[2023-03-15 17:46:31,747] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:46:31,747] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:46:31,748] [INFO] DQC Reference Directory: /var/lib/cwl/stg034bbd6b-4d01-462f-bc3b-6b414c2b14c0/dqc_reference
[2023-03-15 17:46:32,849] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:46:32,849] [INFO] Task started: Prodigal
[2023-03-15 17:46:32,849] [INFO] Running command: cat /var/lib/cwl/stg84d20bbb-9cc1-4f5c-8c39-764a4dbe16cb/OceanDNA-a4987.fa | prodigal -d OceanDNA-a4987/cds.fna -a OceanDNA-a4987/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:46:38,801] [INFO] Task succeeded: Prodigal
[2023-03-15 17:46:38,802] [INFO] Task started: HMMsearch
[2023-03-15 17:46:38,802] [INFO] Running command: hmmsearch --tblout OceanDNA-a4987/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg034bbd6b-4d01-462f-bc3b-6b414c2b14c0/dqc_reference/reference_markers.hmm OceanDNA-a4987/protein.faa > /dev/null
[2023-03-15 17:46:38,966] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:46:38,966] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg84d20bbb-9cc1-4f5c-8c39-764a4dbe16cb/OceanDNA-a4987.fa]
[2023-03-15 17:46:38,977] [INFO] Query marker FASTA was written to OceanDNA-a4987/markers.fasta
[2023-03-15 17:46:38,979] [INFO] Task started: Blastn
[2023-03-15 17:46:38,979] [INFO] Running command: blastn -query OceanDNA-a4987/markers.fasta -db /var/lib/cwl/stg034bbd6b-4d01-462f-bc3b-6b414c2b14c0/dqc_reference/reference_markers.fasta -out OceanDNA-a4987/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:46:39,452] [INFO] Task succeeded: Blastn
[2023-03-15 17:46:39,453] [INFO] Selected 5 target genomes.
[2023-03-15 17:46:39,454] [INFO] Target genome list was writen to OceanDNA-a4987/target_genomes.txt
[2023-03-15 17:46:39,460] [INFO] Task started: fastANI
[2023-03-15 17:46:39,461] [INFO] Running command: fastANI --query /var/lib/cwl/stg84d20bbb-9cc1-4f5c-8c39-764a4dbe16cb/OceanDNA-a4987.fa --refList OceanDNA-a4987/target_genomes.txt --output OceanDNA-a4987/fastani_result.tsv --threads 1
[2023-03-15 17:46:42,666] [INFO] Task succeeded: fastANI
[2023-03-15 17:46:42,666] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg034bbd6b-4d01-462f-bc3b-6b414c2b14c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:46:42,666] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg034bbd6b-4d01-462f-bc3b-6b414c2b14c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:46:42,666] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:46:42,666] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 17:46:42,666] [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
--------------------------------------------------------------------------------
[2023-03-15 17:46:42,668] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4987/tc_result.tsv
[2023-03-15 17:46:42,668] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:46:42,669] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:46:42,669] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg034bbd6b-4d01-462f-bc3b-6b414c2b14c0/dqc_reference/checkm_data
[2023-03-15 17:46:42,679] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:46:42,683] [INFO] Task started: CheckM
[2023-03-15 17:46:42,683] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4987/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4987/checkm_input OceanDNA-a4987/checkm_result
[2023-03-15 17:47:04,349] [INFO] Task succeeded: CheckM
[2023-03-15 17:47:04,349] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.40%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 17:47:04,352] [INFO] ===== Completeness check finished =====
[2023-03-15 17:47:04,353] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:47:04,353] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4987/markers.fasta)
[2023-03-15 17:47:04,354] [INFO] Task started: Blastn
[2023-03-15 17:47:04,354] [INFO] Running command: blastn -query OceanDNA-a4987/markers.fasta -db /var/lib/cwl/stg034bbd6b-4d01-462f-bc3b-6b414c2b14c0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4987/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:47:04,937] [INFO] Task succeeded: Blastn
[2023-03-15 17:47:04,940] [INFO] Selected 7 target genomes.
[2023-03-15 17:47:04,940] [INFO] Target genome list was writen to OceanDNA-a4987/target_genomes_gtdb.txt
[2023-03-15 17:47:04,973] [INFO] Task started: fastANI
[2023-03-15 17:47:04,973] [INFO] Running command: fastANI --query /var/lib/cwl/stg84d20bbb-9cc1-4f5c-8c39-764a4dbe16cb/OceanDNA-a4987.fa --refList OceanDNA-a4987/target_genomes_gtdb.txt --output OceanDNA-a4987/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:47:06,743] [INFO] Task succeeded: fastANI
[2023-03-15 17:47:06,748] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 17:47:06,748] [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_002457605.1	s__Thalassarchaeum sp002457605	99.3319	254	326	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002505325.1	s__Thalassarchaeum sp002505325	91.7695	240	326	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002495735.1	s__Thalassarchaeum sp002495735	88.823	231	326	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004195715.1	s__Thalassarchaeum sp004195715	88.4134	297	326	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	99.87	99.86	0.95	0.94	3	-
GCA_014240285.1	s__Thalassarchaeum sp014240285	84.6616	251	326	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002507125.1	s__Thalassarchaeum sp002507125	78.6493	126	326	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	98.54	98.42	0.77	0.74	3	-
GCA_002501885.1	s__Thalassarchaeum sp002501885	76.9668	53	326	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	98.85	97.05	0.83	0.68	9	-
--------------------------------------------------------------------------------
[2023-03-15 17:47:06,749] [INFO] GTDB search result was written to OceanDNA-a4987/result_gtdb.tsv
[2023-03-15 17:47:06,751] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:47:06,752] [INFO] DFAST_QC result json was written to OceanDNA-a4987/dqc_result.json
[2023-03-15 17:47:06,753] [INFO] DFAST_QC completed!
[2023-03-15 17:47:06,753] [INFO] Total running time: 0h0m35s