[2023-03-15 15:06:33,959] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:06:33,959] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:06:33,959] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c0f0164-ecfb-4096-b090-056a44b98d38/dqc_reference
[2023-03-15 15:06:35,047] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:06:35,047] [INFO] Task started: Prodigal
[2023-03-15 15:06:35,047] [INFO] Running command: cat /var/lib/cwl/stg43254f52-ca38-40cb-b6ae-afbca5de368d/OceanDNA-b14525.fa | prodigal -d OceanDNA-b14525/cds.fna -a OceanDNA-b14525/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:06:41,468] [INFO] Task succeeded: Prodigal
[2023-03-15 15:06:41,468] [INFO] Task started: HMMsearch
[2023-03-15 15:06:41,468] [INFO] Running command: hmmsearch --tblout OceanDNA-b14525/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c0f0164-ecfb-4096-b090-056a44b98d38/dqc_reference/reference_markers.hmm OceanDNA-b14525/protein.faa > /dev/null
[2023-03-15 15:06:41,625] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:06:41,625] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg43254f52-ca38-40cb-b6ae-afbca5de368d/OceanDNA-b14525.fa]
[2023-03-15 15:06:41,652] [INFO] Query marker FASTA was written to OceanDNA-b14525/markers.fasta
[2023-03-15 15:06:41,653] [INFO] Task started: Blastn
[2023-03-15 15:06:41,653] [INFO] Running command: blastn -query OceanDNA-b14525/markers.fasta -db /var/lib/cwl/stg8c0f0164-ecfb-4096-b090-056a44b98d38/dqc_reference/reference_markers.fasta -out OceanDNA-b14525/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:06:42,138] [INFO] Task succeeded: Blastn
[2023-03-15 15:06:42,148] [INFO] Selected 17 target genomes.
[2023-03-15 15:06:42,148] [INFO] Target genome list was writen to OceanDNA-b14525/target_genomes.txt
[2023-03-15 15:06:42,157] [INFO] Task started: fastANI
[2023-03-15 15:06:42,157] [INFO] Running command: fastANI --query /var/lib/cwl/stg43254f52-ca38-40cb-b6ae-afbca5de368d/OceanDNA-b14525.fa --refList OceanDNA-b14525/target_genomes.txt --output OceanDNA-b14525/fastani_result.tsv --threads 1
[2023-03-15 15:06:49,039] [INFO] Task succeeded: fastANI
[2023-03-15 15:06:49,039] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c0f0164-ecfb-4096-b090-056a44b98d38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:06:49,040] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c0f0164-ecfb-4096-b090-056a44b98d38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:06:49,040] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:06:49,040] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 15:06:49,040] [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 15:06:49,042] [INFO] DFAST Taxonomy check result was written to OceanDNA-b14525/tc_result.tsv
[2023-03-15 15:06:49,047] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:06:49,047] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:06:49,047] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c0f0164-ecfb-4096-b090-056a44b98d38/dqc_reference/checkm_data
[2023-03-15 15:06:49,050] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:06:49,069] [INFO] Task started: CheckM
[2023-03-15 15:06:49,069] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b14525/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b14525/checkm_input OceanDNA-b14525/checkm_result
[2023-03-15 15:07:10,731] [INFO] Task succeeded: CheckM
[2023-03-15 15:07:10,731] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 15:07:10,828] [INFO] ===== Completeness check finished =====
[2023-03-15 15:07:10,829] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:07:10,829] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b14525/markers.fasta)
[2023-03-15 15:07:10,830] [INFO] Task started: Blastn
[2023-03-15 15:07:10,830] [INFO] Running command: blastn -query OceanDNA-b14525/markers.fasta -db /var/lib/cwl/stg8c0f0164-ecfb-4096-b090-056a44b98d38/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b14525/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:07:11,472] [INFO] Task succeeded: Blastn
[2023-03-15 15:07:11,484] [INFO] Selected 16 target genomes.
[2023-03-15 15:07:11,484] [INFO] Target genome list was writen to OceanDNA-b14525/target_genomes_gtdb.txt
[2023-03-15 15:07:11,529] [INFO] Task started: fastANI
[2023-03-15 15:07:11,529] [INFO] Running command: fastANI --query /var/lib/cwl/stg43254f52-ca38-40cb-b6ae-afbca5de368d/OceanDNA-b14525.fa --refList OceanDNA-b14525/target_genomes_gtdb.txt --output OceanDNA-b14525/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:07:15,472] [INFO] Task succeeded: fastANI
[2023-03-15 15:07:15,475] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 15:07:15,475] [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_002717385.1	s__GCA-2717385 sp002717385	99.713	348	424	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__GCA-2717385	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002718415.1	s__GCA-2718415 sp002718415	79.1473	131	424	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__GCA-2718415	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 15:07:15,478] [INFO] GTDB search result was written to OceanDNA-b14525/result_gtdb.tsv
[2023-03-15 15:07:15,485] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:07:15,492] [INFO] DFAST_QC result json was written to OceanDNA-b14525/dqc_result.json
[2023-03-15 15:07:15,492] [INFO] DFAST_QC completed!
[2023-03-15 15:07:15,492] [INFO] Total running time: 0h0m42s