[2023-03-15 07:03:38,853] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:03:38,854] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:03:38,854] [INFO] DQC Reference Directory: /var/lib/cwl/stg9fda2c4b-01ab-4d66-a851-c2306ad45e2b/dqc_reference
[2023-03-15 07:03:40,045] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:03:40,045] [INFO] Task started: Prodigal
[2023-03-15 07:03:40,046] [INFO] Running command: cat /var/lib/cwl/stgcb516263-7c8d-43ff-bf99-5128dcb7b638/OceanDNA-b15459.fa | prodigal -d OceanDNA-b15459/cds.fna -a OceanDNA-b15459/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:03:48,779] [INFO] Task succeeded: Prodigal
[2023-03-15 07:03:48,780] [INFO] Task started: HMMsearch
[2023-03-15 07:03:48,780] [INFO] Running command: hmmsearch --tblout OceanDNA-b15459/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9fda2c4b-01ab-4d66-a851-c2306ad45e2b/dqc_reference/reference_markers.hmm OceanDNA-b15459/protein.faa > /dev/null
[2023-03-15 07:03:48,933] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:03:48,934] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgcb516263-7c8d-43ff-bf99-5128dcb7b638/OceanDNA-b15459.fa]
[2023-03-15 07:03:48,960] [INFO] Query marker FASTA was written to OceanDNA-b15459/markers.fasta
[2023-03-15 07:03:48,960] [INFO] Task started: Blastn
[2023-03-15 07:03:48,960] [INFO] Running command: blastn -query OceanDNA-b15459/markers.fasta -db /var/lib/cwl/stg9fda2c4b-01ab-4d66-a851-c2306ad45e2b/dqc_reference/reference_markers.fasta -out OceanDNA-b15459/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:03:49,407] [INFO] Task succeeded: Blastn
[2023-03-15 07:03:49,421] [INFO] Selected 11 target genomes.
[2023-03-15 07:03:49,421] [INFO] Target genome list was writen to OceanDNA-b15459/target_genomes.txt
[2023-03-15 07:03:49,429] [INFO] Task started: fastANI
[2023-03-15 07:03:49,429] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb516263-7c8d-43ff-bf99-5128dcb7b638/OceanDNA-b15459.fa --refList OceanDNA-b15459/target_genomes.txt --output OceanDNA-b15459/fastani_result.tsv --threads 1
[2023-03-15 07:03:57,837] [INFO] Task succeeded: fastANI
[2023-03-15 07:03:57,837] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9fda2c4b-01ab-4d66-a851-c2306ad45e2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:03:57,838] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9fda2c4b-01ab-4d66-a851-c2306ad45e2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:03:57,838] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:03:57,838] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 07:03:57,838] [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
--------------------------------------------------------------------------------
[2023-03-15 07:03:57,841] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15459/tc_result.tsv
[2023-03-15 07:03:57,847] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:03:57,848] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:03:57,848] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9fda2c4b-01ab-4d66-a851-c2306ad45e2b/dqc_reference/checkm_data
[2023-03-15 07:03:57,851] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:03:57,914] [INFO] Task started: CheckM
[2023-03-15 07:03:57,915] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15459/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15459/checkm_input OceanDNA-b15459/checkm_result
[2023-03-15 07:04:24,127] [INFO] Task succeeded: CheckM
[2023-03-15 07:04:24,127] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.64%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:04:24,188] [INFO] ===== Completeness check finished =====
[2023-03-15 07:04:24,188] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:04:24,188] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15459/markers.fasta)
[2023-03-15 07:04:24,189] [INFO] Task started: Blastn
[2023-03-15 07:04:24,189] [INFO] Running command: blastn -query OceanDNA-b15459/markers.fasta -db /var/lib/cwl/stg9fda2c4b-01ab-4d66-a851-c2306ad45e2b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15459/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:04:24,626] [INFO] Task succeeded: Blastn
[2023-03-15 07:04:24,633] [INFO] Selected 13 target genomes.
[2023-03-15 07:04:24,633] [INFO] Target genome list was writen to OceanDNA-b15459/target_genomes_gtdb.txt
[2023-03-15 07:04:24,753] [INFO] Task started: fastANI
[2023-03-15 07:04:24,753] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb516263-7c8d-43ff-bf99-5128dcb7b638/OceanDNA-b15459.fa --refList OceanDNA-b15459/target_genomes_gtdb.txt --output OceanDNA-b15459/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:04:29,598] [INFO] Task succeeded: fastANI
[2023-03-15 07:04:29,601] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 07:04:29,601] [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_002721995.1	s__UBA9611 sp002721995	76.4176	72	450	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	99.09	98.66	0.88	0.85	7	-
GCA_002816575.1	s__UBA9611 sp002816575	76.3893	72	450	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009392095.1	s__UBA9611 sp009391975	76.0608	58	450	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	98.46	97.52	0.83	0.73	9	-
--------------------------------------------------------------------------------
[2023-03-15 07:04:29,603] [INFO] GTDB search result was written to OceanDNA-b15459/result_gtdb.tsv
[2023-03-15 07:04:29,605] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:04:29,610] [INFO] DFAST_QC result json was written to OceanDNA-b15459/dqc_result.json
[2023-03-15 07:04:29,610] [INFO] DFAST_QC completed!
[2023-03-15 07:04:29,610] [INFO] Total running time: 0h0m51s