[2023-03-19 02:10:16,859] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:10:16,859] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:10:16,859] [INFO] DQC Reference Directory: /var/lib/cwl/stge463c350-4614-474e-8cad-e56a3a85f209/dqc_reference
[2023-03-19 02:10:18,813] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:10:18,814] [INFO] Task started: Prodigal
[2023-03-19 02:10:18,814] [INFO] Running command: cat /var/lib/cwl/stg28a7b993-b157-4ccd-9b2b-93be24d72235/OceanDNA-b3612.fa | prodigal -d OceanDNA-b3612/cds.fna -a OceanDNA-b3612/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:10:40,199] [INFO] Task succeeded: Prodigal
[2023-03-19 02:10:40,200] [INFO] Task started: HMMsearch
[2023-03-19 02:10:40,200] [INFO] Running command: hmmsearch --tblout OceanDNA-b3612/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge463c350-4614-474e-8cad-e56a3a85f209/dqc_reference/reference_markers.hmm OceanDNA-b3612/protein.faa > /dev/null
[2023-03-19 02:10:40,397] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:10:40,398] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg28a7b993-b157-4ccd-9b2b-93be24d72235/OceanDNA-b3612.fa]
[2023-03-19 02:10:40,436] [INFO] Query marker FASTA was written to OceanDNA-b3612/markers.fasta
[2023-03-19 02:10:40,438] [INFO] Task started: Blastn
[2023-03-19 02:10:40,438] [INFO] Running command: blastn -query OceanDNA-b3612/markers.fasta -db /var/lib/cwl/stge463c350-4614-474e-8cad-e56a3a85f209/dqc_reference/reference_markers.fasta -out OceanDNA-b3612/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:10:40,985] [INFO] Task succeeded: Blastn
[2023-03-19 02:10:40,985] [INFO] Selected 18 target genomes.
[2023-03-19 02:10:40,986] [INFO] Target genome list was writen to OceanDNA-b3612/target_genomes.txt
[2023-03-19 02:10:41,031] [INFO] Task started: fastANI
[2023-03-19 02:10:41,031] [INFO] Running command: fastANI --query /var/lib/cwl/stg28a7b993-b157-4ccd-9b2b-93be24d72235/OceanDNA-b3612.fa --refList OceanDNA-b3612/target_genomes.txt --output OceanDNA-b3612/fastani_result.tsv --threads 1
[2023-03-19 02:10:56,004] [INFO] Task succeeded: fastANI
[2023-03-19 02:10:56,005] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge463c350-4614-474e-8cad-e56a3a85f209/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:10:56,005] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge463c350-4614-474e-8cad-e56a3a85f209/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:10:56,005] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:10:56,005] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 02:10:56,005] [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
--------------------------------------------------------------------------------
[2023-03-19 02:10:56,006] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3612/tc_result.tsv
[2023-03-19 02:10:56,006] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:10:56,006] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:10:56,006] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge463c350-4614-474e-8cad-e56a3a85f209/dqc_reference/checkm_data
[2023-03-19 02:10:56,009] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:10:56,242] [INFO] Task started: CheckM
[2023-03-19 02:10:56,242] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3612/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3612/checkm_input OceanDNA-b3612/checkm_result
[2023-03-19 02:11:51,892] [INFO] Task succeeded: CheckM
[2023-03-19 02:11:51,892] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.13%
Contamintation: 0.90%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 02:11:51,929] [INFO] ===== Completeness check finished =====
[2023-03-19 02:11:51,930] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:11:51,930] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3612/markers.fasta)
[2023-03-19 02:11:51,931] [INFO] Task started: Blastn
[2023-03-19 02:11:51,931] [INFO] Running command: blastn -query OceanDNA-b3612/markers.fasta -db /var/lib/cwl/stge463c350-4614-474e-8cad-e56a3a85f209/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3612/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:11:52,666] [INFO] Task succeeded: Blastn
[2023-03-19 02:11:52,669] [INFO] Selected 24 target genomes.
[2023-03-19 02:11:52,669] [INFO] Target genome list was writen to OceanDNA-b3612/target_genomes_gtdb.txt
[2023-03-19 02:11:52,924] [INFO] Task started: fastANI
[2023-03-19 02:11:52,925] [INFO] Running command: fastANI --query /var/lib/cwl/stg28a7b993-b157-4ccd-9b2b-93be24d72235/OceanDNA-b3612.fa --refList OceanDNA-b3612/target_genomes_gtdb.txt --output OceanDNA-b3612/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:12:10,222] [INFO] Task succeeded: fastANI
[2023-03-19 02:12:10,222] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:12:10,222] [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
--------------------------------------------------------------------------------
[2023-03-19 02:12:10,223] [INFO] GTDB search result was written to OceanDNA-b3612/result_gtdb.tsv
[2023-03-19 02:12:10,223] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:12:10,223] [INFO] DFAST_QC result json was written to OceanDNA-b3612/dqc_result.json
[2023-03-19 02:12:10,224] [INFO] DFAST_QC completed!
[2023-03-19 02:12:10,224] [INFO] Total running time: 0h1m53s