[2023-03-18 01:41:22,935] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:41:22,935] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:41:22,935] [INFO] DQC Reference Directory: /var/lib/cwl/stg03791c7e-8113-4170-ae25-3a302927780b/dqc_reference
[2023-03-18 01:41:24,017] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:41:24,017] [INFO] Task started: Prodigal
[2023-03-18 01:41:24,017] [INFO] Running command: cat /var/lib/cwl/stg36012d29-d971-49ec-8e47-9ad85a7bc7f5/OceanDNA-b1597.fa | prodigal -d OceanDNA-b1597/cds.fna -a OceanDNA-b1597/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:41:34,234] [INFO] Task succeeded: Prodigal
[2023-03-18 01:41:34,235] [INFO] Task started: HMMsearch
[2023-03-18 01:41:34,235] [INFO] Running command: hmmsearch --tblout OceanDNA-b1597/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03791c7e-8113-4170-ae25-3a302927780b/dqc_reference/reference_markers.hmm OceanDNA-b1597/protein.faa > /dev/null
[2023-03-18 01:41:34,397] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:41:34,397] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg36012d29-d971-49ec-8e47-9ad85a7bc7f5/OceanDNA-b1597.fa]
[2023-03-18 01:41:34,411] [INFO] Query marker FASTA was written to OceanDNA-b1597/markers.fasta
[2023-03-18 01:41:34,412] [INFO] Task started: Blastn
[2023-03-18 01:41:34,412] [INFO] Running command: blastn -query OceanDNA-b1597/markers.fasta -db /var/lib/cwl/stg03791c7e-8113-4170-ae25-3a302927780b/dqc_reference/reference_markers.fasta -out OceanDNA-b1597/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:41:34,911] [INFO] Task succeeded: Blastn
[2023-03-18 01:41:34,912] [INFO] Selected 11 target genomes.
[2023-03-18 01:41:34,912] [INFO] Target genome list was writen to OceanDNA-b1597/target_genomes.txt
[2023-03-18 01:41:34,920] [INFO] Task started: fastANI
[2023-03-18 01:41:34,920] [INFO] Running command: fastANI --query /var/lib/cwl/stg36012d29-d971-49ec-8e47-9ad85a7bc7f5/OceanDNA-b1597.fa --refList OceanDNA-b1597/target_genomes.txt --output OceanDNA-b1597/fastani_result.tsv --threads 1
[2023-03-18 01:41:40,667] [INFO] Task succeeded: fastANI
[2023-03-18 01:41:40,667] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03791c7e-8113-4170-ae25-3a302927780b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:41:40,667] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03791c7e-8113-4170-ae25-3a302927780b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:41:40,667] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:41:40,667] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 01:41:40,668] [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 01:41:40,668] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1597/tc_result.tsv
[2023-03-18 01:41:40,668] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:41:40,668] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:41:40,668] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03791c7e-8113-4170-ae25-3a302927780b/dqc_reference/checkm_data
[2023-03-18 01:41:40,671] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:41:40,675] [INFO] Task started: CheckM
[2023-03-18 01:41:40,675] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1597/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1597/checkm_input OceanDNA-b1597/checkm_result
[2023-03-18 01:42:10,783] [INFO] Task succeeded: CheckM
[2023-03-18 01:42:10,783] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.02%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:42:10,785] [INFO] ===== Completeness check finished =====
[2023-03-18 01:42:10,785] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:42:10,785] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1597/markers.fasta)
[2023-03-18 01:42:10,786] [INFO] Task started: Blastn
[2023-03-18 01:42:10,786] [INFO] Running command: blastn -query OceanDNA-b1597/markers.fasta -db /var/lib/cwl/stg03791c7e-8113-4170-ae25-3a302927780b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1597/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:42:11,522] [INFO] Task succeeded: Blastn
[2023-03-18 01:42:11,523] [INFO] Selected 14 target genomes.
[2023-03-18 01:42:11,523] [INFO] Target genome list was writen to OceanDNA-b1597/target_genomes_gtdb.txt
[2023-03-18 01:42:11,539] [INFO] Task started: fastANI
[2023-03-18 01:42:11,539] [INFO] Running command: fastANI --query /var/lib/cwl/stg36012d29-d971-49ec-8e47-9ad85a7bc7f5/OceanDNA-b1597.fa --refList OceanDNA-b1597/target_genomes_gtdb.txt --output OceanDNA-b1597/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:42:18,037] [INFO] Task succeeded: fastANI
[2023-03-18 01:42:18,041] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:42:18,042] [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_002724355.1	s__UBA6944 sp002724355	97.9222	488	573	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA6944	95.0	98.32	97.68	0.80	0.76	5	conclusive
GCA_002296525.1	s__UBA6944 sp002296525	86.0976	521	573	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA6944	95.0	98.78	97.54	0.95	0.91	12	-
GCA_002448715.1	s__UBA6944 sp002448715	85.8268	496	573	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA6944	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002708935.1	s__MedAcidi-G3 sp002708935	77.6995	106	573	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__MedAcidi-G3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722565.1	s__MedAcidi-G3 sp002722565	76.5607	106	573	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__MedAcidi-G3	95.0	96.30	96.09	0.94	0.94	4	-
GCA_002705305.1	s__UBA2110 sp002705305	76.3169	72	573	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA2110	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012960315.1	s__UBA2110 sp012960315	76.0894	76	573	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA2110	95.0	99.85	99.85	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-03-18 01:42:18,042] [INFO] GTDB search result was written to OceanDNA-b1597/result_gtdb.tsv
[2023-03-18 01:42:18,042] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:42:18,043] [INFO] DFAST_QC result json was written to OceanDNA-b1597/dqc_result.json
[2023-03-18 01:42:18,043] [INFO] DFAST_QC completed!
[2023-03-18 01:42:18,043] [INFO] Total running time: 0h0m55s