[2023-03-16 17:10:21,410] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:10:21,411] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:10:21,411] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf594708-8b7c-446c-a6f3-de54951e35f2/dqc_reference
[2023-03-16 17:10:22,517] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:10:22,518] [INFO] Task started: Prodigal
[2023-03-16 17:10:22,518] [INFO] Running command: cat /var/lib/cwl/stg9f87aadc-8f1b-4927-8728-be7249d0c865/OceanDNA-b46826.fa | prodigal -d OceanDNA-b46826/cds.fna -a OceanDNA-b46826/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:10:34,211] [INFO] Task succeeded: Prodigal
[2023-03-16 17:10:34,211] [INFO] Task started: HMMsearch
[2023-03-16 17:10:34,211] [INFO] Running command: hmmsearch --tblout OceanDNA-b46826/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf594708-8b7c-446c-a6f3-de54951e35f2/dqc_reference/reference_markers.hmm OceanDNA-b46826/protein.faa > /dev/null
[2023-03-16 17:10:34,368] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:10:34,368] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg9f87aadc-8f1b-4927-8728-be7249d0c865/OceanDNA-b46826.fa]
[2023-03-16 17:10:34,386] [INFO] Query marker FASTA was written to OceanDNA-b46826/markers.fasta
[2023-03-16 17:10:34,387] [INFO] Task started: Blastn
[2023-03-16 17:10:34,387] [INFO] Running command: blastn -query OceanDNA-b46826/markers.fasta -db /var/lib/cwl/stgcf594708-8b7c-446c-a6f3-de54951e35f2/dqc_reference/reference_markers.fasta -out OceanDNA-b46826/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:10:34,876] [INFO] Task succeeded: Blastn
[2023-03-16 17:10:34,878] [INFO] Selected 11 target genomes.
[2023-03-16 17:10:34,878] [INFO] Target genome list was writen to OceanDNA-b46826/target_genomes.txt
[2023-03-16 17:10:34,930] [INFO] Task started: fastANI
[2023-03-16 17:10:34,930] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f87aadc-8f1b-4927-8728-be7249d0c865/OceanDNA-b46826.fa --refList OceanDNA-b46826/target_genomes.txt --output OceanDNA-b46826/fastani_result.tsv --threads 1
[2023-03-16 17:10:44,112] [INFO] Task succeeded: fastANI
[2023-03-16 17:10:44,112] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf594708-8b7c-446c-a6f3-de54951e35f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:10:44,112] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf594708-8b7c-446c-a6f3-de54951e35f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:10:44,113] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:10:44,113] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 17:10:44,113] [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 17:10:44,113] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46826/tc_result.tsv
[2023-03-16 17:10:44,113] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:10:44,113] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:10:44,113] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf594708-8b7c-446c-a6f3-de54951e35f2/dqc_reference/checkm_data
[2023-03-16 17:10:44,116] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:10:44,120] [INFO] Task started: CheckM
[2023-03-16 17:10:44,120] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46826/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46826/checkm_input OceanDNA-b46826/checkm_result
[2023-03-16 17:11:18,472] [INFO] Task succeeded: CheckM
[2023-03-16 17:11:18,472] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.05%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 17:11:18,479] [INFO] ===== Completeness check finished =====
[2023-03-16 17:11:18,479] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:11:18,479] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46826/markers.fasta)
[2023-03-16 17:11:18,481] [INFO] Task started: Blastn
[2023-03-16 17:11:18,481] [INFO] Running command: blastn -query OceanDNA-b46826/markers.fasta -db /var/lib/cwl/stgcf594708-8b7c-446c-a6f3-de54951e35f2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46826/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:11:18,967] [INFO] Task succeeded: Blastn
[2023-03-16 17:11:18,971] [INFO] Selected 14 target genomes.
[2023-03-16 17:11:18,971] [INFO] Target genome list was writen to OceanDNA-b46826/target_genomes_gtdb.txt
[2023-03-16 17:11:18,985] [INFO] Task started: fastANI
[2023-03-16 17:11:18,985] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f87aadc-8f1b-4927-8728-be7249d0c865/OceanDNA-b46826.fa --refList OceanDNA-b46826/target_genomes_gtdb.txt --output OceanDNA-b46826/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:11:28,341] [INFO] Task succeeded: fastANI
[2023-03-16 17:11:28,345] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 17:11:28,345] [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_002729295.1	s__SW10 sp002729295	93.5609	112	135	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	99.31	99.31	0.79	0.79	2	-
GCA_002172625.1	s__SW10 sp002172625	92.1749	114	135	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	98.72	98.72	0.89	0.89	2	-
GCA_018222765.1	s__SW10 sp018222765	91.8259	128	135	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 17:11:28,345] [INFO] GTDB search result was written to OceanDNA-b46826/result_gtdb.tsv
[2023-03-16 17:11:28,345] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:11:28,346] [INFO] DFAST_QC result json was written to OceanDNA-b46826/dqc_result.json
[2023-03-16 17:11:28,346] [INFO] DFAST_QC completed!
[2023-03-16 17:11:28,346] [INFO] Total running time: 0h1m7s