[2023-03-17 02:49:37,511] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:49:37,511] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:49:37,511] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5b17f63-cda2-4559-b6dc-fcfa3d33edf0/dqc_reference
[2023-03-17 02:49:38,739] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:49:38,739] [INFO] Task started: Prodigal
[2023-03-17 02:49:38,739] [INFO] Running command: cat /var/lib/cwl/stgdf1c6aad-8728-4faa-a7cb-7881008a1a75/OceanDNA-b15938.fa | prodigal -d OceanDNA-b15938/cds.fna -a OceanDNA-b15938/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:49:45,119] [INFO] Task succeeded: Prodigal
[2023-03-17 02:49:45,119] [INFO] Task started: HMMsearch
[2023-03-17 02:49:45,119] [INFO] Running command: hmmsearch --tblout OceanDNA-b15938/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5b17f63-cda2-4559-b6dc-fcfa3d33edf0/dqc_reference/reference_markers.hmm OceanDNA-b15938/protein.faa > /dev/null
[2023-03-17 02:49:45,274] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:49:45,275] [INFO] Found 6/6 markers.
[2023-03-17 02:49:45,285] [INFO] Query marker FASTA was written to OceanDNA-b15938/markers.fasta
[2023-03-17 02:49:45,286] [INFO] Task started: Blastn
[2023-03-17 02:49:45,286] [INFO] Running command: blastn -query OceanDNA-b15938/markers.fasta -db /var/lib/cwl/stgb5b17f63-cda2-4559-b6dc-fcfa3d33edf0/dqc_reference/reference_markers.fasta -out OceanDNA-b15938/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:49:45,805] [INFO] Task succeeded: Blastn
[2023-03-17 02:49:45,806] [INFO] Selected 10 target genomes.
[2023-03-17 02:49:45,806] [INFO] Target genome list was writen to OceanDNA-b15938/target_genomes.txt
[2023-03-17 02:49:45,914] [INFO] Task started: fastANI
[2023-03-17 02:49:45,914] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf1c6aad-8728-4faa-a7cb-7881008a1a75/OceanDNA-b15938.fa --refList OceanDNA-b15938/target_genomes.txt --output OceanDNA-b15938/fastani_result.tsv --threads 1
[2023-03-17 02:49:51,329] [INFO] Task succeeded: fastANI
[2023-03-17 02:49:51,329] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5b17f63-cda2-4559-b6dc-fcfa3d33edf0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:49:51,329] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5b17f63-cda2-4559-b6dc-fcfa3d33edf0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:49:51,329] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:49:51,330] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 02:49:51,330] [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 02:49:51,330] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15938/tc_result.tsv
[2023-03-17 02:49:51,330] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:49:51,330] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:49:51,330] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5b17f63-cda2-4559-b6dc-fcfa3d33edf0/dqc_reference/checkm_data
[2023-03-17 02:49:51,333] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:49:51,336] [INFO] Task started: CheckM
[2023-03-17 02:49:51,336] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15938/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15938/checkm_input OceanDNA-b15938/checkm_result
[2023-03-17 02:50:13,016] [INFO] Task succeeded: CheckM
[2023-03-17 02:50:13,016] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 02:50:13,020] [INFO] ===== Completeness check finished =====
[2023-03-17 02:50:13,020] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:50:13,020] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15938/markers.fasta)
[2023-03-17 02:50:13,020] [INFO] Task started: Blastn
[2023-03-17 02:50:13,020] [INFO] Running command: blastn -query OceanDNA-b15938/markers.fasta -db /var/lib/cwl/stgb5b17f63-cda2-4559-b6dc-fcfa3d33edf0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15938/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:50:13,724] [INFO] Task succeeded: Blastn
[2023-03-17 02:50:13,725] [INFO] Selected 13 target genomes.
[2023-03-17 02:50:13,725] [INFO] Target genome list was writen to OceanDNA-b15938/target_genomes_gtdb.txt
[2023-03-17 02:50:14,034] [INFO] Task started: fastANI
[2023-03-17 02:50:14,034] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf1c6aad-8728-4faa-a7cb-7881008a1a75/OceanDNA-b15938.fa --refList OceanDNA-b15938/target_genomes_gtdb.txt --output OceanDNA-b15938/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:50:19,471] [INFO] Task succeeded: fastANI
[2023-03-17 02:50:19,473] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 02:50:19,473] [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_002450515.1	s__UBA6952 sp002450515	97.1806	328	412	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA6952;f__UBA6952;g__UBA6952	95.0	97.13	97.13	0.86	0.86	2	conclusive
GCA_009392515.1	s__UBA6952 sp009392515	88.8082	368	412	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA6952;f__UBA6952;g__UBA6952	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 02:50:19,474] [INFO] GTDB search result was written to OceanDNA-b15938/result_gtdb.tsv
[2023-03-17 02:50:19,475] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:50:19,477] [INFO] DFAST_QC result json was written to OceanDNA-b15938/dqc_result.json
[2023-03-17 02:50:19,477] [INFO] DFAST_QC completed!
[2023-03-17 02:50:19,477] [INFO] Total running time: 0h0m42s