[2023-03-17 09:41:39,503] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:41:39,503] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:41:39,503] [INFO] DQC Reference Directory: /var/lib/cwl/stgd289fb35-4006-47ee-a76b-cff47dba823e/dqc_reference
[2023-03-17 09:41:40,720] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:41:40,720] [INFO] Task started: Prodigal
[2023-03-17 09:41:40,721] [INFO] Running command: cat /var/lib/cwl/stgff1f60c1-32a1-4534-ab62-c6c38e7c7eb0/OceanDNA-a4412.fa | prodigal -d OceanDNA-a4412/cds.fna -a OceanDNA-a4412/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:41:49,465] [INFO] Task succeeded: Prodigal
[2023-03-17 09:41:49,466] [INFO] Task started: HMMsearch
[2023-03-17 09:41:49,466] [INFO] Running command: hmmsearch --tblout OceanDNA-a4412/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd289fb35-4006-47ee-a76b-cff47dba823e/dqc_reference/reference_markers.hmm OceanDNA-a4412/protein.faa > /dev/null
[2023-03-17 09:41:49,617] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:41:49,617] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgff1f60c1-32a1-4534-ab62-c6c38e7c7eb0/OceanDNA-a4412.fa]
[2023-03-17 09:41:49,627] [INFO] Query marker FASTA was written to OceanDNA-a4412/markers.fasta
[2023-03-17 09:41:49,628] [INFO] Task started: Blastn
[2023-03-17 09:41:49,629] [INFO] Running command: blastn -query OceanDNA-a4412/markers.fasta -db /var/lib/cwl/stgd289fb35-4006-47ee-a76b-cff47dba823e/dqc_reference/reference_markers.fasta -out OceanDNA-a4412/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:41:50,236] [INFO] Task succeeded: Blastn
[2023-03-17 09:41:50,237] [INFO] Selected 3 target genomes.
[2023-03-17 09:41:50,237] [INFO] Target genome list was writen to OceanDNA-a4412/target_genomes.txt
[2023-03-17 09:41:50,245] [INFO] Task started: fastANI
[2023-03-17 09:41:50,245] [INFO] Running command: fastANI --query /var/lib/cwl/stgff1f60c1-32a1-4534-ab62-c6c38e7c7eb0/OceanDNA-a4412.fa --refList OceanDNA-a4412/target_genomes.txt --output OceanDNA-a4412/fastani_result.tsv --threads 1
[2023-03-17 09:41:52,486] [INFO] Task succeeded: fastANI
[2023-03-17 09:41:52,486] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd289fb35-4006-47ee-a76b-cff47dba823e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:41:52,486] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd289fb35-4006-47ee-a76b-cff47dba823e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:41:52,486] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:41:52,486] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 09:41:52,486] [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 09:41:52,487] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4412/tc_result.tsv
[2023-03-17 09:41:52,487] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:41:52,487] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:41:52,487] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd289fb35-4006-47ee-a76b-cff47dba823e/dqc_reference/checkm_data
[2023-03-17 09:41:52,578] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:41:52,581] [INFO] Task started: CheckM
[2023-03-17 09:41:52,581] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4412/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4412/checkm_input OceanDNA-a4412/checkm_result
[2023-03-17 09:42:21,661] [INFO] Task succeeded: CheckM
[2023-03-17 09:42:21,662] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.16%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 09:42:21,663] [INFO] ===== Completeness check finished =====
[2023-03-17 09:42:21,663] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:42:21,663] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4412/markers.fasta)
[2023-03-17 09:42:21,665] [INFO] Task started: Blastn
[2023-03-17 09:42:21,665] [INFO] Running command: blastn -query OceanDNA-a4412/markers.fasta -db /var/lib/cwl/stgd289fb35-4006-47ee-a76b-cff47dba823e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4412/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:42:22,553] [INFO] Task succeeded: Blastn
[2023-03-17 09:42:22,553] [INFO] Selected 8 target genomes.
[2023-03-17 09:42:22,553] [INFO] Target genome list was writen to OceanDNA-a4412/target_genomes_gtdb.txt
[2023-03-17 09:42:22,650] [INFO] Task started: fastANI
[2023-03-17 09:42:22,651] [INFO] Running command: fastANI --query /var/lib/cwl/stgff1f60c1-32a1-4534-ab62-c6c38e7c7eb0/OceanDNA-a4412.fa --refList OceanDNA-a4412/target_genomes_gtdb.txt --output OceanDNA-a4412/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:42:24,446] [INFO] Task succeeded: fastANI
[2023-03-17 09:42:24,450] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 09:42:24,450] [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_002722735.1	s__MGIIb-O3 sp002722735	99.6449	427	469	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	99.60	99.54	0.93	0.90	4	conclusive
GCA_003193925.1	s__Thalassarchaeum betae	77.46	99	469	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	99.52	98.11	0.96	0.90	6	-
GCA_004195715.1	s__Thalassarchaeum sp004195715	76.9697	68	469	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	99.87	99.86	0.95	0.94	3	-
GCA_002507125.1	s__Thalassarchaeum sp002507125	76.8809	63	469	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	98.54	98.42	0.77	0.74	3	-
GCA_002505325.1	s__Thalassarchaeum sp002505325	76.424	52	469	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 09:42:24,450] [INFO] GTDB search result was written to OceanDNA-a4412/result_gtdb.tsv
[2023-03-17 09:42:24,450] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:42:24,451] [INFO] DFAST_QC result json was written to OceanDNA-a4412/dqc_result.json
[2023-03-17 09:42:24,451] [INFO] DFAST_QC completed!
[2023-03-17 09:42:24,451] [INFO] Total running time: 0h0m45s