[2023-03-18 09:41:07,119] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:41:07,119] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:41:07,119] [INFO] DQC Reference Directory: /var/lib/cwl/stgb24f593a-93ad-47e8-a769-39863ee59379/dqc_reference
[2023-03-18 09:41:08,237] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:41:08,238] [INFO] Task started: Prodigal
[2023-03-18 09:41:08,238] [INFO] Running command: cat /var/lib/cwl/stgde8101e4-4bd8-4295-8f76-81235e8ef61d/OceanDNA-b5126.fa | prodigal -d OceanDNA-b5126/cds.fna -a OceanDNA-b5126/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:41:14,970] [INFO] Task succeeded: Prodigal
[2023-03-18 09:41:14,971] [INFO] Task started: HMMsearch
[2023-03-18 09:41:14,971] [INFO] Running command: hmmsearch --tblout OceanDNA-b5126/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb24f593a-93ad-47e8-a769-39863ee59379/dqc_reference/reference_markers.hmm OceanDNA-b5126/protein.faa > /dev/null
[2023-03-18 09:41:15,151] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:41:15,152] [INFO] Found 6/6 markers.
[2023-03-18 09:41:15,162] [INFO] Query marker FASTA was written to OceanDNA-b5126/markers.fasta
[2023-03-18 09:41:15,163] [INFO] Task started: Blastn
[2023-03-18 09:41:15,163] [INFO] Running command: blastn -query OceanDNA-b5126/markers.fasta -db /var/lib/cwl/stgb24f593a-93ad-47e8-a769-39863ee59379/dqc_reference/reference_markers.fasta -out OceanDNA-b5126/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:41:15,688] [INFO] Task succeeded: Blastn
[2023-03-18 09:41:15,689] [INFO] Selected 29 target genomes.
[2023-03-18 09:41:15,689] [INFO] Target genome list was writen to OceanDNA-b5126/target_genomes.txt
[2023-03-18 09:41:15,764] [INFO] Task started: fastANI
[2023-03-18 09:41:15,764] [INFO] Running command: fastANI --query /var/lib/cwl/stgde8101e4-4bd8-4295-8f76-81235e8ef61d/OceanDNA-b5126.fa --refList OceanDNA-b5126/target_genomes.txt --output OceanDNA-b5126/fastani_result.tsv --threads 1
[2023-03-18 09:41:30,285] [INFO] Task succeeded: fastANI
[2023-03-18 09:41:30,286] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb24f593a-93ad-47e8-a769-39863ee59379/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:41:30,286] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb24f593a-93ad-47e8-a769-39863ee59379/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:41:30,286] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:41:30,286] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:41:30,286] [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
--------------------------------------------------------------------------------
[2023-03-18 09:41:30,286] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5126/tc_result.tsv
[2023-03-18 09:41:30,286] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:41:30,287] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:41:30,287] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb24f593a-93ad-47e8-a769-39863ee59379/dqc_reference/checkm_data
[2023-03-18 09:41:30,289] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:41:30,292] [INFO] Task started: CheckM
[2023-03-18 09:41:30,292] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5126/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5126/checkm_input OceanDNA-b5126/checkm_result
[2023-03-18 09:41:52,977] [INFO] Task succeeded: CheckM
[2023-03-18 09:41:52,978] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.65%
Contamintation: 5.56%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2023-03-18 09:41:52,980] [INFO] ===== Completeness check finished =====
[2023-03-18 09:41:52,980] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:41:52,980] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5126/markers.fasta)
[2023-03-18 09:41:52,980] [INFO] Task started: Blastn
[2023-03-18 09:41:52,980] [INFO] Running command: blastn -query OceanDNA-b5126/markers.fasta -db /var/lib/cwl/stgb24f593a-93ad-47e8-a769-39863ee59379/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5126/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:41:53,776] [INFO] Task succeeded: Blastn
[2023-03-18 09:41:53,777] [INFO] Selected 31 target genomes.
[2023-03-18 09:41:53,778] [INFO] Target genome list was writen to OceanDNA-b5126/target_genomes_gtdb.txt
[2023-03-18 09:41:53,807] [INFO] Task started: fastANI
[2023-03-18 09:41:53,808] [INFO] Running command: fastANI --query /var/lib/cwl/stgde8101e4-4bd8-4295-8f76-81235e8ef61d/OceanDNA-b5126.fa --refList OceanDNA-b5126/target_genomes_gtdb.txt --output OceanDNA-b5126/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:42:03,151] [INFO] Task succeeded: fastANI
[2023-03-18 09:42:03,154] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 09:42:03,154] [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_002712715.1	s__GCA-2712715 sp002712715	99.9002	323	343	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2712715	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905478555.1	s__GCA-002697625 sp905478555	76.0029	57	343	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	96.63	96.63	0.87	0.87	2	-
GCA_002710495.1	s__GCA-002697625 sp002710495	75.931	53	343	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 09:42:03,155] [INFO] GTDB search result was written to OceanDNA-b5126/result_gtdb.tsv
[2023-03-18 09:42:03,155] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:42:03,155] [INFO] DFAST_QC result json was written to OceanDNA-b5126/dqc_result.json
[2023-03-18 09:42:03,155] [INFO] DFAST_QC completed!
[2023-03-18 09:42:03,155] [INFO] Total running time: 0h0m56s