[2023-03-15 21:01:44,359] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:01:44,359] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:01:44,359] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ee77639-b31f-4fb2-824c-390e0d7df1af/dqc_reference
[2023-03-15 21:01:45,701] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:01:45,701] [INFO] Task started: Prodigal
[2023-03-15 21:01:45,701] [INFO] Running command: cat /var/lib/cwl/stg18b9eb91-5891-402a-a6e7-010469e828c3/OceanDNA-b4785.fa | prodigal -d OceanDNA-b4785/cds.fna -a OceanDNA-b4785/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:01:52,073] [INFO] Task succeeded: Prodigal
[2023-03-15 21:01:52,073] [INFO] Task started: HMMsearch
[2023-03-15 21:01:52,073] [INFO] Running command: hmmsearch --tblout OceanDNA-b4785/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ee77639-b31f-4fb2-824c-390e0d7df1af/dqc_reference/reference_markers.hmm OceanDNA-b4785/protein.faa > /dev/null
[2023-03-15 21:01:52,219] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:01:52,220] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg18b9eb91-5891-402a-a6e7-010469e828c3/OceanDNA-b4785.fa]
[2023-03-15 21:01:52,231] [INFO] Query marker FASTA was written to OceanDNA-b4785/markers.fasta
[2023-03-15 21:01:52,231] [INFO] Task started: Blastn
[2023-03-15 21:01:52,231] [INFO] Running command: blastn -query OceanDNA-b4785/markers.fasta -db /var/lib/cwl/stg5ee77639-b31f-4fb2-824c-390e0d7df1af/dqc_reference/reference_markers.fasta -out OceanDNA-b4785/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:01:52,787] [INFO] Task succeeded: Blastn
[2023-03-15 21:01:52,788] [INFO] Selected 28 target genomes.
[2023-03-15 21:01:52,788] [INFO] Target genome list was writen to OceanDNA-b4785/target_genomes.txt
[2023-03-15 21:01:52,802] [INFO] Task started: fastANI
[2023-03-15 21:01:52,802] [INFO] Running command: fastANI --query /var/lib/cwl/stg18b9eb91-5891-402a-a6e7-010469e828c3/OceanDNA-b4785.fa --refList OceanDNA-b4785/target_genomes.txt --output OceanDNA-b4785/fastani_result.tsv --threads 1
[2023-03-15 21:02:08,236] [INFO] Task succeeded: fastANI
[2023-03-15 21:02:08,236] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ee77639-b31f-4fb2-824c-390e0d7df1af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:02:08,236] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ee77639-b31f-4fb2-824c-390e0d7df1af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:02:08,237] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:02:08,237] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 21:02:08,237] [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 21:02:08,237] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4785/tc_result.tsv
[2023-03-15 21:02:08,237] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:02:08,237] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:02:08,237] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ee77639-b31f-4fb2-824c-390e0d7df1af/dqc_reference/checkm_data
[2023-03-15 21:02:08,240] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:02:08,242] [INFO] Task started: CheckM
[2023-03-15 21:02:08,243] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4785/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4785/checkm_input OceanDNA-b4785/checkm_result
[2023-03-15 21:02:29,921] [INFO] Task succeeded: CheckM
[2023-03-15 21:02:29,922] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.98%
Contamintation: 5.67%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-15 21:02:29,924] [INFO] ===== Completeness check finished =====
[2023-03-15 21:02:29,924] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:02:29,924] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4785/markers.fasta)
[2023-03-15 21:02:29,924] [INFO] Task started: Blastn
[2023-03-15 21:02:29,924] [INFO] Running command: blastn -query OceanDNA-b4785/markers.fasta -db /var/lib/cwl/stg5ee77639-b31f-4fb2-824c-390e0d7df1af/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4785/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:02:30,827] [INFO] Task succeeded: Blastn
[2023-03-15 21:02:30,828] [INFO] Selected 28 target genomes.
[2023-03-15 21:02:30,828] [INFO] Target genome list was writen to OceanDNA-b4785/target_genomes_gtdb.txt
[2023-03-15 21:02:31,310] [INFO] Task started: fastANI
[2023-03-15 21:02:31,310] [INFO] Running command: fastANI --query /var/lib/cwl/stg18b9eb91-5891-402a-a6e7-010469e828c3/OceanDNA-b4785.fa --refList OceanDNA-b4785/target_genomes_gtdb.txt --output OceanDNA-b4785/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:02:39,325] [INFO] Task succeeded: fastANI
[2023-03-15 21:02:39,329] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:02:39,329] [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_002711125.1	s__GCA-2711125 sp002711125	76.1422	66	301	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2711125	95.0	97.93	96.61	0.96	0.94	3	-
GCA_905181585.1	s__CAJIYG01 sp905181585	76.0641	61	301	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__CAJIYG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002728175.1	s__GCA-2697505 sp002728175	76.0404	54	301	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2697505	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478185.1	s__UWMA-0277 sp905478185	75.7976	50	301	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	96.67	96.67	0.88	0.88	2	-
GCA_905478765.1	s__UWMA-0277 sp905478765	75.5247	51	301	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:02:39,329] [INFO] GTDB search result was written to OceanDNA-b4785/result_gtdb.tsv
[2023-03-15 21:02:39,329] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:02:39,330] [INFO] DFAST_QC result json was written to OceanDNA-b4785/dqc_result.json
[2023-03-15 21:02:39,330] [INFO] DFAST_QC completed!
[2023-03-15 21:02:39,330] [INFO] Total running time: 0h0m55s