[2023-03-16 12:37:44,829] [INFO] DFAST_QC pipeline started.
[2023-03-16 12:37:44,829] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 12:37:44,829] [INFO] DQC Reference Directory: /var/lib/cwl/stg145562bf-c487-4516-94cf-c92e69c6d1f0/dqc_reference
[2023-03-16 12:37:45,956] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 12:37:45,956] [INFO] Task started: Prodigal
[2023-03-16 12:37:45,956] [INFO] Running command: cat /var/lib/cwl/stge19ff42b-4f1e-43c6-a66b-ab8ff9cb3243/OceanDNA-b18504.fa | prodigal -d OceanDNA-b18504/cds.fna -a OceanDNA-b18504/protein.faa -g 11 -q > /dev/null
[2023-03-16 12:37:58,458] [INFO] Task succeeded: Prodigal
[2023-03-16 12:37:58,458] [INFO] Task started: HMMsearch
[2023-03-16 12:37:58,458] [INFO] Running command: hmmsearch --tblout OceanDNA-b18504/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg145562bf-c487-4516-94cf-c92e69c6d1f0/dqc_reference/reference_markers.hmm OceanDNA-b18504/protein.faa > /dev/null
[2023-03-16 12:37:58,632] [INFO] Task succeeded: HMMsearch
[2023-03-16 12:37:58,632] [INFO] Found 6/6 markers.
[2023-03-16 12:37:58,648] [INFO] Query marker FASTA was written to OceanDNA-b18504/markers.fasta
[2023-03-16 12:37:58,648] [INFO] Task started: Blastn
[2023-03-16 12:37:58,648] [INFO] Running command: blastn -query OceanDNA-b18504/markers.fasta -db /var/lib/cwl/stg145562bf-c487-4516-94cf-c92e69c6d1f0/dqc_reference/reference_markers.fasta -out OceanDNA-b18504/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 12:37:59,156] [INFO] Task succeeded: Blastn
[2023-03-16 12:37:59,157] [INFO] Selected 16 target genomes.
[2023-03-16 12:37:59,157] [INFO] Target genome list was writen to OceanDNA-b18504/target_genomes.txt
[2023-03-16 12:37:59,169] [INFO] Task started: fastANI
[2023-03-16 12:37:59,169] [INFO] Running command: fastANI --query /var/lib/cwl/stge19ff42b-4f1e-43c6-a66b-ab8ff9cb3243/OceanDNA-b18504.fa --refList OceanDNA-b18504/target_genomes.txt --output OceanDNA-b18504/fastani_result.tsv --threads 1
[2023-03-16 12:38:06,021] [INFO] Task succeeded: fastANI
[2023-03-16 12:38:06,021] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg145562bf-c487-4516-94cf-c92e69c6d1f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 12:38:06,022] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg145562bf-c487-4516-94cf-c92e69c6d1f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 12:38:06,022] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 12:38:06,022] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 12:38:06,022] [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 12:38:06,022] [INFO] DFAST Taxonomy check result was written to OceanDNA-b18504/tc_result.tsv
[2023-03-16 12:38:06,022] [INFO] ===== Taxonomy check completed =====
[2023-03-16 12:38:06,022] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 12:38:06,022] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg145562bf-c487-4516-94cf-c92e69c6d1f0/dqc_reference/checkm_data
[2023-03-16 12:38:06,025] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 12:38:06,029] [INFO] Task started: CheckM
[2023-03-16 12:38:06,029] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b18504/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b18504/checkm_input OceanDNA-b18504/checkm_result
[2023-03-16 12:38:44,379] [INFO] Task succeeded: CheckM
[2023-03-16 12:38:44,379] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 12:38:44,381] [INFO] ===== Completeness check finished =====
[2023-03-16 12:38:44,381] [INFO] ===== Start GTDB Search =====
[2023-03-16 12:38:44,381] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b18504/markers.fasta)
[2023-03-16 12:38:44,383] [INFO] Task started: Blastn
[2023-03-16 12:38:44,383] [INFO] Running command: blastn -query OceanDNA-b18504/markers.fasta -db /var/lib/cwl/stg145562bf-c487-4516-94cf-c92e69c6d1f0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b18504/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 12:38:45,159] [INFO] Task succeeded: Blastn
[2023-03-16 12:38:45,160] [INFO] Selected 20 target genomes.
[2023-03-16 12:38:45,160] [INFO] Target genome list was writen to OceanDNA-b18504/target_genomes_gtdb.txt
[2023-03-16 12:38:45,630] [INFO] Task started: fastANI
[2023-03-16 12:38:45,631] [INFO] Running command: fastANI --query /var/lib/cwl/stge19ff42b-4f1e-43c6-a66b-ab8ff9cb3243/OceanDNA-b18504.fa --refList OceanDNA-b18504/target_genomes_gtdb.txt --output OceanDNA-b18504/fastani_result_gtdb.tsv --threads 1
[2023-03-16 12:38:59,498] [INFO] Task succeeded: fastANI
[2023-03-16 12:38:59,501] [INFO] Found 3 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-16 12:38:59,501] [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_004124535.1	s__UBA2126 sp004124535	96.5747	311	734	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__UBA2126	95.0	97.80	97.80	0.52	0.52	2	inconclusive
GCA_012964215.1	s__GCA-002701945 sp012964215	96.1559	492	734	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__GCA-002701945	95.0	98.56	98.56	0.81	0.81	2	inconclusive
GCA_004321715.1	s__GCA-002701945 sp004321715	76.6505	60	734	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__GCA-002701945	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 12:38:59,501] [INFO] GTDB search result was written to OceanDNA-b18504/result_gtdb.tsv
[2023-03-16 12:38:59,502] [INFO] ===== GTDB Search completed =====
[2023-03-16 12:38:59,502] [INFO] DFAST_QC result json was written to OceanDNA-b18504/dqc_result.json
[2023-03-16 12:38:59,502] [INFO] DFAST_QC completed!
[2023-03-16 12:38:59,502] [INFO] Total running time: 0h1m15s