tsv
[2023-03-17 10:00:21,672] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:00:21,677] [INFO] DFAST_QC result json was written to OceanDNA-b5279/dqc_result.json
[2023-03-17 10:00:21,677] [INFO] DFAST_QC completed!
[2023-03-17 10:00:21,677] [INFO] Total running time: 0h1m21s