[2023-03-14 14:27:09,983] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:27:09,983] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:27:09,983] [INFO] DQC Reference Directory: /var/lib/cwl/stg8dbd75dd-73c5-4f3b-951c-fc0e1035c854/dqc_reference
[2023-03-14 14:27:13,563] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:27:13,566] [INFO] Task started: Prodigal
[2023-03-14 14:27:13,567] [INFO] Running command: cat /var/lib/cwl/stg9ef2459f-1cdc-4a22-a5a4-332046071b26/OceanDNA-b11072.fa | prodigal -d OceanDNA-b11072/cds.fna -a OceanDNA-b11072/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:27:25,521] [INFO] Task succeeded: Prodigal
[2023-03-14 14:27:25,522] [INFO] Task started: HMMsearch
[2023-03-14 14:27:25,522] [INFO] Running command: hmmsearch --tblout OceanDNA-b11072/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8dbd75dd-73c5-4f3b-951c-fc0e1035c854/dqc_reference/reference_markers.hmm OceanDNA-b11072/protein.faa > /dev/null
[2023-03-14 14:27:25,762] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:27:25,762] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9ef2459f-1cdc-4a22-a5a4-332046071b26/OceanDNA-b11072.fa]
[2023-03-14 14:27:25,770] [INFO] Query marker FASTA was written to OceanDNA-b11072/markers.fasta
[2023-03-14 14:27:25,772] [INFO] Task started: Blastn
[2023-03-14 14:27:25,772] [INFO] Running command: blastn -query OceanDNA-b11072/markers.fasta -db /var/lib/cwl/stg8dbd75dd-73c5-4f3b-951c-fc0e1035c854/dqc_reference/reference_markers.fasta -out OceanDNA-b11072/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:27:26,442] [INFO] Task succeeded: Blastn
[2023-03-14 14:27:26,443] [INFO] Selected 27 target genomes.
[2023-03-14 14:27:26,444] [INFO] Target genome list was writen to OceanDNA-b11072/target_genomes.txt
[2023-03-14 14:27:26,476] [INFO] Task started: fastANI
[2023-03-14 14:27:26,476] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ef2459f-1cdc-4a22-a5a4-332046071b26/OceanDNA-b11072.fa --refList OceanDNA-b11072/target_genomes.txt --output OceanDNA-b11072/fastani_result.tsv --threads 1
[2023-03-14 14:27:44,893] [INFO] Task succeeded: fastANI
[2023-03-14 14:27:44,893] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8dbd75dd-73c5-4f3b-951c-fc0e1035c854/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:27:44,894] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8dbd75dd-73c5-4f3b-951c-fc0e1035c854/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:27:44,894] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 14:27:44,894] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 14:27:44,894] [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
--------------------------------------------------------------------------------
[2023-03-14 14:27:44,894] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11072/tc_result.tsv
[2023-03-14 14:27:44,894] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:27:44,894] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:27:44,895] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8dbd75dd-73c5-4f3b-951c-fc0e1035c854/dqc_reference/checkm_data
[2023-03-14 14:27:44,905] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:27:44,915] [INFO] Task started: CheckM
[2023-03-14 14:27:44,915] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11072/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11072/checkm_input OceanDNA-b11072/checkm_result
[2023-03-14 14:28:16,440] [INFO] Task succeeded: CheckM
[2023-03-14 14:28:16,441] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 14:28:16,442] [INFO] ===== Completeness check finished =====
[2023-03-14 14:28:16,442] [INFO] ===== Start GTDB Search =====
[2023-03-14 14:28:16,442] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11072/markers.fasta)
[2023-03-14 14:28:16,443] [INFO] Task started: Blastn
[2023-03-14 14:28:16,443] [INFO] Running command: blastn -query OceanDNA-b11072/markers.fasta -db /var/lib/cwl/stg8dbd75dd-73c5-4f3b-951c-fc0e1035c854/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11072/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:28:17,326] [INFO] Task succeeded: Blastn
[2023-03-14 14:28:17,327] [INFO] Selected 9 target genomes.
[2023-03-14 14:28:17,327] [INFO] Target genome list was writen to OceanDNA-b11072/target_genomes_gtdb.txt
[2023-03-14 14:28:17,335] [INFO] Task started: fastANI
[2023-03-14 14:28:17,335] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ef2459f-1cdc-4a22-a5a4-332046071b26/OceanDNA-b11072.fa --refList OceanDNA-b11072/target_genomes_gtdb.txt --output OceanDNA-b11072/fastani_result_gtdb.tsv --threads 1
[2023-03-14 14:28:20,342] [INFO] Task succeeded: fastANI
[2023-03-14 14:28:20,347] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 14:28:20,347] [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_009886265.1	s__UBA7446 sp009886265	83.9866	216	250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862705.1	s__UBA7446 sp002862705	82.3732	218	250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	99.06	98.27	0.87	0.83	14	-
GCA_002313325.1	s__UBA7446 sp002313325	81.6542	165	250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	99.90	99.90	0.92	0.92	2	-
GCA_002862645.1	s__UBA7446 sp002862645	81.3152	193	250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	95.15	95.15	0.79	0.79	2	-
GCA_002698745.1	s__UBA7446 sp002698745	81.221	174	250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937085.1	s__UBA7446 sp009937085	77.4758	75	250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017856205.1	s__UBA7446 sp017856205	77.4678	59	250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 14:28:20,348] [INFO] GTDB search result was written to OceanDNA-b11072/result_gtdb.tsv
[2023-03-14 14:28:20,348] [INFO] ===== GTDB Search completed =====
[2023-03-14 14:28:20,348] [INFO] DFAST_QC result json was written to OceanDNA-b11072/dqc_result.json
[2023-03-14 14:28:20,349] [INFO] DFAST_QC completed!
[2023-03-14 14:28:20,349] [INFO] Total running time: 0h1m10s