[2023-03-17 22:46:02,565] [INFO] DFAST_QC pipeline started.
[2023-03-17 22:46:02,565] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 22:46:02,565] [INFO] DQC Reference Directory: /var/lib/cwl/stg35ae08f1-5f24-4034-9c34-6e30ad03b5ad/dqc_reference
[2023-03-17 22:46:03,671] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 22:46:03,672] [INFO] Task started: Prodigal
[2023-03-17 22:46:03,672] [INFO] Running command: cat /var/lib/cwl/stg809b6beb-36a5-442a-939e-c31dcda3319c/OceanDNA-a40.fa | prodigal -d OceanDNA-a40/cds.fna -a OceanDNA-a40/protein.faa -g 11 -q > /dev/null
[2023-03-17 22:46:07,929] [INFO] Task succeeded: Prodigal
[2023-03-17 22:46:07,930] [INFO] Task started: HMMsearch
[2023-03-17 22:46:07,930] [INFO] Running command: hmmsearch --tblout OceanDNA-a40/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35ae08f1-5f24-4034-9c34-6e30ad03b5ad/dqc_reference/reference_markers.hmm OceanDNA-a40/protein.faa > /dev/null
[2023-03-17 22:46:08,039] [INFO] Task succeeded: HMMsearch
[2023-03-17 22:46:08,040] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg809b6beb-36a5-442a-939e-c31dcda3319c/OceanDNA-a40.fa]
[2023-03-17 22:46:08,046] [INFO] Query marker FASTA was written to OceanDNA-a40/markers.fasta
[2023-03-17 22:46:08,048] [INFO] Task started: Blastn
[2023-03-17 22:46:08,049] [INFO] Running command: blastn -query OceanDNA-a40/markers.fasta -db /var/lib/cwl/stg35ae08f1-5f24-4034-9c34-6e30ad03b5ad/dqc_reference/reference_markers.fasta -out OceanDNA-a40/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:46:08,601] [INFO] Task succeeded: Blastn
[2023-03-17 22:46:08,601] [INFO] Selected 2 target genomes.
[2023-03-17 22:46:08,602] [INFO] Target genome list was writen to OceanDNA-a40/target_genomes.txt
[2023-03-17 22:46:08,603] [INFO] Task started: fastANI
[2023-03-17 22:46:08,603] [INFO] Running command: fastANI --query /var/lib/cwl/stg809b6beb-36a5-442a-939e-c31dcda3319c/OceanDNA-a40.fa --refList OceanDNA-a40/target_genomes.txt --output OceanDNA-a40/fastani_result.tsv --threads 1
[2023-03-17 22:46:09,069] [INFO] Task succeeded: fastANI
[2023-03-17 22:46:09,070] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35ae08f1-5f24-4034-9c34-6e30ad03b5ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 22:46:09,070] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35ae08f1-5f24-4034-9c34-6e30ad03b5ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 22:46:09,070] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 22:46:09,070] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 22:46:09,070] [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 22:46:09,070] [INFO] DFAST Taxonomy check result was written to OceanDNA-a40/tc_result.tsv
[2023-03-17 22:46:09,071] [INFO] ===== Taxonomy check completed =====
[2023-03-17 22:46:09,071] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 22:46:09,071] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35ae08f1-5f24-4034-9c34-6e30ad03b5ad/dqc_reference/checkm_data
[2023-03-17 22:46:09,123] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 22:46:09,125] [INFO] Task started: CheckM
[2023-03-17 22:46:09,125] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a40/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a40/checkm_input OceanDNA-a40/checkm_result
[2023-03-17 22:46:25,880] [INFO] Task succeeded: CheckM
[2023-03-17 22:46:25,881] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.79%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 22:46:25,882] [INFO] ===== Completeness check finished =====
[2023-03-17 22:46:25,882] [INFO] ===== Start GTDB Search =====
[2023-03-17 22:46:25,882] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a40/markers.fasta)
[2023-03-17 22:46:25,884] [INFO] Task started: Blastn
[2023-03-17 22:46:25,884] [INFO] Running command: blastn -query OceanDNA-a40/markers.fasta -db /var/lib/cwl/stg35ae08f1-5f24-4034-9c34-6e30ad03b5ad/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a40/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:46:26,435] [INFO] Task succeeded: Blastn
[2023-03-17 22:46:26,435] [INFO] Selected 5 target genomes.
[2023-03-17 22:46:26,435] [INFO] Target genome list was writen to OceanDNA-a40/target_genomes_gtdb.txt
[2023-03-17 22:46:26,441] [INFO] Task started: fastANI
[2023-03-17 22:46:26,441] [INFO] Running command: fastANI --query /var/lib/cwl/stg809b6beb-36a5-442a-939e-c31dcda3319c/OceanDNA-a40.fa --refList OceanDNA-a40/target_genomes_gtdb.txt --output OceanDNA-a40/fastani_result_gtdb.tsv --threads 1
[2023-03-17 22:46:27,274] [INFO] Task succeeded: fastANI
[2023-03-17 22:46:27,278] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 22:46:27,278] [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_013390785.1	s__Nitrosopelagicus sp013390785	80.005	110	191	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018263495.1	s__Nitrosopelagicus sp018263495	79.8799	96	191	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013390745.1	s__Nitrosopelagicus sp013390745	79.5388	106	191	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000402075.1	s__Nitrosopelagicus sp000402075	79.3504	125	191	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	95.01	95.01	0.87	0.87	2	-
GCA_902590655.1	s__Nitrosopelagicus sp902590655	79.1187	88	191	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 22:46:27,278] [INFO] GTDB search result was written to OceanDNA-a40/result_gtdb.tsv
[2023-03-17 22:46:27,278] [INFO] ===== GTDB Search completed =====
[2023-03-17 22:46:27,279] [INFO] DFAST_QC result json was written to OceanDNA-a40/dqc_result.json
[2023-03-17 22:46:27,279] [INFO] DFAST_QC completed!
[2023-03-17 22:46:27,279] [INFO] Total running time: 0h0m25s