[2023-03-15 16:25:57,984] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:25:57,984] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:25:57,984] [INFO] DQC Reference Directory: /var/lib/cwl/stg43a542cd-2ef8-4b34-8952-86203512d7c6/dqc_reference
[2023-03-15 16:26:01,652] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:26:01,653] [INFO] Task started: Prodigal
[2023-03-15 16:26:01,653] [INFO] Running command: cat /var/lib/cwl/stg135882dc-046a-4b61-9404-5d312fc3a556/OceanDNA-b17199.fa | prodigal -d OceanDNA-b17199/cds.fna -a OceanDNA-b17199/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:26:04,797] [INFO] Task succeeded: Prodigal
[2023-03-15 16:26:04,797] [INFO] Task started: HMMsearch
[2023-03-15 16:26:04,798] [INFO] Running command: hmmsearch --tblout OceanDNA-b17199/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43a542cd-2ef8-4b34-8952-86203512d7c6/dqc_reference/reference_markers.hmm OceanDNA-b17199/protein.faa > /dev/null
[2023-03-15 16:26:04,980] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:26:04,981] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg135882dc-046a-4b61-9404-5d312fc3a556/OceanDNA-b17199.fa]
[2023-03-15 16:26:05,009] [INFO] Query marker FASTA was written to OceanDNA-b17199/markers.fasta
[2023-03-15 16:26:05,011] [INFO] Task started: Blastn
[2023-03-15 16:26:05,011] [INFO] Running command: blastn -query OceanDNA-b17199/markers.fasta -db /var/lib/cwl/stg43a542cd-2ef8-4b34-8952-86203512d7c6/dqc_reference/reference_markers.fasta -out OceanDNA-b17199/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:26:08,601] [INFO] Task succeeded: Blastn
[2023-03-15 16:26:08,608] [INFO] Selected 15 target genomes.
[2023-03-15 16:26:08,608] [INFO] Target genome list was writen to OceanDNA-b17199/target_genomes.txt
[2023-03-15 16:26:08,623] [INFO] Task started: fastANI
[2023-03-15 16:26:08,624] [INFO] Running command: fastANI --query /var/lib/cwl/stg135882dc-046a-4b61-9404-5d312fc3a556/OceanDNA-b17199.fa --refList OceanDNA-b17199/target_genomes.txt --output OceanDNA-b17199/fastani_result.tsv --threads 1
[2023-03-15 16:26:14,996] [INFO] Task succeeded: fastANI
[2023-03-15 16:26:14,997] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43a542cd-2ef8-4b34-8952-86203512d7c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:26:14,997] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43a542cd-2ef8-4b34-8952-86203512d7c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:26:14,997] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:26:14,997] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 16:26:14,997] [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 16:26:15,000] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17199/tc_result.tsv
[2023-03-15 16:26:15,002] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:26:15,002] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:26:15,002] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43a542cd-2ef8-4b34-8952-86203512d7c6/dqc_reference/checkm_data
[2023-03-15 16:26:15,013] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:26:15,018] [INFO] Task started: CheckM
[2023-03-15 16:26:15,018] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17199/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17199/checkm_input OceanDNA-b17199/checkm_result
[2023-03-15 16:26:31,869] [INFO] Task succeeded: CheckM
[2023-03-15 16:26:31,870] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 16:26:31,872] [INFO] ===== Completeness check finished =====
[2023-03-15 16:26:31,872] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:26:31,872] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17199/markers.fasta)
[2023-03-15 16:26:31,874] [INFO] Task started: Blastn
[2023-03-15 16:26:31,874] [INFO] Running command: blastn -query OceanDNA-b17199/markers.fasta -db /var/lib/cwl/stg43a542cd-2ef8-4b34-8952-86203512d7c6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17199/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:26:32,655] [INFO] Task succeeded: Blastn
[2023-03-15 16:26:32,657] [INFO] Selected 15 target genomes.
[2023-03-15 16:26:32,657] [INFO] Target genome list was writen to OceanDNA-b17199/target_genomes_gtdb.txt
[2023-03-15 16:26:32,675] [INFO] Task started: fastANI
[2023-03-15 16:26:32,675] [INFO] Running command: fastANI --query /var/lib/cwl/stg135882dc-046a-4b61-9404-5d312fc3a556/OceanDNA-b17199.fa --refList OceanDNA-b17199/target_genomes_gtdb.txt --output OceanDNA-b17199/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:26:37,802] [INFO] Task succeeded: fastANI
[2023-03-15 16:26:37,804] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 16:26:37,804] [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_002313635.1	s__UBA816 sp002313635	99.9546	195	199	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Bac17;f__UBA816;g__UBA816	95.0	99.90	99.81	0.97	0.94	6	conclusive
--------------------------------------------------------------------------------
[2023-03-15 16:26:37,805] [INFO] GTDB search result was written to OceanDNA-b17199/result_gtdb.tsv
[2023-03-15 16:26:37,806] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:26:37,806] [INFO] DFAST_QC result json was written to OceanDNA-b17199/dqc_result.json
[2023-03-15 16:26:37,807] [INFO] DFAST_QC completed!
[2023-03-15 16:26:37,807] [INFO] Total running time: 0h0m40s