[2023-03-18 03:27:00,919] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:27:00,920] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:27:00,920] [INFO] DQC Reference Directory: /var/lib/cwl/stgc38ad023-23ad-4ace-94fd-3452b0cefbd8/dqc_reference
[2023-03-18 03:27:02,635] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:27:02,636] [INFO] Task started: Prodigal
[2023-03-18 03:27:02,636] [INFO] Running command: cat /var/lib/cwl/stg7597098f-bffc-4072-93d3-0b56eacb5f59/OceanDNA-a3219.fa | prodigal -d OceanDNA-a3219/cds.fna -a OceanDNA-a3219/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:27:12,513] [INFO] Task succeeded: Prodigal
[2023-03-18 03:27:12,514] [INFO] Task started: HMMsearch
[2023-03-18 03:27:12,514] [INFO] Running command: hmmsearch --tblout OceanDNA-a3219/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc38ad023-23ad-4ace-94fd-3452b0cefbd8/dqc_reference/reference_markers.hmm OceanDNA-a3219/protein.faa > /dev/null
[2023-03-18 03:27:12,686] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:27:12,686] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg7597098f-bffc-4072-93d3-0b56eacb5f59/OceanDNA-a3219.fa]
[2023-03-18 03:27:12,698] [INFO] Query marker FASTA was written to OceanDNA-a3219/markers.fasta
[2023-03-18 03:27:12,698] [INFO] Task started: Blastn
[2023-03-18 03:27:12,698] [INFO] Running command: blastn -query OceanDNA-a3219/markers.fasta -db /var/lib/cwl/stgc38ad023-23ad-4ace-94fd-3452b0cefbd8/dqc_reference/reference_markers.fasta -out OceanDNA-a3219/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:27:13,122] [INFO] Task succeeded: Blastn
[2023-03-18 03:27:13,123] [INFO] Selected 6 target genomes.
[2023-03-18 03:27:13,123] [INFO] Target genome list was writen to OceanDNA-a3219/target_genomes.txt
[2023-03-18 03:27:13,126] [INFO] Task started: fastANI
[2023-03-18 03:27:13,127] [INFO] Running command: fastANI --query /var/lib/cwl/stg7597098f-bffc-4072-93d3-0b56eacb5f59/OceanDNA-a3219.fa --refList OceanDNA-a3219/target_genomes.txt --output OceanDNA-a3219/fastani_result.tsv --threads 1
[2023-03-18 03:27:15,134] [INFO] Task succeeded: fastANI
[2023-03-18 03:27:15,134] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc38ad023-23ad-4ace-94fd-3452b0cefbd8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:27:15,134] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc38ad023-23ad-4ace-94fd-3452b0cefbd8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:27:15,135] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:27:15,135] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 03:27:15,135] [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
--------------------------------------------------------------------------------
[2023-03-18 03:27:15,135] [INFO] DFAST Taxonomy check result was written to OceanDNA-a3219/tc_result.tsv
[2023-03-18 03:27:15,135] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:27:15,135] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:27:15,135] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc38ad023-23ad-4ace-94fd-3452b0cefbd8/dqc_reference/checkm_data
[2023-03-18 03:27:15,138] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:27:15,142] [INFO] Task started: CheckM
[2023-03-18 03:27:15,142] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3219/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3219/checkm_input OceanDNA-a3219/checkm_result
[2023-03-18 03:27:45,222] [INFO] Task succeeded: CheckM
[2023-03-18 03:27:45,222] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.61%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:27:45,224] [INFO] ===== Completeness check finished =====
[2023-03-18 03:27:45,224] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:27:45,225] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3219/markers.fasta)
[2023-03-18 03:27:45,225] [INFO] Task started: Blastn
[2023-03-18 03:27:45,225] [INFO] Running command: blastn -query OceanDNA-a3219/markers.fasta -db /var/lib/cwl/stgc38ad023-23ad-4ace-94fd-3452b0cefbd8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3219/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:27:45,647] [INFO] Task succeeded: Blastn
[2023-03-18 03:27:45,648] [INFO] Selected 8 target genomes.
[2023-03-18 03:27:45,648] [INFO] Target genome list was writen to OceanDNA-a3219/target_genomes_gtdb.txt
[2023-03-18 03:27:45,655] [INFO] Task started: fastANI
[2023-03-18 03:27:45,656] [INFO] Running command: fastANI --query /var/lib/cwl/stg7597098f-bffc-4072-93d3-0b56eacb5f59/OceanDNA-a3219.fa --refList OceanDNA-a3219/target_genomes_gtdb.txt --output OceanDNA-a3219/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:27:48,467] [INFO] Task succeeded: fastANI
[2023-03-18 03:27:48,471] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 03:27:48,471] [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_018650285.1	s__MGIIb-Q1 sp018650285	99.9656	560	565	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-Q1	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016845345.1	s__MGIIb-Q1 sp016845345	78.7788	206	565	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-Q1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012964335.1	s__MGIIb-Q1 sp012964335	78.5825	226	565	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-Q1	95.0	99.77	99.71	0.95	0.94	8	-
GCA_014384685.1	s__MGIIb-Q1 sp014384685	78.3298	142	565	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-Q1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:27:48,471] [INFO] GTDB search result was written to OceanDNA-a3219/result_gtdb.tsv
[2023-03-18 03:27:48,471] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:27:48,472] [INFO] DFAST_QC result json was written to OceanDNA-a3219/dqc_result.json
[2023-03-18 03:27:48,472] [INFO] DFAST_QC completed!
[2023-03-18 03:27:48,472] [INFO] Total running time: 0h0m48s