[2023-03-15 19:39:19,143] [INFO] DFAST_QC pipeline started.
[2023-03-15 19:39:19,143] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 19:39:19,143] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ae3a2bb-5a36-4b14-b788-76af6e6fcff2/dqc_reference
[2023-03-15 19:39:22,366] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 19:39:22,367] [INFO] Task started: Prodigal
[2023-03-15 19:39:22,367] [INFO] Running command: cat /var/lib/cwl/stgd5efeb78-50af-4338-aed5-9d5603cd1318/OceanDNA-b22487.fa | prodigal -d OceanDNA-b22487/cds.fna -a OceanDNA-b22487/protein.faa -g 11 -q > /dev/null
[2023-03-15 19:39:44,451] [INFO] Task succeeded: Prodigal
[2023-03-15 19:39:44,451] [INFO] Task started: HMMsearch
[2023-03-15 19:39:44,451] [INFO] Running command: hmmsearch --tblout OceanDNA-b22487/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ae3a2bb-5a36-4b14-b788-76af6e6fcff2/dqc_reference/reference_markers.hmm OceanDNA-b22487/protein.faa > /dev/null
[2023-03-15 19:39:44,699] [INFO] Task succeeded: HMMsearch
[2023-03-15 19:39:44,699] [INFO] Found 6/6 markers.
[2023-03-15 19:39:44,732] [INFO] Query marker FASTA was written to OceanDNA-b22487/markers.fasta
[2023-03-15 19:39:44,734] [INFO] Task started: Blastn
[2023-03-15 19:39:44,734] [INFO] Running command: blastn -query OceanDNA-b22487/markers.fasta -db /var/lib/cwl/stg4ae3a2bb-5a36-4b14-b788-76af6e6fcff2/dqc_reference/reference_markers.fasta -out OceanDNA-b22487/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 19:39:45,250] [INFO] Task succeeded: Blastn
[2023-03-15 19:39:45,251] [INFO] Selected 27 target genomes.
[2023-03-15 19:39:45,251] [INFO] Target genome list was writen to OceanDNA-b22487/target_genomes.txt
[2023-03-15 19:39:45,268] [INFO] Task started: fastANI
[2023-03-15 19:39:45,268] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5efeb78-50af-4338-aed5-9d5603cd1318/OceanDNA-b22487.fa --refList OceanDNA-b22487/target_genomes.txt --output OceanDNA-b22487/fastani_result.tsv --threads 1
[2023-03-15 19:40:10,858] [INFO] Task succeeded: fastANI
[2023-03-15 19:40:10,858] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ae3a2bb-5a36-4b14-b788-76af6e6fcff2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 19:40:10,859] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ae3a2bb-5a36-4b14-b788-76af6e6fcff2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 19:40:10,859] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 19:40:10,859] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 19:40:10,859] [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
--------------------------------------------------------------------------------
[2023-03-15 19:40:10,918] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22487/tc_result.tsv
[2023-03-15 19:40:10,918] [INFO] ===== Taxonomy check completed =====
[2023-03-15 19:40:10,918] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 19:40:10,918] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ae3a2bb-5a36-4b14-b788-76af6e6fcff2/dqc_reference/checkm_data
[2023-03-15 19:40:10,922] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 19:40:10,953] [INFO] Task started: CheckM
[2023-03-15 19:40:10,953] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22487/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22487/checkm_input OceanDNA-b22487/checkm_result
[2023-03-15 19:41:08,967] [INFO] Task succeeded: CheckM
[2023-03-15 19:41:08,968] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.10%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 19:41:08,971] [INFO] ===== Completeness check finished =====
[2023-03-15 19:41:08,971] [INFO] ===== Start GTDB Search =====
[2023-03-15 19:41:08,972] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22487/markers.fasta)
[2023-03-15 19:41:08,973] [INFO] Task started: Blastn
[2023-03-15 19:41:08,973] [INFO] Running command: blastn -query OceanDNA-b22487/markers.fasta -db /var/lib/cwl/stg4ae3a2bb-5a36-4b14-b788-76af6e6fcff2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22487/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 19:41:09,685] [INFO] Task succeeded: Blastn
[2023-03-15 19:41:09,686] [INFO] Selected 14 target genomes.
[2023-03-15 19:41:09,686] [INFO] Target genome list was writen to OceanDNA-b22487/target_genomes_gtdb.txt
[2023-03-15 19:41:10,151] [INFO] Task started: fastANI
[2023-03-15 19:41:10,151] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5efeb78-50af-4338-aed5-9d5603cd1318/OceanDNA-b22487.fa --refList OceanDNA-b22487/target_genomes_gtdb.txt --output OceanDNA-b22487/fastani_result_gtdb.tsv --threads 1
[2023-03-15 19:41:25,106] [INFO] Task succeeded: fastANI
[2023-03-15 19:41:25,111] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 19:41:25,111] [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_002712845.1	s__Rubripirellula sp002712845	82.6713	390	969	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689655.1	s__Rubripirellula sp002689655	81.5006	726	969	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	100.00	100.00	0.98	0.98	2	-
GCA_003513555.1	s__Rubripirellula sp003513555	81.4562	716	969	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002690925.1	s__Rubripirellula sp002690925	81.2108	681	969	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862205.1	s__Rubripirellula sp002862205	79.0575	488	969	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012270065.1	s__Rubripirellula sp012270065	77.6125	270	969	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	98.24	98.24	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-03-15 19:41:25,111] [INFO] GTDB search result was written to OceanDNA-b22487/result_gtdb.tsv
[2023-03-15 19:41:25,111] [INFO] ===== GTDB Search completed =====
[2023-03-15 19:41:25,112] [INFO] DFAST_QC result json was written to OceanDNA-b22487/dqc_result.json
[2023-03-15 19:41:25,112] [INFO] DFAST_QC completed!
[2023-03-15 19:41:25,112] [INFO] Total running time: 0h2m6s