[2023-03-15 13:52:04,722] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:52:04,722] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:52:04,722] [INFO] DQC Reference Directory: /var/lib/cwl/stgacb3fe16-6021-45b0-81b7-67bb08f6cc47/dqc_reference
[2023-03-15 13:52:05,838] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:52:05,838] [INFO] Task started: Prodigal
[2023-03-15 13:52:05,839] [INFO] Running command: cat /var/lib/cwl/stg5f00fc94-5ff6-449f-a7e5-a2dada7ed0ea/OceanDNA-b20479.fa | prodigal -d OceanDNA-b20479/cds.fna -a OceanDNA-b20479/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:52:12,133] [INFO] Task succeeded: Prodigal
[2023-03-15 13:52:12,133] [INFO] Task started: HMMsearch
[2023-03-15 13:52:12,133] [INFO] Running command: hmmsearch --tblout OceanDNA-b20479/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgacb3fe16-6021-45b0-81b7-67bb08f6cc47/dqc_reference/reference_markers.hmm OceanDNA-b20479/protein.faa > /dev/null
[2023-03-15 13:52:12,285] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:52:12,285] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg5f00fc94-5ff6-449f-a7e5-a2dada7ed0ea/OceanDNA-b20479.fa]
[2023-03-15 13:52:12,298] [INFO] Query marker FASTA was written to OceanDNA-b20479/markers.fasta
[2023-03-15 13:52:12,298] [INFO] Task started: Blastn
[2023-03-15 13:52:12,298] [INFO] Running command: blastn -query OceanDNA-b20479/markers.fasta -db /var/lib/cwl/stgacb3fe16-6021-45b0-81b7-67bb08f6cc47/dqc_reference/reference_markers.fasta -out OceanDNA-b20479/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:52:12,798] [INFO] Task succeeded: Blastn
[2023-03-15 13:52:12,799] [INFO] Selected 16 target genomes.
[2023-03-15 13:52:12,799] [INFO] Target genome list was writen to OceanDNA-b20479/target_genomes.txt
[2023-03-15 13:52:12,809] [INFO] Task started: fastANI
[2023-03-15 13:52:12,809] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f00fc94-5ff6-449f-a7e5-a2dada7ed0ea/OceanDNA-b20479.fa --refList OceanDNA-b20479/target_genomes.txt --output OceanDNA-b20479/fastani_result.tsv --threads 1
[2023-03-15 13:52:19,806] [INFO] Task succeeded: fastANI
[2023-03-15 13:52:19,806] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgacb3fe16-6021-45b0-81b7-67bb08f6cc47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:52:19,807] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgacb3fe16-6021-45b0-81b7-67bb08f6cc47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:52:19,807] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:52:19,807] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 13:52:19,807] [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
--------------------------------------------------------------------------------
[2023-03-15 13:52:19,807] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20479/tc_result.tsv
[2023-03-15 13:52:19,807] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:52:19,807] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:52:19,807] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgacb3fe16-6021-45b0-81b7-67bb08f6cc47/dqc_reference/checkm_data
[2023-03-15 13:52:19,810] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:52:19,813] [INFO] Task started: CheckM
[2023-03-15 13:52:19,813] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20479/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20479/checkm_input OceanDNA-b20479/checkm_result
[2023-03-15 13:52:40,968] [INFO] Task succeeded: CheckM
[2023-03-15 13:52:40,969] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.38%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:52:40,971] [INFO] ===== Completeness check finished =====
[2023-03-15 13:52:40,971] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:52:40,971] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20479/markers.fasta)
[2023-03-15 13:52:40,972] [INFO] Task started: Blastn
[2023-03-15 13:52:40,972] [INFO] Running command: blastn -query OceanDNA-b20479/markers.fasta -db /var/lib/cwl/stgacb3fe16-6021-45b0-81b7-67bb08f6cc47/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20479/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:52:41,664] [INFO] Task succeeded: Blastn
[2023-03-15 13:52:41,665] [INFO] Selected 18 target genomes.
[2023-03-15 13:52:41,665] [INFO] Target genome list was writen to OceanDNA-b20479/target_genomes_gtdb.txt
[2023-03-15 13:52:41,684] [INFO] Task started: fastANI
[2023-03-15 13:52:41,685] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f00fc94-5ff6-449f-a7e5-a2dada7ed0ea/OceanDNA-b20479.fa --refList OceanDNA-b20479/target_genomes_gtdb.txt --output OceanDNA-b20479/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:52:46,657] [INFO] Task succeeded: fastANI
[2023-03-15 13:52:46,660] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 13:52:46,660] [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_002703375.1	s__GCA-002704045 sp002703375	77.6865	155	421	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002704045;g__GCA-002704045	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002704045.1	s__GCA-002704045 sp002704045	77.4076	124	421	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002704045;g__GCA-002704045	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:52:46,660] [INFO] GTDB search result was written to OceanDNA-b20479/result_gtdb.tsv
[2023-03-15 13:52:46,660] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:52:46,661] [INFO] DFAST_QC result json was written to OceanDNA-b20479/dqc_result.json
[2023-03-15 13:52:46,661] [INFO] DFAST_QC completed!
[2023-03-15 13:52:46,661] [INFO] Total running time: 0h0m42s