[2023-03-18 09:41:07,115] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:41:07,115] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:41:07,115] [INFO] DQC Reference Directory: /var/lib/cwl/stgb78452a6-cbba-484e-ad8d-ff8c570db27f/dqc_reference
[2023-03-18 09:41:08,237] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:41:08,238] [INFO] Task started: Prodigal
[2023-03-18 09:41:08,238] [INFO] Running command: cat /var/lib/cwl/stg0eb0f14e-a348-43d9-aa90-260cb63f5096/OceanDNA-b19355.fa | prodigal -d OceanDNA-b19355/cds.fna -a OceanDNA-b19355/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:41:16,438] [INFO] Task succeeded: Prodigal
[2023-03-18 09:41:16,438] [INFO] Task started: HMMsearch
[2023-03-18 09:41:16,438] [INFO] Running command: hmmsearch --tblout OceanDNA-b19355/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb78452a6-cbba-484e-ad8d-ff8c570db27f/dqc_reference/reference_markers.hmm OceanDNA-b19355/protein.faa > /dev/null
[2023-03-18 09:41:16,617] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:41:16,617] [INFO] Found 6/6 markers.
[2023-03-18 09:41:16,629] [INFO] Query marker FASTA was written to OceanDNA-b19355/markers.fasta
[2023-03-18 09:41:16,630] [INFO] Task started: Blastn
[2023-03-18 09:41:16,630] [INFO] Running command: blastn -query OceanDNA-b19355/markers.fasta -db /var/lib/cwl/stgb78452a6-cbba-484e-ad8d-ff8c570db27f/dqc_reference/reference_markers.fasta -out OceanDNA-b19355/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:41:17,169] [INFO] Task succeeded: Blastn
[2023-03-18 09:41:17,170] [INFO] Selected 15 target genomes.
[2023-03-18 09:41:17,170] [INFO] Target genome list was writen to OceanDNA-b19355/target_genomes.txt
[2023-03-18 09:41:17,179] [INFO] Task started: fastANI
[2023-03-18 09:41:17,179] [INFO] Running command: fastANI --query /var/lib/cwl/stg0eb0f14e-a348-43d9-aa90-260cb63f5096/OceanDNA-b19355.fa --refList OceanDNA-b19355/target_genomes.txt --output OceanDNA-b19355/fastani_result.tsv --threads 1
[2023-03-18 09:41:24,089] [INFO] Task succeeded: fastANI
[2023-03-18 09:41:24,089] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb78452a6-cbba-484e-ad8d-ff8c570db27f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:41:24,090] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb78452a6-cbba-484e-ad8d-ff8c570db27f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:41:24,090] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:41:24,090] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:41:24,090] [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 09:41:24,090] [INFO] DFAST Taxonomy check result was written to OceanDNA-b19355/tc_result.tsv
[2023-03-18 09:41:24,090] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:41:24,090] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:41:24,091] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb78452a6-cbba-484e-ad8d-ff8c570db27f/dqc_reference/checkm_data
[2023-03-18 09:41:24,093] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:41:24,097] [INFO] Task started: CheckM
[2023-03-18 09:41:24,097] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b19355/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b19355/checkm_input OceanDNA-b19355/checkm_result
[2023-03-18 09:41:49,423] [INFO] Task succeeded: CheckM
[2023-03-18 09:41:49,424] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 09:41:49,426] [INFO] ===== Completeness check finished =====
[2023-03-18 09:41:49,426] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:41:49,426] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b19355/markers.fasta)
[2023-03-18 09:41:49,426] [INFO] Task started: Blastn
[2023-03-18 09:41:49,426] [INFO] Running command: blastn -query OceanDNA-b19355/markers.fasta -db /var/lib/cwl/stgb78452a6-cbba-484e-ad8d-ff8c570db27f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b19355/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:41:50,309] [INFO] Task succeeded: Blastn
[2023-03-18 09:41:50,310] [INFO] Selected 29 target genomes.
[2023-03-18 09:41:50,310] [INFO] Target genome list was writen to OceanDNA-b19355/target_genomes_gtdb.txt
[2023-03-18 09:41:50,337] [INFO] Task started: fastANI
[2023-03-18 09:41:50,337] [INFO] Running command: fastANI --query /var/lib/cwl/stg0eb0f14e-a348-43d9-aa90-260cb63f5096/OceanDNA-b19355.fa --refList OceanDNA-b19355/target_genomes_gtdb.txt --output OceanDNA-b19355/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:42:00,311] [INFO] Task succeeded: fastANI
[2023-03-18 09:42:00,315] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 09:42:00,315] [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_002172545.1	s__TMED108 sp002172545	99.2149	336	505	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TMED108	95.0	99.45	99.45	0.75	0.75	2	conclusive
GCA_002717765.1	s__TMED108 sp002717765	77.4731	117	505	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TMED108	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724735.1	s__TMED108 sp002724735	77.3069	104	505	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TMED108	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002712245.1	s__TMED108 sp002712245	77.291	76	505	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TMED108	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724475.1	s__TMED108 sp002724475	77.2593	94	505	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TMED108	95.0	97.60	97.08	0.73	0.61	4	-
--------------------------------------------------------------------------------
[2023-03-18 09:42:00,316] [INFO] GTDB search result was written to OceanDNA-b19355/result_gtdb.tsv
[2023-03-18 09:42:00,316] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:42:00,316] [INFO] DFAST_QC result json was written to OceanDNA-b19355/dqc_result.json
[2023-03-18 09:42:00,317] [INFO] DFAST_QC completed!
[2023-03-18 09:42:00,317] [INFO] Total running time: 0h0m53s