[2023-03-18 22:17:12,668] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:17:12,668] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:17:12,668] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d33e47f-0390-481b-a579-5b1ef99330be/dqc_reference
[2023-03-18 22:17:13,840] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:17:13,840] [INFO] Task started: Prodigal
[2023-03-18 22:17:13,840] [INFO] Running command: cat /var/lib/cwl/stgb5b83512-f346-4114-ac30-4fc590a0f4cb/OceanDNA-b45789.fa | prodigal -d OceanDNA-b45789/cds.fna -a OceanDNA-b45789/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:17:29,977] [INFO] Task succeeded: Prodigal
[2023-03-18 22:17:29,978] [INFO] Task started: HMMsearch
[2023-03-18 22:17:29,978] [INFO] Running command: hmmsearch --tblout OceanDNA-b45789/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d33e47f-0390-481b-a579-5b1ef99330be/dqc_reference/reference_markers.hmm OceanDNA-b45789/protein.faa > /dev/null
[2023-03-18 22:17:30,167] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:17:30,167] [INFO] Found 6/6 markers.
[2023-03-18 22:17:30,183] [INFO] Query marker FASTA was written to OceanDNA-b45789/markers.fasta
[2023-03-18 22:17:30,184] [INFO] Task started: Blastn
[2023-03-18 22:17:30,185] [INFO] Running command: blastn -query OceanDNA-b45789/markers.fasta -db /var/lib/cwl/stg6d33e47f-0390-481b-a579-5b1ef99330be/dqc_reference/reference_markers.fasta -out OceanDNA-b45789/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:17:30,735] [INFO] Task succeeded: Blastn
[2023-03-18 22:17:30,735] [INFO] Selected 17 target genomes.
[2023-03-18 22:17:30,736] [INFO] Target genome list was writen to OceanDNA-b45789/target_genomes.txt
[2023-03-18 22:17:30,744] [INFO] Task started: fastANI
[2023-03-18 22:17:30,744] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5b83512-f346-4114-ac30-4fc590a0f4cb/OceanDNA-b45789.fa --refList OceanDNA-b45789/target_genomes.txt --output OceanDNA-b45789/fastani_result.tsv --threads 1
[2023-03-18 22:17:37,667] [INFO] Task succeeded: fastANI
[2023-03-18 22:17:37,668] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d33e47f-0390-481b-a579-5b1ef99330be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:17:37,668] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d33e47f-0390-481b-a579-5b1ef99330be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:17:37,668] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:17:37,668] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 22:17:37,668] [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 22:17:37,669] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45789/tc_result.tsv
[2023-03-18 22:17:37,669] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:17:37,669] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:17:37,669] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d33e47f-0390-481b-a579-5b1ef99330be/dqc_reference/checkm_data
[2023-03-18 22:17:37,672] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:17:37,696] [INFO] Task started: CheckM
[2023-03-18 22:17:37,696] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45789/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45789/checkm_input OceanDNA-b45789/checkm_result
[2023-03-18 22:18:21,546] [INFO] Task succeeded: CheckM
[2023-03-18 22:18:21,546] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:18:21,585] [INFO] ===== Completeness check finished =====
[2023-03-18 22:18:21,585] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:18:21,585] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45789/markers.fasta)
[2023-03-18 22:18:21,586] [INFO] Task started: Blastn
[2023-03-18 22:18:21,586] [INFO] Running command: blastn -query OceanDNA-b45789/markers.fasta -db /var/lib/cwl/stg6d33e47f-0390-481b-a579-5b1ef99330be/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45789/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:18:22,505] [INFO] Task succeeded: Blastn
[2023-03-18 22:18:22,506] [INFO] Selected 24 target genomes.
[2023-03-18 22:18:22,506] [INFO] Target genome list was writen to OceanDNA-b45789/target_genomes_gtdb.txt
[2023-03-18 22:18:22,526] [INFO] Task started: fastANI
[2023-03-18 22:18:22,526] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5b83512-f346-4114-ac30-4fc590a0f4cb/OceanDNA-b45789.fa --refList OceanDNA-b45789/target_genomes_gtdb.txt --output OceanDNA-b45789/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:18:30,199] [INFO] Task succeeded: fastANI
[2023-03-18 22:18:30,203] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 22:18:30,203] [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_002694035.1	s__MB11C04 sp002694035	99.4978	648	729	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902580225.1	s__MB11C04 sp902580225	77.7645	58	729	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018646565.1	s__MB11C04 sp018646565	76.6289	54	729	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478775.1	s__MB11C04 sp002477515	76.3973	95	729	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	98.93	98.38	0.86	0.80	5	-
GCA_018645475.1	s__MB11C04 sp018645475	76.095	91	729	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 22:18:30,211] [INFO] GTDB search result was written to OceanDNA-b45789/result_gtdb.tsv
[2023-03-18 22:18:30,211] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:18:30,212] [INFO] DFAST_QC result json was written to OceanDNA-b45789/dqc_result.json
[2023-03-18 22:18:30,212] [INFO] DFAST_QC completed!
[2023-03-18 22:18:30,212] [INFO] Total running time: 0h1m18s