[2023-03-16 19:18:54,483] [INFO] DFAST_QC pipeline started.
[2023-03-16 19:18:54,483] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 19:18:54,483] [INFO] DQC Reference Directory: /var/lib/cwl/stg00ed825c-b790-4fd1-a9c4-7c5e17a13dd1/dqc_reference
[2023-03-16 19:18:55,562] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 19:18:55,563] [INFO] Task started: Prodigal
[2023-03-16 19:18:55,563] [INFO] Running command: cat /var/lib/cwl/stgc77e5757-c8ee-40f3-a73b-f7ea51cfbaed/OceanDNA-b3498.fa | prodigal -d OceanDNA-b3498/cds.fna -a OceanDNA-b3498/protein.faa -g 11 -q > /dev/null
[2023-03-16 19:19:12,117] [INFO] Task succeeded: Prodigal
[2023-03-16 19:19:12,118] [INFO] Task started: HMMsearch
[2023-03-16 19:19:12,118] [INFO] Running command: hmmsearch --tblout OceanDNA-b3498/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg00ed825c-b790-4fd1-a9c4-7c5e17a13dd1/dqc_reference/reference_markers.hmm OceanDNA-b3498/protein.faa > /dev/null
[2023-03-16 19:19:12,318] [INFO] Task succeeded: HMMsearch
[2023-03-16 19:19:12,319] [INFO] Found 6/6 markers.
[2023-03-16 19:19:12,336] [INFO] Query marker FASTA was written to OceanDNA-b3498/markers.fasta
[2023-03-16 19:19:12,338] [INFO] Task started: Blastn
[2023-03-16 19:19:12,338] [INFO] Running command: blastn -query OceanDNA-b3498/markers.fasta -db /var/lib/cwl/stg00ed825c-b790-4fd1-a9c4-7c5e17a13dd1/dqc_reference/reference_markers.fasta -out OceanDNA-b3498/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:19:12,900] [INFO] Task succeeded: Blastn
[2023-03-16 19:19:12,901] [INFO] Selected 25 target genomes.
[2023-03-16 19:19:12,902] [INFO] Target genome list was writen to OceanDNA-b3498/target_genomes.txt
[2023-03-16 19:19:12,915] [INFO] Task started: fastANI
[2023-03-16 19:19:12,915] [INFO] Running command: fastANI --query /var/lib/cwl/stgc77e5757-c8ee-40f3-a73b-f7ea51cfbaed/OceanDNA-b3498.fa --refList OceanDNA-b3498/target_genomes.txt --output OceanDNA-b3498/fastani_result.tsv --threads 1
[2023-03-16 19:19:26,714] [INFO] Task succeeded: fastANI
[2023-03-16 19:19:26,715] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg00ed825c-b790-4fd1-a9c4-7c5e17a13dd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 19:19:26,715] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg00ed825c-b790-4fd1-a9c4-7c5e17a13dd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 19:19:26,715] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 19:19:26,715] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 19:19:26,715] [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 19:19:26,716] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3498/tc_result.tsv
[2023-03-16 19:19:26,717] [INFO] ===== Taxonomy check completed =====
[2023-03-16 19:19:26,717] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 19:19:26,717] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg00ed825c-b790-4fd1-a9c4-7c5e17a13dd1/dqc_reference/checkm_data
[2023-03-16 19:19:26,720] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 19:19:26,888] [INFO] Task started: CheckM
[2023-03-16 19:19:26,888] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3498/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3498/checkm_input OceanDNA-b3498/checkm_result
[2023-03-16 19:20:28,796] [INFO] Task succeeded: CheckM
[2023-03-16 19:20:28,797] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 19:20:28,803] [INFO] ===== Completeness check finished =====
[2023-03-16 19:20:28,804] [INFO] ===== Start GTDB Search =====
[2023-03-16 19:20:28,804] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3498/markers.fasta)
[2023-03-16 19:20:28,805] [INFO] Task started: Blastn
[2023-03-16 19:20:28,805] [INFO] Running command: blastn -query OceanDNA-b3498/markers.fasta -db /var/lib/cwl/stg00ed825c-b790-4fd1-a9c4-7c5e17a13dd1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3498/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:20:29,975] [INFO] Task succeeded: Blastn
[2023-03-16 19:20:29,978] [INFO] Selected 24 target genomes.
[2023-03-16 19:20:29,978] [INFO] Target genome list was writen to OceanDNA-b3498/target_genomes_gtdb.txt
[2023-03-16 19:20:30,004] [INFO] Task started: fastANI
[2023-03-16 19:20:30,004] [INFO] Running command: fastANI --query /var/lib/cwl/stgc77e5757-c8ee-40f3-a73b-f7ea51cfbaed/OceanDNA-b3498.fa --refList OceanDNA-b3498/target_genomes_gtdb.txt --output OceanDNA-b3498/fastani_result_gtdb.tsv --threads 1
[2023-03-16 19:20:52,121] [INFO] Task succeeded: fastANI
[2023-03-16 19:20:52,125] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 19:20:52,125] [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_018661505.1	s__GCA-002708315 sp018661505	99.8676	748	820	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__GCA-002708315	95.0	99.95	99.92	0.97	0.96	16	conclusive
GCA_002708315.1	s__GCA-002708315 sp002708315	91.255	580	820	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__GCA-002708315	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686705.1	s__GCA-002708315 sp002686705	77.829	95	820	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__GCA-002708315	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845105.1	s__GCA-002708315 sp016845105	77.2335	143	820	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__GCA-002708315	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013203805.1	s__GCA-002708315 sp013203805	76.5262	113	820	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__GCA-002708315	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 19:20:52,126] [INFO] GTDB search result was written to OceanDNA-b3498/result_gtdb.tsv
[2023-03-16 19:20:52,127] [INFO] ===== GTDB Search completed =====
[2023-03-16 19:20:52,128] [INFO] DFAST_QC result json was written to OceanDNA-b3498/dqc_result.json
[2023-03-16 19:20:52,128] [INFO] DFAST_QC completed!
[2023-03-16 19:20:52,128] [INFO] Total running time: 0h1m58s