[2023-03-17 22:54:20,717] [INFO] DFAST_QC pipeline started.
[2023-03-17 22:54:20,718] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 22:54:20,718] [INFO] DQC Reference Directory: /var/lib/cwl/stg6494215d-9f01-4641-803e-bf4017b24b0a/dqc_reference
[2023-03-17 22:54:21,830] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 22:54:21,830] [INFO] Task started: Prodigal
[2023-03-17 22:54:21,830] [INFO] Running command: cat /var/lib/cwl/stg249c6f1b-b624-4034-b53d-2e72ff15e665/OceanDNA-a4201.fa | prodigal -d OceanDNA-a4201/cds.fna -a OceanDNA-a4201/protein.faa -g 11 -q > /dev/null
[2023-03-17 22:54:26,344] [INFO] Task succeeded: Prodigal
[2023-03-17 22:54:26,345] [INFO] Task started: HMMsearch
[2023-03-17 22:54:26,345] [INFO] Running command: hmmsearch --tblout OceanDNA-a4201/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6494215d-9f01-4641-803e-bf4017b24b0a/dqc_reference/reference_markers.hmm OceanDNA-a4201/protein.faa > /dev/null
[2023-03-17 22:54:26,459] [INFO] Task succeeded: HMMsearch
[2023-03-17 22:54:26,459] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg249c6f1b-b624-4034-b53d-2e72ff15e665/OceanDNA-a4201.fa]
[2023-03-17 22:54:26,467] [INFO] Query marker FASTA was written to OceanDNA-a4201/markers.fasta
[2023-03-17 22:54:26,467] [INFO] Task started: Blastn
[2023-03-17 22:54:26,467] [INFO] Running command: blastn -query OceanDNA-a4201/markers.fasta -db /var/lib/cwl/stg6494215d-9f01-4641-803e-bf4017b24b0a/dqc_reference/reference_markers.fasta -out OceanDNA-a4201/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:54:26,895] [INFO] Task succeeded: Blastn
[2023-03-17 22:54:26,896] [INFO] Selected 1 target genomes.
[2023-03-17 22:54:26,896] [INFO] Target genome list was writen to OceanDNA-a4201/target_genomes.txt
[2023-03-17 22:54:26,897] [INFO] Task started: fastANI
[2023-03-17 22:54:26,897] [INFO] Running command: fastANI --query /var/lib/cwl/stg249c6f1b-b624-4034-b53d-2e72ff15e665/OceanDNA-a4201.fa --refList OceanDNA-a4201/target_genomes.txt --output OceanDNA-a4201/fastani_result.tsv --threads 1
[2023-03-17 22:54:27,476] [INFO] Task succeeded: fastANI
[2023-03-17 22:54:27,476] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6494215d-9f01-4641-803e-bf4017b24b0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 22:54:27,476] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6494215d-9f01-4641-803e-bf4017b24b0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 22:54:27,476] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 22:54:27,476] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 22:54:27,477] [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 22:54:27,477] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4201/tc_result.tsv
[2023-03-17 22:54:27,477] [INFO] ===== Taxonomy check completed =====
[2023-03-17 22:54:27,477] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 22:54:27,477] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6494215d-9f01-4641-803e-bf4017b24b0a/dqc_reference/checkm_data
[2023-03-17 22:54:27,480] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 22:54:27,482] [INFO] Task started: CheckM
[2023-03-17 22:54:27,482] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4201/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4201/checkm_input OceanDNA-a4201/checkm_result
[2023-03-17 22:54:44,799] [INFO] Task succeeded: CheckM
[2023-03-17 22:54:44,800] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.90%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 22:54:44,801] [INFO] ===== Completeness check finished =====
[2023-03-17 22:54:44,802] [INFO] ===== Start GTDB Search =====
[2023-03-17 22:54:44,802] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4201/markers.fasta)
[2023-03-17 22:54:44,803] [INFO] Task started: Blastn
[2023-03-17 22:54:44,803] [INFO] Running command: blastn -query OceanDNA-a4201/markers.fasta -db /var/lib/cwl/stg6494215d-9f01-4641-803e-bf4017b24b0a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4201/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:54:45,250] [INFO] Task succeeded: Blastn
[2023-03-17 22:54:45,250] [INFO] Selected 6 target genomes.
[2023-03-17 22:54:45,250] [INFO] Target genome list was writen to OceanDNA-a4201/target_genomes_gtdb.txt
[2023-03-17 22:54:45,258] [INFO] Task started: fastANI
[2023-03-17 22:54:45,258] [INFO] Running command: fastANI --query /var/lib/cwl/stg249c6f1b-b624-4034-b53d-2e72ff15e665/OceanDNA-a4201.fa --refList OceanDNA-a4201/target_genomes_gtdb.txt --output OceanDNA-a4201/fastani_result_gtdb.tsv --threads 1
[2023-03-17 22:54:46,699] [INFO] Task succeeded: fastANI
[2023-03-17 22:54:46,704] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 22:54:46,704] [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_002457155.1	s__MGIIb-O3 sp002457155	92.9283	201	238	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002723045.1	s__MGIIb-O3 sp002723045	84.5763	124	238	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003602515.1	s__MGIIb-O3 sp003602515	83.72	193	238	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	99.42	99.42	0.80	0.80	2	-
GCA_014239955.1	s__MGIIb-O3 sp014239955	80.865	189	238	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004195615.1	s__MGIIb-O3 sp004195615	80.7679	203	238	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	99.94	99.91	0.95	0.93	3	-
GCA_002716085.1	s__MGIIb-O3 sp002716085	77.1868	61	238	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	97.47	97.47	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-03-17 22:54:46,704] [INFO] GTDB search result was written to OceanDNA-a4201/result_gtdb.tsv
[2023-03-17 22:54:46,704] [INFO] ===== GTDB Search completed =====
[2023-03-17 22:54:46,705] [INFO] DFAST_QC result json was written to OceanDNA-a4201/dqc_result.json
[2023-03-17 22:54:46,705] [INFO] DFAST_QC completed!
[2023-03-17 22:54:46,705] [INFO] Total running time: 0h0m26s