[2023-03-16 09:06:46,902] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:06:46,902] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:06:46,902] [INFO] DQC Reference Directory: /var/lib/cwl/stg93e2a727-0279-49a3-8e53-e409bf569f3c/dqc_reference
[2023-03-16 09:06:48,023] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:06:48,023] [INFO] Task started: Prodigal
[2023-03-16 09:06:48,024] [INFO] Running command: cat /var/lib/cwl/stga545a9f1-7057-4a7c-923d-b0eea897d9d0/OceanDNA-b9616.fa | prodigal -d OceanDNA-b9616/cds.fna -a OceanDNA-b9616/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:07:00,251] [INFO] Task succeeded: Prodigal
[2023-03-16 09:07:00,251] [INFO] Task started: HMMsearch
[2023-03-16 09:07:00,252] [INFO] Running command: hmmsearch --tblout OceanDNA-b9616/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg93e2a727-0279-49a3-8e53-e409bf569f3c/dqc_reference/reference_markers.hmm OceanDNA-b9616/protein.faa > /dev/null
[2023-03-16 09:07:00,429] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:07:00,429] [INFO] Found 6/6 markers.
[2023-03-16 09:07:00,444] [INFO] Query marker FASTA was written to OceanDNA-b9616/markers.fasta
[2023-03-16 09:07:00,445] [INFO] Task started: Blastn
[2023-03-16 09:07:00,445] [INFO] Running command: blastn -query OceanDNA-b9616/markers.fasta -db /var/lib/cwl/stg93e2a727-0279-49a3-8e53-e409bf569f3c/dqc_reference/reference_markers.fasta -out OceanDNA-b9616/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:07:01,018] [INFO] Task succeeded: Blastn
[2023-03-16 09:07:01,019] [INFO] Selected 34 target genomes.
[2023-03-16 09:07:01,019] [INFO] Target genome list was writen to OceanDNA-b9616/target_genomes.txt
[2023-03-16 09:07:01,215] [INFO] Task started: fastANI
[2023-03-16 09:07:01,215] [INFO] Running command: fastANI --query /var/lib/cwl/stga545a9f1-7057-4a7c-923d-b0eea897d9d0/OceanDNA-b9616.fa --refList OceanDNA-b9616/target_genomes.txt --output OceanDNA-b9616/fastani_result.tsv --threads 1
[2023-03-16 09:07:19,983] [INFO] Task succeeded: fastANI
[2023-03-16 09:07:19,984] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg93e2a727-0279-49a3-8e53-e409bf569f3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:07:19,984] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg93e2a727-0279-49a3-8e53-e409bf569f3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:07:19,984] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:07:19,984] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 09:07:19,984] [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 09:07:19,985] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9616/tc_result.tsv
[2023-03-16 09:07:19,985] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:07:19,985] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:07:19,986] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg93e2a727-0279-49a3-8e53-e409bf569f3c/dqc_reference/checkm_data
[2023-03-16 09:07:19,988] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:07:20,014] [INFO] Task started: CheckM
[2023-03-16 09:07:20,014] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9616/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9616/checkm_input OceanDNA-b9616/checkm_result
[2023-03-16 09:07:54,819] [INFO] Task succeeded: CheckM
[2023-03-16 09:07:54,819] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.94%
Contamintation: 1.85%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-16 09:07:54,869] [INFO] ===== Completeness check finished =====
[2023-03-16 09:07:54,869] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:07:54,869] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9616/markers.fasta)
[2023-03-16 09:07:54,870] [INFO] Task started: Blastn
[2023-03-16 09:07:54,870] [INFO] Running command: blastn -query OceanDNA-b9616/markers.fasta -db /var/lib/cwl/stg93e2a727-0279-49a3-8e53-e409bf569f3c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9616/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:07:55,795] [INFO] Task succeeded: Blastn
[2023-03-16 09:07:55,798] [INFO] Selected 30 target genomes.
[2023-03-16 09:07:55,798] [INFO] Target genome list was writen to OceanDNA-b9616/target_genomes_gtdb.txt
[2023-03-16 09:07:56,196] [INFO] Task started: fastANI
[2023-03-16 09:07:56,196] [INFO] Running command: fastANI --query /var/lib/cwl/stga545a9f1-7057-4a7c-923d-b0eea897d9d0/OceanDNA-b9616.fa --refList OceanDNA-b9616/target_genomes_gtdb.txt --output OceanDNA-b9616/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:08:09,011] [INFO] Task succeeded: fastANI
[2023-03-16 09:08:09,014] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 09:08:09,014] [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_002457295.1	s__MS024-2A sp002457295	92.974	263	605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	98.75	98.17	0.80	0.74	3	-
GCA_002714815.1	s__MS024-2A sp002714815	76.8798	65	605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009886625.1	s__MS024-2A sp009886625	75.7885	52	605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 09:08:09,016] [INFO] GTDB search result was written to OceanDNA-b9616/result_gtdb.tsv
[2023-03-16 09:08:09,017] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:08:09,019] [INFO] DFAST_QC result json was written to OceanDNA-b9616/dqc_result.json
[2023-03-16 09:08:09,019] [INFO] DFAST_QC completed!
[2023-03-16 09:08:09,019] [INFO] Total running time: 0h1m22s