[2023-03-19 04:55:39,485] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:55:39,485] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:55:39,485] [INFO] DQC Reference Directory: /var/lib/cwl/stg612c896d-49ac-4aaf-979b-50976fe4bbda/dqc_reference
[2023-03-19 04:55:40,560] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:55:40,561] [INFO] Task started: Prodigal
[2023-03-19 04:55:40,561] [INFO] Running command: cat /var/lib/cwl/stg23e38a31-2279-4759-872b-1089b164ec55/OceanDNA-b42718.fa | prodigal -d OceanDNA-b42718/cds.fna -a OceanDNA-b42718/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:55:45,244] [INFO] Task succeeded: Prodigal
[2023-03-19 04:55:45,245] [INFO] Task started: HMMsearch
[2023-03-19 04:55:45,245] [INFO] Running command: hmmsearch --tblout OceanDNA-b42718/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg612c896d-49ac-4aaf-979b-50976fe4bbda/dqc_reference/reference_markers.hmm OceanDNA-b42718/protein.faa > /dev/null
[2023-03-19 04:55:45,414] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:55:45,414] [INFO] Found 6/6 markers.
[2023-03-19 04:55:45,434] [INFO] Query marker FASTA was written to OceanDNA-b42718/markers.fasta
[2023-03-19 04:55:45,435] [INFO] Task started: Blastn
[2023-03-19 04:55:45,435] [INFO] Running command: blastn -query OceanDNA-b42718/markers.fasta -db /var/lib/cwl/stg612c896d-49ac-4aaf-979b-50976fe4bbda/dqc_reference/reference_markers.fasta -out OceanDNA-b42718/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:55:45,936] [INFO] Task succeeded: Blastn
[2023-03-19 04:55:45,941] [INFO] Selected 10 target genomes.
[2023-03-19 04:55:45,941] [INFO] Target genome list was writen to OceanDNA-b42718/target_genomes.txt
[2023-03-19 04:55:45,948] [INFO] Task started: fastANI
[2023-03-19 04:55:45,949] [INFO] Running command: fastANI --query /var/lib/cwl/stg23e38a31-2279-4759-872b-1089b164ec55/OceanDNA-b42718.fa --refList OceanDNA-b42718/target_genomes.txt --output OceanDNA-b42718/fastani_result.tsv --threads 1
[2023-03-19 04:55:49,775] [INFO] Task succeeded: fastANI
[2023-03-19 04:55:49,775] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg612c896d-49ac-4aaf-979b-50976fe4bbda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:55:49,776] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg612c896d-49ac-4aaf-979b-50976fe4bbda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:55:49,776] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:55:49,776] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 04:55:49,776] [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
--------------------------------------------------------------------------------
[2023-03-19 04:55:49,779] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42718/tc_result.tsv
[2023-03-19 04:55:49,781] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:55:49,781] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:55:49,781] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg612c896d-49ac-4aaf-979b-50976fe4bbda/dqc_reference/checkm_data
[2023-03-19 04:55:49,834] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:55:49,838] [INFO] Task started: CheckM
[2023-03-19 04:55:49,839] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42718/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42718/checkm_input OceanDNA-b42718/checkm_result
[2023-03-19 04:56:08,759] [INFO] Task succeeded: CheckM
[2023-03-19 04:56:08,759] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:56:08,765] [INFO] ===== Completeness check finished =====
[2023-03-19 04:56:08,765] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:56:08,766] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42718/markers.fasta)
[2023-03-19 04:56:08,768] [INFO] Task started: Blastn
[2023-03-19 04:56:08,768] [INFO] Running command: blastn -query OceanDNA-b42718/markers.fasta -db /var/lib/cwl/stg612c896d-49ac-4aaf-979b-50976fe4bbda/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42718/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:56:09,824] [INFO] Task succeeded: Blastn
[2023-03-19 04:56:09,826] [INFO] Selected 11 target genomes.
[2023-03-19 04:56:09,827] [INFO] Target genome list was writen to OceanDNA-b42718/target_genomes_gtdb.txt
[2023-03-19 04:56:09,837] [INFO] Task started: fastANI
[2023-03-19 04:56:09,837] [INFO] Running command: fastANI --query /var/lib/cwl/stg23e38a31-2279-4759-872b-1089b164ec55/OceanDNA-b42718.fa --refList OceanDNA-b42718/target_genomes_gtdb.txt --output OceanDNA-b42718/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:56:11,936] [INFO] Task succeeded: fastANI
[2023-03-19 04:56:11,940] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 04:56:11,940] [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_002716745.1	s__TMED112 sp002716745	96.7506	281	301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	96.67	96.57	0.91	0.90	3	conclusive
GCA_902610995.1	s__TMED112 sp902610995	79.3882	138	301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	98.48	96.99	0.80	0.72	6	-
GCA_002170245.2	s__TMED112 sp002170245	76.7019	53	301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:56:11,942] [INFO] GTDB search result was written to OceanDNA-b42718/result_gtdb.tsv
[2023-03-19 04:56:11,945] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:56:11,947] [INFO] DFAST_QC result json was written to OceanDNA-b42718/dqc_result.json
[2023-03-19 04:56:11,948] [INFO] DFAST_QC completed!
[2023-03-19 04:56:11,948] [INFO] Total running time: 0h0m32s