[2023-03-18 01:37:05,996] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:37:05,997] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:37:05,997] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf4e6df6-b0bb-4940-aab7-64f014ec999d/dqc_reference
[2023-03-18 01:37:07,104] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:37:07,105] [INFO] Task started: Prodigal
[2023-03-18 01:37:07,105] [INFO] Running command: cat /var/lib/cwl/stgff17e650-128b-44cb-906b-9431eb964969/OceanDNA-a1135.fa | prodigal -d OceanDNA-a1135/cds.fna -a OceanDNA-a1135/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:37:10,260] [INFO] Task succeeded: Prodigal
[2023-03-18 01:37:10,260] [INFO] Task started: HMMsearch
[2023-03-18 01:37:10,260] [INFO] Running command: hmmsearch --tblout OceanDNA-a1135/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf4e6df6-b0bb-4940-aab7-64f014ec999d/dqc_reference/reference_markers.hmm OceanDNA-a1135/protein.faa > /dev/null
[2023-03-18 01:37:10,378] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:37:10,378] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgff17e650-128b-44cb-906b-9431eb964969/OceanDNA-a1135.fa]
[2023-03-18 01:37:10,384] [INFO] Query marker FASTA was written to OceanDNA-a1135/markers.fasta
[2023-03-18 01:37:10,386] [INFO] Task started: Blastn
[2023-03-18 01:37:10,386] [INFO] Running command: blastn -query OceanDNA-a1135/markers.fasta -db /var/lib/cwl/stgbf4e6df6-b0bb-4940-aab7-64f014ec999d/dqc_reference/reference_markers.fasta -out OceanDNA-a1135/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:37:10,894] [INFO] Task succeeded: Blastn
[2023-03-18 01:37:10,898] [INFO] Selected 5 target genomes.
[2023-03-18 01:37:10,899] [INFO] Target genome list was writen to OceanDNA-a1135/target_genomes.txt
[2023-03-18 01:37:10,901] [INFO] Task started: fastANI
[2023-03-18 01:37:10,902] [INFO] Running command: fastANI --query /var/lib/cwl/stgff17e650-128b-44cb-906b-9431eb964969/OceanDNA-a1135.fa --refList OceanDNA-a1135/target_genomes.txt --output OceanDNA-a1135/fastani_result.tsv --threads 1
[2023-03-18 01:37:12,201] [INFO] Task succeeded: fastANI
[2023-03-18 01:37:12,201] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf4e6df6-b0bb-4940-aab7-64f014ec999d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:37:12,202] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf4e6df6-b0bb-4940-aab7-64f014ec999d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:37:12,202] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:37:12,202] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 01:37:12,202] [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 01:37:12,204] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1135/tc_result.tsv
[2023-03-18 01:37:12,210] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:37:12,210] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:37:12,211] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf4e6df6-b0bb-4940-aab7-64f014ec999d/dqc_reference/checkm_data
[2023-03-18 01:37:12,214] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:37:12,216] [INFO] Task started: CheckM
[2023-03-18 01:37:12,216] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1135/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1135/checkm_input OceanDNA-a1135/checkm_result
[2023-03-18 01:37:26,769] [INFO] Task succeeded: CheckM
[2023-03-18 01:37:26,770] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.81%
Contamintation: 2.60%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-18 01:37:26,779] [INFO] ===== Completeness check finished =====
[2023-03-18 01:37:26,779] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:37:26,779] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1135/markers.fasta)
[2023-03-18 01:37:26,780] [INFO] Task started: Blastn
[2023-03-18 01:37:26,780] [INFO] Running command: blastn -query OceanDNA-a1135/markers.fasta -db /var/lib/cwl/stgbf4e6df6-b0bb-4940-aab7-64f014ec999d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1135/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:37:27,349] [INFO] Task succeeded: Blastn
[2023-03-18 01:37:27,360] [INFO] Selected 8 target genomes.
[2023-03-18 01:37:27,360] [INFO] Target genome list was writen to OceanDNA-a1135/target_genomes_gtdb.txt
[2023-03-18 01:37:27,368] [INFO] Task started: fastANI
[2023-03-18 01:37:27,368] [INFO] Running command: fastANI --query /var/lib/cwl/stgff17e650-128b-44cb-906b-9431eb964969/OceanDNA-a1135.fa --refList OceanDNA-a1135/target_genomes_gtdb.txt --output OceanDNA-a1135/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:37:28,634] [INFO] Task succeeded: fastANI
[2023-03-18 01:37:28,637] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:37:28,637] [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_018693795.1	s__JABJPM01 sp018693795	99.7759	152	206	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__SCGC-AAA011-G17;f__PNOQ01;g__JABJPM01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018663865.1	s__JABJPM01 sp018663865	79.6762	96	206	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__SCGC-AAA011-G17;f__PNOQ01;g__JABJPM01	95.0	99.82	99.71	0.88	0.82	5	-
--------------------------------------------------------------------------------
[2023-03-18 01:37:28,641] [INFO] GTDB search result was written to OceanDNA-a1135/result_gtdb.tsv
[2023-03-18 01:37:28,644] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:37:28,649] [INFO] DFAST_QC result json was written to OceanDNA-a1135/dqc_result.json
[2023-03-18 01:37:28,649] [INFO] DFAST_QC completed!
[2023-03-18 01:37:28,649] [INFO] Total running time: 0h0m23s