[2023-03-16 23:55:45,852] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:55:45,863] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:55:45,863] [INFO] DQC Reference Directory: /var/lib/cwl/stg93d30e6f-01d9-43e7-b13c-568a23f0a1eb/dqc_reference
[2023-03-16 23:55:46,971] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:55:46,971] [INFO] Task started: Prodigal
[2023-03-16 23:55:46,972] [INFO] Running command: cat /var/lib/cwl/stg74c6deca-c944-427b-96f4-ae64aa3565df/OceanDNA-b32897.fa | prodigal -d OceanDNA-b32897/cds.fna -a OceanDNA-b32897/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:55:55,114] [INFO] Task succeeded: Prodigal
[2023-03-16 23:55:55,114] [INFO] Task started: HMMsearch
[2023-03-16 23:55:55,114] [INFO] Running command: hmmsearch --tblout OceanDNA-b32897/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg93d30e6f-01d9-43e7-b13c-568a23f0a1eb/dqc_reference/reference_markers.hmm OceanDNA-b32897/protein.faa > /dev/null
[2023-03-16 23:55:55,274] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:55:55,274] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg74c6deca-c944-427b-96f4-ae64aa3565df/OceanDNA-b32897.fa]
[2023-03-16 23:55:55,332] [INFO] Query marker FASTA was written to OceanDNA-b32897/markers.fasta
[2023-03-16 23:55:55,333] [INFO] Task started: Blastn
[2023-03-16 23:55:55,333] [INFO] Running command: blastn -query OceanDNA-b32897/markers.fasta -db /var/lib/cwl/stg93d30e6f-01d9-43e7-b13c-568a23f0a1eb/dqc_reference/reference_markers.fasta -out OceanDNA-b32897/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:55:55,922] [INFO] Task succeeded: Blastn
[2023-03-16 23:55:55,929] [INFO] Selected 27 target genomes.
[2023-03-16 23:55:55,929] [INFO] Target genome list was writen to OceanDNA-b32897/target_genomes.txt
[2023-03-16 23:55:55,944] [INFO] Task started: fastANI
[2023-03-16 23:55:55,944] [INFO] Running command: fastANI --query /var/lib/cwl/stg74c6deca-c944-427b-96f4-ae64aa3565df/OceanDNA-b32897.fa --refList OceanDNA-b32897/target_genomes.txt --output OceanDNA-b32897/fastani_result.tsv --threads 1
[2023-03-16 23:56:16,168] [INFO] Task succeeded: fastANI
[2023-03-16 23:56:16,168] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg93d30e6f-01d9-43e7-b13c-568a23f0a1eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:56:16,168] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg93d30e6f-01d9-43e7-b13c-568a23f0a1eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:56:16,174] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:56:16,174] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 23:56:16,174] [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
Hypericibacter terrae	strain=R5913	GCA_008728855.1	2602015	2602015	type	True	76.9449	51	387	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.0092	64	387	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	75.966	54	387	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	75.8853	53	387	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 23:56:16,178] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32897/tc_result.tsv
[2023-03-16 23:56:16,181] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:56:16,181] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:56:16,181] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg93d30e6f-01d9-43e7-b13c-568a23f0a1eb/dqc_reference/checkm_data
[2023-03-16 23:56:16,182] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:56:16,188] [INFO] Task started: CheckM
[2023-03-16 23:56:16,188] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32897/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32897/checkm_input OceanDNA-b32897/checkm_result
[2023-03-16 23:56:41,538] [INFO] Task succeeded: CheckM
[2023-03-16 23:56:41,539] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.80%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 23:56:41,592] [INFO] ===== Completeness check finished =====
[2023-03-16 23:56:41,593] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:56:41,593] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32897/markers.fasta)
[2023-03-16 23:56:41,594] [INFO] Task started: Blastn
[2023-03-16 23:56:41,594] [INFO] Running command: blastn -query OceanDNA-b32897/markers.fasta -db /var/lib/cwl/stg93d30e6f-01d9-43e7-b13c-568a23f0a1eb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32897/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:56:42,485] [INFO] Task succeeded: Blastn
[2023-03-16 23:56:42,493] [INFO] Selected 30 target genomes.
[2023-03-16 23:56:42,493] [INFO] Target genome list was writen to OceanDNA-b32897/target_genomes_gtdb.txt
[2023-03-16 23:56:43,323] [INFO] Task started: fastANI
[2023-03-16 23:56:43,324] [INFO] Running command: fastANI --query /var/lib/cwl/stg74c6deca-c944-427b-96f4-ae64aa3565df/OceanDNA-b32897.fa --refList OceanDNA-b32897/target_genomes_gtdb.txt --output OceanDNA-b32897/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:57:02,571] [INFO] Task succeeded: fastANI
[2023-03-16 23:57:02,571] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 23:57:02,571] [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
--------------------------------------------------------------------------------
[2023-03-16 23:57:02,578] [INFO] GTDB search result was written to OceanDNA-b32897/result_gtdb.tsv
[2023-03-16 23:57:02,586] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:57:02,595] [INFO] DFAST_QC result json was written to OceanDNA-b32897/dqc_result.json
[2023-03-16 23:57:02,595] [INFO] DFAST_QC completed!
[2023-03-16 23:57:02,595] [INFO] Total running time: 0h1m17s