[2023-03-16 05:41:22,620] [INFO] DFAST_QC pipeline started.
[2023-03-16 05:41:22,620] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 05:41:22,620] [INFO] DQC Reference Directory: /var/lib/cwl/stgf197de56-9a29-42e2-a58c-b4eb8cfb0ae4/dqc_reference
[2023-03-16 05:41:23,718] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 05:41:23,718] [INFO] Task started: Prodigal
[2023-03-16 05:41:23,718] [INFO] Running command: cat /var/lib/cwl/stgacc9fd6d-1c90-47cd-a97a-685ed4bc1a06/OceanDNA-b45508.fa | prodigal -d OceanDNA-b45508/cds.fna -a OceanDNA-b45508/protein.faa -g 11 -q > /dev/null
[2023-03-16 05:41:37,018] [INFO] Task succeeded: Prodigal
[2023-03-16 05:41:37,018] [INFO] Task started: HMMsearch
[2023-03-16 05:41:37,018] [INFO] Running command: hmmsearch --tblout OceanDNA-b45508/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf197de56-9a29-42e2-a58c-b4eb8cfb0ae4/dqc_reference/reference_markers.hmm OceanDNA-b45508/protein.faa > /dev/null
[2023-03-16 05:41:37,189] [INFO] Task succeeded: HMMsearch
[2023-03-16 05:41:37,189] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgacc9fd6d-1c90-47cd-a97a-685ed4bc1a06/OceanDNA-b45508.fa]
[2023-03-16 05:41:37,206] [INFO] Query marker FASTA was written to OceanDNA-b45508/markers.fasta
[2023-03-16 05:41:37,206] [INFO] Task started: Blastn
[2023-03-16 05:41:37,206] [INFO] Running command: blastn -query OceanDNA-b45508/markers.fasta -db /var/lib/cwl/stgf197de56-9a29-42e2-a58c-b4eb8cfb0ae4/dqc_reference/reference_markers.fasta -out OceanDNA-b45508/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:41:37,702] [INFO] Task succeeded: Blastn
[2023-03-16 05:41:37,703] [INFO] Selected 23 target genomes.
[2023-03-16 05:41:37,703] [INFO] Target genome list was writen to OceanDNA-b45508/target_genomes.txt
[2023-03-16 05:41:37,714] [INFO] Task started: fastANI
[2023-03-16 05:41:37,714] [INFO] Running command: fastANI --query /var/lib/cwl/stgacc9fd6d-1c90-47cd-a97a-685ed4bc1a06/OceanDNA-b45508.fa --refList OceanDNA-b45508/target_genomes.txt --output OceanDNA-b45508/fastani_result.tsv --threads 1
[2023-03-16 05:41:50,348] [INFO] Task succeeded: fastANI
[2023-03-16 05:41:50,348] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf197de56-9a29-42e2-a58c-b4eb8cfb0ae4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 05:41:50,349] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf197de56-9a29-42e2-a58c-b4eb8cfb0ae4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 05:41:50,349] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 05:41:50,349] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 05:41:50,349] [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 05:41:50,349] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45508/tc_result.tsv
[2023-03-16 05:41:50,349] [INFO] ===== Taxonomy check completed =====
[2023-03-16 05:41:50,349] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 05:41:50,350] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf197de56-9a29-42e2-a58c-b4eb8cfb0ae4/dqc_reference/checkm_data
[2023-03-16 05:41:50,352] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 05:41:50,356] [INFO] Task started: CheckM
[2023-03-16 05:41:50,356] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45508/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45508/checkm_input OceanDNA-b45508/checkm_result
[2023-03-16 05:42:28,464] [INFO] Task succeeded: CheckM
[2023-03-16 05:42:28,465] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.03%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 05:42:28,494] [INFO] ===== Completeness check finished =====
[2023-03-16 05:42:28,494] [INFO] ===== Start GTDB Search =====
[2023-03-16 05:42:28,494] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45508/markers.fasta)
[2023-03-16 05:42:28,494] [INFO] Task started: Blastn
[2023-03-16 05:42:28,494] [INFO] Running command: blastn -query OceanDNA-b45508/markers.fasta -db /var/lib/cwl/stgf197de56-9a29-42e2-a58c-b4eb8cfb0ae4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45508/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:42:29,214] [INFO] Task succeeded: Blastn
[2023-03-16 05:42:29,214] [INFO] Selected 22 target genomes.
[2023-03-16 05:42:29,215] [INFO] Target genome list was writen to OceanDNA-b45508/target_genomes_gtdb.txt
[2023-03-16 05:42:29,232] [INFO] Task started: fastANI
[2023-03-16 05:42:29,232] [INFO] Running command: fastANI --query /var/lib/cwl/stgacc9fd6d-1c90-47cd-a97a-685ed4bc1a06/OceanDNA-b45508.fa --refList OceanDNA-b45508/target_genomes_gtdb.txt --output OceanDNA-b45508/fastani_result_gtdb.tsv --threads 1
[2023-03-16 05:42:38,881] [INFO] Task succeeded: fastANI
[2023-03-16 05:42:38,885] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 05:42:38,885] [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	92.5547	211	305	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__GCA-2730975	95.0	98.14	98.04	0.72	0.68	4	-
GCA_002730975.1	s__GCA-2730975 sp002730975	87.5194	257	305	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_905612515.1	s__GCA-2730975 sp905612515	86.583	122	305	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_014382645.1	s__GCA-2730975 sp014382645	85.7033	243	305	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__GCA-2730975	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 05:42:38,885] [INFO] GTDB search result was written to OceanDNA-b45508/result_gtdb.tsv
[2023-03-16 05:42:38,885] [INFO] ===== GTDB Search completed =====
[2023-03-16 05:42:38,886] [INFO] DFAST_QC result json was written to OceanDNA-b45508/dqc_result.json
[2023-03-16 05:42:38,886] [INFO] DFAST_QC completed!
[2023-03-16 05:42:38,886] [INFO] Total running time: 0h1m16s