[2023-03-16 17:57:51,586] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:57:51,586] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:57:51,586] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b253772-a4af-426c-8a24-667e4e41fb61/dqc_reference
[2023-03-16 17:57:54,062] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:57:54,065] [INFO] Task started: Prodigal
[2023-03-16 17:57:54,065] [INFO] Running command: cat /var/lib/cwl/stgdd834ac0-1d2d-4ce4-b3d3-7355e9e01e72/OceanDNA-b17590.fa | prodigal -d OceanDNA-b17590/cds.fna -a OceanDNA-b17590/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:58:27,181] [INFO] Task succeeded: Prodigal
[2023-03-16 17:58:27,181] [INFO] Task started: HMMsearch
[2023-03-16 17:58:27,181] [INFO] Running command: hmmsearch --tblout OceanDNA-b17590/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b253772-a4af-426c-8a24-667e4e41fb61/dqc_reference/reference_markers.hmm OceanDNA-b17590/protein.faa > /dev/null
[2023-03-16 17:58:27,830] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:58:27,831] [INFO] Found 6/6 markers.
[2023-03-16 17:58:27,927] [INFO] Query marker FASTA was written to OceanDNA-b17590/markers.fasta
[2023-03-16 17:58:27,933] [INFO] Task started: Blastn
[2023-03-16 17:58:27,933] [INFO] Running command: blastn -query OceanDNA-b17590/markers.fasta -db /var/lib/cwl/stg0b253772-a4af-426c-8a24-667e4e41fb61/dqc_reference/reference_markers.fasta -out OceanDNA-b17590/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:58:28,601] [INFO] Task succeeded: Blastn
[2023-03-16 17:58:28,603] [INFO] Selected 17 target genomes.
[2023-03-16 17:58:28,603] [INFO] Target genome list was writen to OceanDNA-b17590/target_genomes.txt
[2023-03-16 17:58:28,613] [INFO] Task started: fastANI
[2023-03-16 17:58:28,613] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd834ac0-1d2d-4ce4-b3d3-7355e9e01e72/OceanDNA-b17590.fa --refList OceanDNA-b17590/target_genomes.txt --output OceanDNA-b17590/fastani_result.tsv --threads 1
[2023-03-16 17:58:48,282] [INFO] Task succeeded: fastANI
[2023-03-16 17:58:48,282] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b253772-a4af-426c-8a24-667e4e41fb61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:58:48,283] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b253772-a4af-426c-8a24-667e4e41fb61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:58:48,283] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:58:48,283] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 17:58:48,283] [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
--------------------------------------------------------------------------------
[2023-03-16 17:58:48,284] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17590/tc_result.tsv
[2023-03-16 17:58:48,284] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:58:48,284] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:58:48,284] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b253772-a4af-426c-8a24-667e4e41fb61/dqc_reference/checkm_data
[2023-03-16 17:58:48,287] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:58:48,295] [INFO] Task started: CheckM
[2023-03-16 17:58:48,295] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17590/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17590/checkm_input OceanDNA-b17590/checkm_result
[2023-03-16 18:00:09,742] [INFO] Task succeeded: CheckM
[2023-03-16 18:00:09,742] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.14%
Contamintation: 0.93%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 18:00:09,751] [INFO] ===== Completeness check finished =====
[2023-03-16 18:00:09,751] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:00:09,752] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17590/markers.fasta)
[2023-03-16 18:00:09,753] [INFO] Task started: Blastn
[2023-03-16 18:00:09,753] [INFO] Running command: blastn -query OceanDNA-b17590/markers.fasta -db /var/lib/cwl/stg0b253772-a4af-426c-8a24-667e4e41fb61/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17590/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:00:11,388] [INFO] Task succeeded: Blastn
[2023-03-16 18:00:11,391] [INFO] Selected 27 target genomes.
[2023-03-16 18:00:11,391] [INFO] Target genome list was writen to OceanDNA-b17590/target_genomes_gtdb.txt
[2023-03-16 18:00:11,485] [INFO] Task started: fastANI
[2023-03-16 18:00:11,485] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd834ac0-1d2d-4ce4-b3d3-7355e9e01e72/OceanDNA-b17590.fa --refList OceanDNA-b17590/target_genomes_gtdb.txt --output OceanDNA-b17590/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:00:28,872] [INFO] Task succeeded: fastANI
[2023-03-16 18:00:28,875] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 18:00:28,875] [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_002727195.1	s__UBA2968 sp002727195	77.4354	364	1602	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA2968;f__UBA2968;g__UBA2968	95.0	98.72	97.66	0.95	0.94	3	-
GCA_002714465.1	s__UBA2968 sp002714465	76.7901	238	1602	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA2968;f__UBA2968;g__UBA2968	95.0	99.49	99.49	0.96	0.96	2	-
GCA_002433075.1	s__UBA6620 sp002433075	75.7447	112	1602	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA2968;f__UBA2968;g__UBA6620	95.0	99.96	99.96	0.96	0.95	3	-
--------------------------------------------------------------------------------
[2023-03-16 18:00:28,876] [INFO] GTDB search result was written to OceanDNA-b17590/result_gtdb.tsv
[2023-03-16 18:00:28,876] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:00:28,878] [INFO] DFAST_QC result json was written to OceanDNA-b17590/dqc_result.json
[2023-03-16 18:00:28,878] [INFO] DFAST_QC completed!
[2023-03-16 18:00:28,878] [INFO] Total running time: 0h2m37s