[2023-03-17 22:37:12,599] [INFO] DFAST_QC pipeline started.
[2023-03-17 22:37:12,599] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 22:37:12,599] [INFO] DQC Reference Directory: /var/lib/cwl/stg037d8af5-6eef-4be4-bece-026133221578/dqc_reference
[2023-03-17 22:37:14,345] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 22:37:14,346] [INFO] Task started: Prodigal
[2023-03-17 22:37:14,346] [INFO] Running command: cat /var/lib/cwl/stg0e65d6f9-7d58-4220-bcef-38780d24211d/OceanDNA-b11586.fa | prodigal -d OceanDNA-b11586/cds.fna -a OceanDNA-b11586/protein.faa -g 11 -q > /dev/null
[2023-03-17 22:37:20,966] [INFO] Task succeeded: Prodigal
[2023-03-17 22:37:20,966] [INFO] Task started: HMMsearch
[2023-03-17 22:37:20,966] [INFO] Running command: hmmsearch --tblout OceanDNA-b11586/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg037d8af5-6eef-4be4-bece-026133221578/dqc_reference/reference_markers.hmm OceanDNA-b11586/protein.faa > /dev/null
[2023-03-17 22:37:21,124] [INFO] Task succeeded: HMMsearch
[2023-03-17 22:37:21,124] [INFO] Found 6/6 markers.
[2023-03-17 22:37:21,135] [INFO] Query marker FASTA was written to OceanDNA-b11586/markers.fasta
[2023-03-17 22:37:21,136] [INFO] Task started: Blastn
[2023-03-17 22:37:21,136] [INFO] Running command: blastn -query OceanDNA-b11586/markers.fasta -db /var/lib/cwl/stg037d8af5-6eef-4be4-bece-026133221578/dqc_reference/reference_markers.fasta -out OceanDNA-b11586/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:37:21,666] [INFO] Task succeeded: Blastn
[2023-03-17 22:37:21,666] [INFO] Selected 26 target genomes.
[2023-03-17 22:37:21,667] [INFO] Target genome list was writen to OceanDNA-b11586/target_genomes.txt
[2023-03-17 22:37:21,680] [INFO] Task started: fastANI
[2023-03-17 22:37:21,680] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e65d6f9-7d58-4220-bcef-38780d24211d/OceanDNA-b11586.fa --refList OceanDNA-b11586/target_genomes.txt --output OceanDNA-b11586/fastani_result.tsv --threads 1
[2023-03-17 22:37:36,092] [INFO] Task succeeded: fastANI
[2023-03-17 22:37:36,092] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg037d8af5-6eef-4be4-bece-026133221578/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 22:37:36,093] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg037d8af5-6eef-4be4-bece-026133221578/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 22:37:36,093] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 22:37:36,093] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 22:37:36,093] [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
--------------------------------------------------------------------------------
[2023-03-17 22:37:36,093] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11586/tc_result.tsv
[2023-03-17 22:37:36,093] [INFO] ===== Taxonomy check completed =====
[2023-03-17 22:37:36,093] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 22:37:36,093] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg037d8af5-6eef-4be4-bece-026133221578/dqc_reference/checkm_data
[2023-03-17 22:37:36,096] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 22:37:36,101] [INFO] Task started: CheckM
[2023-03-17 22:37:36,101] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11586/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11586/checkm_input OceanDNA-b11586/checkm_result
[2023-03-17 22:37:58,192] [INFO] Task succeeded: CheckM
[2023-03-17 22:37:58,193] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.19%
Contamintation: 2.55%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-17 22:37:58,194] [INFO] ===== Completeness check finished =====
[2023-03-17 22:37:58,194] [INFO] ===== Start GTDB Search =====
[2023-03-17 22:37:58,195] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11586/markers.fasta)
[2023-03-17 22:37:58,195] [INFO] Task started: Blastn
[2023-03-17 22:37:58,196] [INFO] Running command: blastn -query OceanDNA-b11586/markers.fasta -db /var/lib/cwl/stg037d8af5-6eef-4be4-bece-026133221578/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11586/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:37:59,007] [INFO] Task succeeded: Blastn
[2023-03-17 22:37:59,008] [INFO] Selected 25 target genomes.
[2023-03-17 22:37:59,008] [INFO] Target genome list was writen to OceanDNA-b11586/target_genomes_gtdb.txt
[2023-03-17 22:37:59,077] [INFO] Task started: fastANI
[2023-03-17 22:37:59,077] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e65d6f9-7d58-4220-bcef-38780d24211d/OceanDNA-b11586.fa --refList OceanDNA-b11586/target_genomes_gtdb.txt --output OceanDNA-b11586/fastani_result_gtdb.tsv --threads 1
[2023-03-17 22:38:07,689] [INFO] Task succeeded: fastANI
[2023-03-17 22:38:07,693] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 22:38:07,693] [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_002718035.1	s__GCA-2718035 sp002718035	91.8144	257	343	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-2718035	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902533035.1	s__GCA-2718035 sp902533035	78.2978	127	343	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-2718035	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902520385.1	s__GCA-2718035 sp902520385	78.2502	95	343	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-2718035	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 22:38:07,693] [INFO] GTDB search result was written to OceanDNA-b11586/result_gtdb.tsv
[2023-03-17 22:38:07,693] [INFO] ===== GTDB Search completed =====
[2023-03-17 22:38:07,694] [INFO] DFAST_QC result json was written to OceanDNA-b11586/dqc_result.json
[2023-03-17 22:38:07,694] [INFO] DFAST_QC completed!
[2023-03-17 22:38:07,694] [INFO] Total running time: 0h0m55s