[2023-03-17 13:01:52,508] [INFO] DFAST_QC pipeline started.
[2023-03-17 13:01:52,509] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 13:01:52,509] [INFO] DQC Reference Directory: /var/lib/cwl/stg173cd3c1-708e-419e-9b96-33770636a6e8/dqc_reference
[2023-03-17 13:01:55,103] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 13:01:55,108] [INFO] Task started: Prodigal
[2023-03-17 13:01:55,109] [INFO] Running command: cat /var/lib/cwl/stg22876462-9864-4fd2-99f6-991f22c8b54a/OceanDNA-b20207.fa | prodigal -d OceanDNA-b20207/cds.fna -a OceanDNA-b20207/protein.faa -g 11 -q > /dev/null
[2023-03-17 13:02:02,714] [INFO] Task succeeded: Prodigal
[2023-03-17 13:02:02,714] [INFO] Task started: HMMsearch
[2023-03-17 13:02:02,714] [INFO] Running command: hmmsearch --tblout OceanDNA-b20207/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg173cd3c1-708e-419e-9b96-33770636a6e8/dqc_reference/reference_markers.hmm OceanDNA-b20207/protein.faa > /dev/null
[2023-03-17 13:02:02,851] [INFO] Task succeeded: HMMsearch
[2023-03-17 13:02:02,851] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg22876462-9864-4fd2-99f6-991f22c8b54a/OceanDNA-b20207.fa]
[2023-03-17 13:02:02,864] [INFO] Query marker FASTA was written to OceanDNA-b20207/markers.fasta
[2023-03-17 13:02:02,864] [INFO] Task started: Blastn
[2023-03-17 13:02:02,864] [INFO] Running command: blastn -query OceanDNA-b20207/markers.fasta -db /var/lib/cwl/stg173cd3c1-708e-419e-9b96-33770636a6e8/dqc_reference/reference_markers.fasta -out OceanDNA-b20207/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:02:03,306] [INFO] Task succeeded: Blastn
[2023-03-17 13:02:03,307] [INFO] Selected 9 target genomes.
[2023-03-17 13:02:03,307] [INFO] Target genome list was writen to OceanDNA-b20207/target_genomes.txt
[2023-03-17 13:02:03,318] [INFO] Task started: fastANI
[2023-03-17 13:02:03,318] [INFO] Running command: fastANI --query /var/lib/cwl/stg22876462-9864-4fd2-99f6-991f22c8b54a/OceanDNA-b20207.fa --refList OceanDNA-b20207/target_genomes.txt --output OceanDNA-b20207/fastani_result.tsv --threads 1
[2023-03-17 13:02:07,314] [INFO] Task succeeded: fastANI
[2023-03-17 13:02:07,315] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg173cd3c1-708e-419e-9b96-33770636a6e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 13:02:07,315] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg173cd3c1-708e-419e-9b96-33770636a6e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 13:02:07,315] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 13:02:07,315] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 13:02:07,315] [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
--------------------------------------------------------------------------------
[2023-03-17 13:02:07,315] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20207/tc_result.tsv
[2023-03-17 13:02:07,316] [INFO] ===== Taxonomy check completed =====
[2023-03-17 13:02:07,316] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 13:02:07,316] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg173cd3c1-708e-419e-9b96-33770636a6e8/dqc_reference/checkm_data
[2023-03-17 13:02:07,403] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 13:02:07,445] [INFO] Task started: CheckM
[2023-03-17 13:02:07,445] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20207/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20207/checkm_input OceanDNA-b20207/checkm_result
[2023-03-17 13:02:37,831] [INFO] Task succeeded: CheckM
[2023-03-17 13:02:37,832] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 13:02:37,833] [INFO] ===== Completeness check finished =====
[2023-03-17 13:02:37,833] [INFO] ===== Start GTDB Search =====
[2023-03-17 13:02:37,834] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20207/markers.fasta)
[2023-03-17 13:02:37,834] [INFO] Task started: Blastn
[2023-03-17 13:02:37,834] [INFO] Running command: blastn -query OceanDNA-b20207/markers.fasta -db /var/lib/cwl/stg173cd3c1-708e-419e-9b96-33770636a6e8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20207/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:02:38,287] [INFO] Task succeeded: Blastn
[2023-03-17 13:02:38,288] [INFO] Selected 13 target genomes.
[2023-03-17 13:02:38,288] [INFO] Target genome list was writen to OceanDNA-b20207/target_genomes_gtdb.txt
[2023-03-17 13:02:38,576] [INFO] Task started: fastANI
[2023-03-17 13:02:38,577] [INFO] Running command: fastANI --query /var/lib/cwl/stg22876462-9864-4fd2-99f6-991f22c8b54a/OceanDNA-b20207.fa --refList OceanDNA-b20207/target_genomes_gtdb.txt --output OceanDNA-b20207/fastani_result_gtdb.tsv --threads 1
[2023-03-17 13:02:46,457] [INFO] Task succeeded: fastANI
[2023-03-17 13:02:46,460] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 13:02:46,460] [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_012964275.1	s__UBA1611 sp012964275	85.345	283	449	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__UBA1611	95.0	98.90	98.90	0.78	0.78	2	-
GCA_002321855.1	s__UBA1611 sp002321855	81.4603	217	449	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__UBA1611	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 13:02:46,460] [INFO] GTDB search result was written to OceanDNA-b20207/result_gtdb.tsv
[2023-03-17 13:02:46,460] [INFO] ===== GTDB Search completed =====
[2023-03-17 13:02:46,461] [INFO] DFAST_QC result json was written to OceanDNA-b20207/dqc_result.json
[2023-03-17 13:02:46,461] [INFO] DFAST_QC completed!
[2023-03-17 13:02:46,461] [INFO] Total running time: 0h0m54s