[2023-03-16 10:57:32,962] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:57:32,962] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:57:32,962] [INFO] DQC Reference Directory: /var/lib/cwl/stg128f4f1f-6057-46ce-9742-ed1ce2cda127/dqc_reference
[2023-03-16 10:57:34,158] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:57:34,158] [INFO] Task started: Prodigal
[2023-03-16 10:57:34,158] [INFO] Running command: cat /var/lib/cwl/stgad73964b-9ff3-427a-8c0e-10dee5d754a8/OceanDNA-b45514.fa | prodigal -d OceanDNA-b45514/cds.fna -a OceanDNA-b45514/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:58:16,836] [INFO] Task succeeded: Prodigal
[2023-03-16 10:58:16,836] [INFO] Task started: HMMsearch
[2023-03-16 10:58:16,836] [INFO] Running command: hmmsearch --tblout OceanDNA-b45514/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg128f4f1f-6057-46ce-9742-ed1ce2cda127/dqc_reference/reference_markers.hmm OceanDNA-b45514/protein.faa > /dev/null
[2023-03-16 10:58:17,038] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:58:17,039] [INFO] Found 6/6 markers.
[2023-03-16 10:58:17,067] [INFO] Query marker FASTA was written to OceanDNA-b45514/markers.fasta
[2023-03-16 10:58:17,068] [INFO] Task started: Blastn
[2023-03-16 10:58:17,068] [INFO] Running command: blastn -query OceanDNA-b45514/markers.fasta -db /var/lib/cwl/stg128f4f1f-6057-46ce-9742-ed1ce2cda127/dqc_reference/reference_markers.fasta -out OceanDNA-b45514/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:58:17,774] [INFO] Task succeeded: Blastn
[2023-03-16 10:58:17,776] [INFO] Selected 7 target genomes.
[2023-03-16 10:58:17,776] [INFO] Target genome list was writen to OceanDNA-b45514/target_genomes.txt
[2023-03-16 10:58:17,781] [INFO] Task started: fastANI
[2023-03-16 10:58:17,781] [INFO] Running command: fastANI --query /var/lib/cwl/stgad73964b-9ff3-427a-8c0e-10dee5d754a8/OceanDNA-b45514.fa --refList OceanDNA-b45514/target_genomes.txt --output OceanDNA-b45514/fastani_result.tsv --threads 1
[2023-03-16 10:58:28,416] [INFO] Task succeeded: fastANI
[2023-03-16 10:58:28,417] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg128f4f1f-6057-46ce-9742-ed1ce2cda127/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:58:28,417] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg128f4f1f-6057-46ce-9742-ed1ce2cda127/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:58:28,417] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:58:28,417] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 10:58:28,417] [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
--------------------------------------------------------------------------------
[2023-03-16 10:58:28,418] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45514/tc_result.tsv
[2023-03-16 10:58:28,418] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:58:28,418] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:58:28,418] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg128f4f1f-6057-46ce-9742-ed1ce2cda127/dqc_reference/checkm_data
[2023-03-16 10:58:28,421] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:58:28,509] [INFO] Task started: CheckM
[2023-03-16 10:58:28,509] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45514/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45514/checkm_input OceanDNA-b45514/checkm_result
[2023-03-16 10:59:52,295] [INFO] Task succeeded: CheckM
[2023-03-16 10:59:52,296] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 10:59:52,299] [INFO] ===== Completeness check finished =====
[2023-03-16 10:59:52,299] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:59:52,299] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45514/markers.fasta)
[2023-03-16 10:59:52,300] [INFO] Task started: Blastn
[2023-03-16 10:59:52,301] [INFO] Running command: blastn -query OceanDNA-b45514/markers.fasta -db /var/lib/cwl/stg128f4f1f-6057-46ce-9742-ed1ce2cda127/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45514/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:59:53,258] [INFO] Task succeeded: Blastn
[2023-03-16 10:59:53,260] [INFO] Selected 16 target genomes.
[2023-03-16 10:59:53,260] [INFO] Target genome list was writen to OceanDNA-b45514/target_genomes_gtdb.txt
[2023-03-16 10:59:53,286] [INFO] Task started: fastANI
[2023-03-16 10:59:53,286] [INFO] Running command: fastANI --query /var/lib/cwl/stgad73964b-9ff3-427a-8c0e-10dee5d754a8/OceanDNA-b45514.fa --refList OceanDNA-b45514/target_genomes_gtdb.txt --output OceanDNA-b45514/fastani_result_gtdb.tsv --threads 1
[2023-03-16 11:00:01,612] [INFO] Task succeeded: fastANI
[2023-03-16 11:00:01,617] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 11:00:01,617] [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_018695085.1	s__GCA-2730975 sp018695085	98.3486	607	1059	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__GCA-2730975	95.0	98.14	98.04	0.72	0.68	4	conclusive
GCA_905612515.1	s__GCA-2730975 sp905612515	87.3892	313	1059	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__GCA-2730975	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002730975.1	s__GCA-2730975 sp002730975	86.8932	692	1059	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__GCA-2730975	95.0	99.68	99.68	0.85	0.85	2	-
GCA_014382645.1	s__GCA-2730975 sp014382645	85.6274	595	1059	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__GCA-2730975	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018645725.1	s__MB11C04 sp018645725	81.9423	134	1059	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002500665.1	s__MB11C04 sp002500665	79.9354	128	1059	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	98.37	95.55	0.93	0.84	7	-
--------------------------------------------------------------------------------
[2023-03-16 11:00:01,618] [INFO] GTDB search result was written to OceanDNA-b45514/result_gtdb.tsv
[2023-03-16 11:00:01,618] [INFO] ===== GTDB Search completed =====
[2023-03-16 11:00:01,619] [INFO] DFAST_QC result json was written to OceanDNA-b45514/dqc_result.json
[2023-03-16 11:00:01,619] [INFO] DFAST_QC completed!
[2023-03-16 11:00:01,619] [INFO] Total running time: 0h2m29s