[2023-03-18 04:38:00,467] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:38:00,467] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:38:00,467] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d2e6fc5-d3b8-49e5-b8e1-3348b87dfe07/dqc_reference
[2023-03-18 04:38:01,599] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:38:01,599] [INFO] Task started: Prodigal
[2023-03-18 04:38:01,600] [INFO] Running command: cat /var/lib/cwl/stgecb716a7-c125-4ad4-bbf6-8b7e54f83c82/OceanDNA-b13726.fa | prodigal -d OceanDNA-b13726/cds.fna -a OceanDNA-b13726/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:38:03,876] [INFO] Task succeeded: Prodigal
[2023-03-18 04:38:03,876] [INFO] Task started: HMMsearch
[2023-03-18 04:38:03,876] [INFO] Running command: hmmsearch --tblout OceanDNA-b13726/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d2e6fc5-d3b8-49e5-b8e1-3348b87dfe07/dqc_reference/reference_markers.hmm OceanDNA-b13726/protein.faa > /dev/null
[2023-03-18 04:38:04,027] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:38:04,027] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgecb716a7-c125-4ad4-bbf6-8b7e54f83c82/OceanDNA-b13726.fa]
[2023-03-18 04:38:04,036] [INFO] Query marker FASTA was written to OceanDNA-b13726/markers.fasta
[2023-03-18 04:38:04,036] [INFO] Task started: Blastn
[2023-03-18 04:38:04,036] [INFO] Running command: blastn -query OceanDNA-b13726/markers.fasta -db /var/lib/cwl/stg4d2e6fc5-d3b8-49e5-b8e1-3348b87dfe07/dqc_reference/reference_markers.fasta -out OceanDNA-b13726/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:38:04,566] [INFO] Task succeeded: Blastn
[2023-03-18 04:38:04,567] [INFO] Selected 11 target genomes.
[2023-03-18 04:38:04,567] [INFO] Target genome list was writen to OceanDNA-b13726/target_genomes.txt
[2023-03-18 04:38:04,577] [INFO] Task started: fastANI
[2023-03-18 04:38:04,577] [INFO] Running command: fastANI --query /var/lib/cwl/stgecb716a7-c125-4ad4-bbf6-8b7e54f83c82/OceanDNA-b13726.fa --refList OceanDNA-b13726/target_genomes.txt --output OceanDNA-b13726/fastani_result.tsv --threads 1
[2023-03-18 04:38:09,640] [INFO] Task succeeded: fastANI
[2023-03-18 04:38:09,641] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d2e6fc5-d3b8-49e5-b8e1-3348b87dfe07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:38:09,641] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d2e6fc5-d3b8-49e5-b8e1-3348b87dfe07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:38:09,641] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:38:09,641] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 04:38:09,641] [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 04:38:09,642] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13726/tc_result.tsv
[2023-03-18 04:38:09,642] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:38:09,642] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:38:09,642] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d2e6fc5-d3b8-49e5-b8e1-3348b87dfe07/dqc_reference/checkm_data
[2023-03-18 04:38:09,645] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:38:09,648] [INFO] Task started: CheckM
[2023-03-18 04:38:09,648] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13726/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13726/checkm_input OceanDNA-b13726/checkm_result
[2023-03-18 04:38:22,441] [INFO] Task succeeded: CheckM
[2023-03-18 04:38:22,441] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.34%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:38:22,442] [INFO] ===== Completeness check finished =====
[2023-03-18 04:38:22,442] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:38:22,443] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13726/markers.fasta)
[2023-03-18 04:38:22,443] [INFO] Task started: Blastn
[2023-03-18 04:38:22,443] [INFO] Running command: blastn -query OceanDNA-b13726/markers.fasta -db /var/lib/cwl/stg4d2e6fc5-d3b8-49e5-b8e1-3348b87dfe07/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13726/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:38:23,103] [INFO] Task succeeded: Blastn
[2023-03-18 04:38:23,104] [INFO] Selected 19 target genomes.
[2023-03-18 04:38:23,104] [INFO] Target genome list was writen to OceanDNA-b13726/target_genomes_gtdb.txt
[2023-03-18 04:38:23,120] [INFO] Task started: fastANI
[2023-03-18 04:38:23,120] [INFO] Running command: fastANI --query /var/lib/cwl/stgecb716a7-c125-4ad4-bbf6-8b7e54f83c82/OceanDNA-b13726.fa --refList OceanDNA-b13726/target_genomes_gtdb.txt --output OceanDNA-b13726/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:38:28,496] [INFO] Task succeeded: fastANI
[2023-03-18 04:38:28,499] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 04:38:28,499] [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_002694895.1	s__GCA-002694895 sp002694895	89.484	74	103	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__GCA-002694895;g__GCA-002694895	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009391605.1	s__GCA-002694895 sp009391605	88.9469	81	103	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__GCA-002694895;g__GCA-002694895	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 04:38:28,499] [INFO] GTDB search result was written to OceanDNA-b13726/result_gtdb.tsv
[2023-03-18 04:38:28,499] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:38:28,500] [INFO] DFAST_QC result json was written to OceanDNA-b13726/dqc_result.json
[2023-03-18 04:38:28,500] [INFO] DFAST_QC completed!
[2023-03-18 04:38:28,500] [INFO] Total running time: 0h0m28s