[2023-03-18 09:41:09,242] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:41:09,242] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:41:09,242] [INFO] DQC Reference Directory: /var/lib/cwl/stga8f65189-362d-4c62-8500-08c69396c90d/dqc_reference
[2023-03-18 09:41:10,420] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:41:10,420] [INFO] Task started: Prodigal
[2023-03-18 09:41:10,420] [INFO] Running command: cat /var/lib/cwl/stg8b89816c-810f-4ff8-b507-7786979d9a12/OceanDNA-b20788.fa | prodigal -d OceanDNA-b20788/cds.fna -a OceanDNA-b20788/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:41:27,114] [INFO] Task succeeded: Prodigal
[2023-03-18 09:41:27,114] [INFO] Task started: HMMsearch
[2023-03-18 09:41:27,114] [INFO] Running command: hmmsearch --tblout OceanDNA-b20788/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8f65189-362d-4c62-8500-08c69396c90d/dqc_reference/reference_markers.hmm OceanDNA-b20788/protein.faa > /dev/null
[2023-03-18 09:41:27,318] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:41:27,318] [INFO] Found 6/6 markers.
[2023-03-18 09:41:27,338] [INFO] Query marker FASTA was written to OceanDNA-b20788/markers.fasta
[2023-03-18 09:41:27,338] [INFO] Task started: Blastn
[2023-03-18 09:41:27,338] [INFO] Running command: blastn -query OceanDNA-b20788/markers.fasta -db /var/lib/cwl/stga8f65189-362d-4c62-8500-08c69396c90d/dqc_reference/reference_markers.fasta -out OceanDNA-b20788/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:41:27,867] [INFO] Task succeeded: Blastn
[2023-03-18 09:41:27,868] [INFO] Selected 21 target genomes.
[2023-03-18 09:41:27,869] [INFO] Target genome list was writen to OceanDNA-b20788/target_genomes.txt
[2023-03-18 09:41:27,882] [INFO] Task started: fastANI
[2023-03-18 09:41:27,882] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b89816c-810f-4ff8-b507-7786979d9a12/OceanDNA-b20788.fa --refList OceanDNA-b20788/target_genomes.txt --output OceanDNA-b20788/fastani_result.tsv --threads 1
[2023-03-18 09:41:42,559] [INFO] Task succeeded: fastANI
[2023-03-18 09:41:42,559] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8f65189-362d-4c62-8500-08c69396c90d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:41:42,559] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8f65189-362d-4c62-8500-08c69396c90d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:41:42,560] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:41:42,560] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:41:42,560] [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 09:41:42,560] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20788/tc_result.tsv
[2023-03-18 09:41:42,560] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:41:42,560] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:41:42,560] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8f65189-362d-4c62-8500-08c69396c90d/dqc_reference/checkm_data
[2023-03-18 09:41:42,563] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:41:42,567] [INFO] Task started: CheckM
[2023-03-18 09:41:42,568] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20788/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20788/checkm_input OceanDNA-b20788/checkm_result
[2023-03-18 09:42:26,896] [INFO] Task succeeded: CheckM
[2023-03-18 09:42:26,896] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.86%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:42:26,899] [INFO] ===== Completeness check finished =====
[2023-03-18 09:42:26,899] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:42:26,899] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20788/markers.fasta)
[2023-03-18 09:42:26,899] [INFO] Task started: Blastn
[2023-03-18 09:42:26,899] [INFO] Running command: blastn -query OceanDNA-b20788/markers.fasta -db /var/lib/cwl/stga8f65189-362d-4c62-8500-08c69396c90d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20788/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:42:27,612] [INFO] Task succeeded: Blastn
[2023-03-18 09:42:27,613] [INFO] Selected 8 target genomes.
[2023-03-18 09:42:27,613] [INFO] Target genome list was writen to OceanDNA-b20788/target_genomes_gtdb.txt
[2023-03-18 09:42:27,621] [INFO] Task started: fastANI
[2023-03-18 09:42:27,621] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b89816c-810f-4ff8-b507-7786979d9a12/OceanDNA-b20788.fa --refList OceanDNA-b20788/target_genomes_gtdb.txt --output OceanDNA-b20788/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:42:33,869] [INFO] Task succeeded: fastANI
[2023-03-18 09:42:33,874] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 09:42:33,884] [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_018650795.1	s__JABMPR01 sp018650795	99.792	885	969	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	99.79	99.56	0.89	0.81	14	conclusive
GCA_018650445.1	s__JABMPR01 sp018650445	82.2573	597	969	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	99.76	99.61	0.86	0.82	5	-
GCA_016784025.1	s__JABMPR01 sp014382565	80.678	555	969	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	99.96	99.93	0.94	0.93	3	-
GCA_018673925.1	s__JABMPR01 sp018673925	80.4296	564	969	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	99.95	99.91	0.96	0.94	16	-
GCA_013202495.1	s__JABMPR01 sp013202495	80.2979	523	969	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016784545.1	s__JABMPR01 sp016784545	80.0035	506	969	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845065.1	s__JABMPR01 sp016845065	79.2314	426	969	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016844945.1	s__JABMPR01 sp016844945	77.8019	236	969	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 09:42:33,884] [INFO] GTDB search result was written to OceanDNA-b20788/result_gtdb.tsv
[2023-03-18 09:42:33,884] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:42:33,885] [INFO] DFAST_QC result json was written to OceanDNA-b20788/dqc_result.json
[2023-03-18 09:42:33,885] [INFO] DFAST_QC completed!
[2023-03-18 09:42:33,885] [INFO] Total running time: 0h1m25s