[2023-03-16 07:49:29,129] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:49:29,129] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:49:29,129] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ebeb23d-e848-4065-a6f6-5c1b26ca2415/dqc_reference
[2023-03-16 07:49:30,906] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:49:30,907] [INFO] Task started: Prodigal
[2023-03-16 07:49:30,907] [INFO] Running command: cat /var/lib/cwl/stge04d00b8-2616-4637-94cb-1570c64b07c1/OceanDNA-b10923.fa | prodigal -d OceanDNA-b10923/cds.fna -a OceanDNA-b10923/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:49:40,614] [INFO] Task succeeded: Prodigal
[2023-03-16 07:49:40,614] [INFO] Task started: HMMsearch
[2023-03-16 07:49:40,615] [INFO] Running command: hmmsearch --tblout OceanDNA-b10923/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ebeb23d-e848-4065-a6f6-5c1b26ca2415/dqc_reference/reference_markers.hmm OceanDNA-b10923/protein.faa > /dev/null
[2023-03-16 07:49:40,791] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:49:40,791] [INFO] Found 6/6 markers.
[2023-03-16 07:49:40,805] [INFO] Query marker FASTA was written to OceanDNA-b10923/markers.fasta
[2023-03-16 07:49:40,806] [INFO] Task started: Blastn
[2023-03-16 07:49:40,806] [INFO] Running command: blastn -query OceanDNA-b10923/markers.fasta -db /var/lib/cwl/stg1ebeb23d-e848-4065-a6f6-5c1b26ca2415/dqc_reference/reference_markers.fasta -out OceanDNA-b10923/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:49:41,367] [INFO] Task succeeded: Blastn
[2023-03-16 07:49:41,368] [INFO] Selected 39 target genomes.
[2023-03-16 07:49:41,368] [INFO] Target genome list was writen to OceanDNA-b10923/target_genomes.txt
[2023-03-16 07:49:41,390] [INFO] Task started: fastANI
[2023-03-16 07:49:41,390] [INFO] Running command: fastANI --query /var/lib/cwl/stge04d00b8-2616-4637-94cb-1570c64b07c1/OceanDNA-b10923.fa --refList OceanDNA-b10923/target_genomes.txt --output OceanDNA-b10923/fastani_result.tsv --threads 1
[2023-03-16 07:50:04,575] [INFO] Task succeeded: fastANI
[2023-03-16 07:50:04,575] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ebeb23d-e848-4065-a6f6-5c1b26ca2415/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:50:04,575] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ebeb23d-e848-4065-a6f6-5c1b26ca2415/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:50:04,575] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:50:04,575] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 07:50:04,575] [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
--------------------------------------------------------------------------------
[2023-03-16 07:50:04,576] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10923/tc_result.tsv
[2023-03-16 07:50:04,576] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:50:04,576] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:50:04,576] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ebeb23d-e848-4065-a6f6-5c1b26ca2415/dqc_reference/checkm_data
[2023-03-16 07:50:04,579] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:50:04,680] [INFO] Task started: CheckM
[2023-03-16 07:50:04,681] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10923/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10923/checkm_input OceanDNA-b10923/checkm_result
[2023-03-16 07:50:33,836] [INFO] Task succeeded: CheckM
[2023-03-16 07:50:33,836] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.95%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 07:50:33,839] [INFO] ===== Completeness check finished =====
[2023-03-16 07:50:33,839] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:50:33,839] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10923/markers.fasta)
[2023-03-16 07:50:33,840] [INFO] Task started: Blastn
[2023-03-16 07:50:33,840] [INFO] Running command: blastn -query OceanDNA-b10923/markers.fasta -db /var/lib/cwl/stg1ebeb23d-e848-4065-a6f6-5c1b26ca2415/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10923/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:50:34,636] [INFO] Task succeeded: Blastn
[2023-03-16 07:50:34,637] [INFO] Selected 33 target genomes.
[2023-03-16 07:50:34,637] [INFO] Target genome list was writen to OceanDNA-b10923/target_genomes_gtdb.txt
[2023-03-16 07:50:35,004] [INFO] Task started: fastANI
[2023-03-16 07:50:35,004] [INFO] Running command: fastANI --query /var/lib/cwl/stge04d00b8-2616-4637-94cb-1570c64b07c1/OceanDNA-b10923.fa --refList OceanDNA-b10923/target_genomes_gtdb.txt --output OceanDNA-b10923/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:50:47,695] [INFO] Task succeeded: fastANI
[2023-03-16 07:50:47,699] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 07:50:47,699] [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_011526285.1	s__UBA7428 sp011526285	77.5948	120	445	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478905.1	s__UBA7428 sp905478905	77.5728	107	445	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	98.97	98.97	0.80	0.80	2	-
GCA_011526275.1	s__UBA7428 sp011526275	77.4979	113	445	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011526335.1	s__UBA7428 sp011526335	77.3046	67	445	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011526265.1	s__UBA7428 sp011526265	76.7898	64	445	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003023645.1	s__UBA7428 sp003023645	76.6391	56	445	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	99.50	99.50	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-03-16 07:50:47,699] [INFO] GTDB search result was written to OceanDNA-b10923/result_gtdb.tsv
[2023-03-16 07:50:47,700] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:50:47,700] [INFO] DFAST_QC result json was written to OceanDNA-b10923/dqc_result.json
[2023-03-16 07:50:47,700] [INFO] DFAST_QC completed!
[2023-03-16 07:50:47,700] [INFO] Total running time: 0h1m19s