[2023-03-14 10:55:58,909] [INFO] DFAST_QC pipeline started.
[2023-03-14 10:55:58,909] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 10:55:58,909] [INFO] DQC Reference Directory: /var/lib/cwl/stg7501b396-de1b-43f3-bde6-4fc98f58c6c2/dqc_reference
[2023-03-14 10:56:00,756] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 10:56:00,756] [INFO] Task started: Prodigal
[2023-03-14 10:56:00,757] [INFO] Running command: cat /var/lib/cwl/stg1bb4feff-9942-42ff-8d50-1a45b984c7ac/OceanDNA-a3737.fa | prodigal -d OceanDNA-a3737/cds.fna -a OceanDNA-a3737/protein.faa -g 11 -q > /dev/null
[2023-03-14 10:56:06,742] [INFO] Task succeeded: Prodigal
[2023-03-14 10:56:06,742] [INFO] Task started: HMMsearch
[2023-03-14 10:56:06,743] [INFO] Running command: hmmsearch --tblout OceanDNA-a3737/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7501b396-de1b-43f3-bde6-4fc98f58c6c2/dqc_reference/reference_markers.hmm OceanDNA-a3737/protein.faa > /dev/null
[2023-03-14 10:56:06,976] [INFO] Task succeeded: HMMsearch
[2023-03-14 10:56:06,977] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg1bb4feff-9942-42ff-8d50-1a45b984c7ac/OceanDNA-a3737.fa]
[2023-03-14 10:56:06,987] [INFO] Query marker FASTA was written to OceanDNA-a3737/markers.fasta
[2023-03-14 10:56:06,987] [INFO] Task started: Blastn
[2023-03-14 10:56:06,987] [INFO] Running command: blastn -query OceanDNA-a3737/markers.fasta -db /var/lib/cwl/stg7501b396-de1b-43f3-bde6-4fc98f58c6c2/dqc_reference/reference_markers.fasta -out OceanDNA-a3737/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:07,447] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:07,447] [INFO] Selected 5 target genomes.
[2023-03-14 10:56:07,448] [INFO] Target genome list was writen to OceanDNA-a3737/target_genomes.txt
[2023-03-14 10:56:07,452] [INFO] Task started: fastANI
[2023-03-14 10:56:07,452] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bb4feff-9942-42ff-8d50-1a45b984c7ac/OceanDNA-a3737.fa --refList OceanDNA-a3737/target_genomes.txt --output OceanDNA-a3737/fastani_result.tsv --threads 1
[2023-03-14 10:56:09,506] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:09,506] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7501b396-de1b-43f3-bde6-4fc98f58c6c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 10:56:09,506] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7501b396-de1b-43f3-bde6-4fc98f58c6c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 10:56:09,507] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 10:56:09,507] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 10:56:09,507] [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
--------------------------------------------------------------------------------
[2023-03-14 10:56:09,507] [INFO] DFAST Taxonomy check result was written to OceanDNA-a3737/tc_result.tsv
[2023-03-14 10:56:09,507] [INFO] ===== Taxonomy check completed =====
[2023-03-14 10:56:09,507] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 10:56:09,507] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7501b396-de1b-43f3-bde6-4fc98f58c6c2/dqc_reference/checkm_data
[2023-03-14 10:56:09,510] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 10:56:09,512] [INFO] Task started: CheckM
[2023-03-14 10:56:09,512] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3737/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3737/checkm_input OceanDNA-a3737/checkm_result
[2023-03-14 10:56:30,418] [INFO] Task succeeded: CheckM
[2023-03-14 10:56:30,419] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.27%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 10:56:30,421] [INFO] ===== Completeness check finished =====
[2023-03-14 10:56:30,421] [INFO] ===== Start GTDB Search =====
[2023-03-14 10:56:30,421] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3737/markers.fasta)
[2023-03-14 10:56:30,421] [INFO] Task started: Blastn
[2023-03-14 10:56:30,421] [INFO] Running command: blastn -query OceanDNA-a3737/markers.fasta -db /var/lib/cwl/stg7501b396-de1b-43f3-bde6-4fc98f58c6c2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3737/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:30,982] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:30,982] [INFO] Selected 5 target genomes.
[2023-03-14 10:56:30,982] [INFO] Target genome list was writen to OceanDNA-a3737/target_genomes_gtdb.txt
[2023-03-14 10:56:30,991] [INFO] Task started: fastANI
[2023-03-14 10:56:30,991] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bb4feff-9942-42ff-8d50-1a45b984c7ac/OceanDNA-a3737.fa --refList OceanDNA-a3737/target_genomes_gtdb.txt --output OceanDNA-a3737/fastani_result_gtdb.tsv --threads 1
[2023-03-14 10:56:32,351] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:32,355] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 10:56:32,356] [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_016777225.1	s__MGIIb-O2 sp016777225	80.7661	286	373	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902511005.1	s__MGIIb-O2 sp902511005	79.9127	216	373	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	98.72	98.72	0.78	0.78	2	-
GCA_902593945.1	s__MGIIb-O2 sp902593945	78.3673	144	373	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002685315.1	s__MGIIb-O2 sp002685315	78.3574	123	373	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002504905.1	s__MGIIb-O2 sp002504905	77.9388	181	373	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	99.85	99.68	0.95	0.91	6	-
--------------------------------------------------------------------------------
[2023-03-14 10:56:32,356] [INFO] GTDB search result was written to OceanDNA-a3737/result_gtdb.tsv
[2023-03-14 10:56:32,356] [INFO] ===== GTDB Search completed =====
[2023-03-14 10:56:32,357] [INFO] DFAST_QC result json was written to OceanDNA-a3737/dqc_result.json
[2023-03-14 10:56:32,357] [INFO] DFAST_QC completed!
[2023-03-14 10:56:32,357] [INFO] Total running time: 0h0m33s