[2023-03-15 08:55:06,626] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:55:06,627] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:55:06,627] [INFO] DQC Reference Directory: /var/lib/cwl/stg1127e3f3-c773-4508-81a9-e65b0879e6b4/dqc_reference
[2023-03-15 08:55:08,347] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:55:08,347] [INFO] Task started: Prodigal
[2023-03-15 08:55:08,347] [INFO] Running command: cat /var/lib/cwl/stg7da19819-577a-41c2-955c-ccf743b3282d/OceanDNA-b13730.fa | prodigal -d OceanDNA-b13730/cds.fna -a OceanDNA-b13730/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:55:13,453] [INFO] Task succeeded: Prodigal
[2023-03-15 08:55:13,454] [INFO] Task started: HMMsearch
[2023-03-15 08:55:13,454] [INFO] Running command: hmmsearch --tblout OceanDNA-b13730/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1127e3f3-c773-4508-81a9-e65b0879e6b4/dqc_reference/reference_markers.hmm OceanDNA-b13730/protein.faa > /dev/null
[2023-03-15 08:55:13,688] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:55:13,689] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg7da19819-577a-41c2-955c-ccf743b3282d/OceanDNA-b13730.fa]
[2023-03-15 08:55:13,697] [INFO] Query marker FASTA was written to OceanDNA-b13730/markers.fasta
[2023-03-15 08:55:13,698] [INFO] Task started: Blastn
[2023-03-15 08:55:13,698] [INFO] Running command: blastn -query OceanDNA-b13730/markers.fasta -db /var/lib/cwl/stg1127e3f3-c773-4508-81a9-e65b0879e6b4/dqc_reference/reference_markers.fasta -out OceanDNA-b13730/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:55:14,448] [INFO] Task succeeded: Blastn
[2023-03-15 08:55:14,448] [INFO] Selected 5 target genomes.
[2023-03-15 08:55:14,449] [INFO] Target genome list was writen to OceanDNA-b13730/target_genomes.txt
[2023-03-15 08:55:14,452] [INFO] Task started: fastANI
[2023-03-15 08:55:14,452] [INFO] Running command: fastANI --query /var/lib/cwl/stg7da19819-577a-41c2-955c-ccf743b3282d/OceanDNA-b13730.fa --refList OceanDNA-b13730/target_genomes.txt --output OceanDNA-b13730/fastani_result.tsv --threads 1
[2023-03-15 08:55:15,405] [INFO] Task succeeded: fastANI
[2023-03-15 08:55:15,406] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1127e3f3-c773-4508-81a9-e65b0879e6b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:55:15,406] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1127e3f3-c773-4508-81a9-e65b0879e6b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:55:15,406] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:55:15,406] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 08:55:15,406] [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 08:55:15,407] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13730/tc_result.tsv
[2023-03-15 08:55:15,407] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:55:15,407] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:55:15,407] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1127e3f3-c773-4508-81a9-e65b0879e6b4/dqc_reference/checkm_data
[2023-03-15 08:55:15,461] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:55:15,621] [INFO] Task started: CheckM
[2023-03-15 08:55:15,621] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13730/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13730/checkm_input OceanDNA-b13730/checkm_result
[2023-03-15 08:55:38,171] [INFO] Task succeeded: CheckM
[2023-03-15 08:55:38,172] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:55:38,173] [INFO] ===== Completeness check finished =====
[2023-03-15 08:55:38,174] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:55:38,174] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13730/markers.fasta)
[2023-03-15 08:55:38,174] [INFO] Task started: Blastn
[2023-03-15 08:55:38,174] [INFO] Running command: blastn -query OceanDNA-b13730/markers.fasta -db /var/lib/cwl/stg1127e3f3-c773-4508-81a9-e65b0879e6b4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13730/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:55:38,781] [INFO] Task succeeded: Blastn
[2023-03-15 08:55:38,782] [INFO] Selected 9 target genomes.
[2023-03-15 08:55:38,782] [INFO] Target genome list was writen to OceanDNA-b13730/target_genomes_gtdb.txt
[2023-03-15 08:55:38,966] [INFO] Task started: fastANI
[2023-03-15 08:55:38,967] [INFO] Running command: fastANI --query /var/lib/cwl/stg7da19819-577a-41c2-955c-ccf743b3282d/OceanDNA-b13730.fa --refList OceanDNA-b13730/target_genomes_gtdb.txt --output OceanDNA-b13730/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:55:41,100] [INFO] Task succeeded: fastANI
[2023-03-15 08:55:41,104] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 08:55:41,104] [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_009391605.1	s__GCA-002694895 sp009391605	89.386	227	326	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__GCA-002694895;g__GCA-002694895	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694895.1	s__GCA-002694895 sp002694895	89.1241	215	326	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__GCA-002694895;g__GCA-002694895	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002711005.1	s__GCA-002694895 sp002711005	77.3374	70	326	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__GCA-002694895;g__GCA-002694895	95.0	95.35	95.35	0.85	0.85	2	-
GCA_002715665.1	s__GCA-002694895 sp002715665	76.9535	66	326	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__GCA-002694895;g__GCA-002694895	95.0	95.83	95.83	0.63	0.63	2	-
--------------------------------------------------------------------------------
[2023-03-15 08:55:41,104] [INFO] GTDB search result was written to OceanDNA-b13730/result_gtdb.tsv
[2023-03-15 08:55:41,105] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:55:41,105] [INFO] DFAST_QC result json was written to OceanDNA-b13730/dqc_result.json
[2023-03-15 08:55:41,105] [INFO] DFAST_QC completed!
[2023-03-15 08:55:41,105] [INFO] Total running time: 0h0m34s