[2023-03-16 07:34:40,566] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:34:40,566] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:34:40,566] [INFO] DQC Reference Directory: /var/lib/cwl/stg15406e30-dfc7-4d9e-9e1d-364b06365480/dqc_reference
[2023-03-16 07:34:42,228] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:34:42,228] [INFO] Task started: Prodigal
[2023-03-16 07:34:42,228] [INFO] Running command: cat /var/lib/cwl/stg7ce44b52-f9bf-4e23-8af0-5d83e27c98ae/OceanDNA-b22548.fa | prodigal -d OceanDNA-b22548/cds.fna -a OceanDNA-b22548/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:35:06,831] [INFO] Task succeeded: Prodigal
[2023-03-16 07:35:06,832] [INFO] Task started: HMMsearch
[2023-03-16 07:35:06,832] [INFO] Running command: hmmsearch --tblout OceanDNA-b22548/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15406e30-dfc7-4d9e-9e1d-364b06365480/dqc_reference/reference_markers.hmm OceanDNA-b22548/protein.faa > /dev/null
[2023-03-16 07:35:07,063] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:35:07,063] [INFO] Found 6/6 markers.
[2023-03-16 07:35:07,091] [INFO] Query marker FASTA was written to OceanDNA-b22548/markers.fasta
[2023-03-16 07:35:07,092] [INFO] Task started: Blastn
[2023-03-16 07:35:07,092] [INFO] Running command: blastn -query OceanDNA-b22548/markers.fasta -db /var/lib/cwl/stg15406e30-dfc7-4d9e-9e1d-364b06365480/dqc_reference/reference_markers.fasta -out OceanDNA-b22548/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:35:07,600] [INFO] Task succeeded: Blastn
[2023-03-16 07:35:07,601] [INFO] Selected 18 target genomes.
[2023-03-16 07:35:07,602] [INFO] Target genome list was writen to OceanDNA-b22548/target_genomes.txt
[2023-03-16 07:35:07,713] [INFO] Task started: fastANI
[2023-03-16 07:35:07,713] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ce44b52-f9bf-4e23-8af0-5d83e27c98ae/OceanDNA-b22548.fa --refList OceanDNA-b22548/target_genomes.txt --output OceanDNA-b22548/fastani_result.tsv --threads 1
[2023-03-16 07:35:21,533] [INFO] Task succeeded: fastANI
[2023-03-16 07:35:21,534] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15406e30-dfc7-4d9e-9e1d-364b06365480/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:35:21,534] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15406e30-dfc7-4d9e-9e1d-364b06365480/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:35:21,534] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:35:21,534] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 07:35:21,534] [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 07:35:21,536] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22548/tc_result.tsv
[2023-03-16 07:35:21,536] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:35:21,536] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:35:21,536] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15406e30-dfc7-4d9e-9e1d-364b06365480/dqc_reference/checkm_data
[2023-03-16 07:35:21,539] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:35:21,545] [INFO] Task started: CheckM
[2023-03-16 07:35:21,545] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22548/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22548/checkm_input OceanDNA-b22548/checkm_result
[2023-03-16 07:36:23,287] [INFO] Task succeeded: CheckM
[2023-03-16 07:36:23,287] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:36:23,305] [INFO] ===== Completeness check finished =====
[2023-03-16 07:36:23,305] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:36:23,305] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22548/markers.fasta)
[2023-03-16 07:36:23,306] [INFO] Task started: Blastn
[2023-03-16 07:36:23,306] [INFO] Running command: blastn -query OceanDNA-b22548/markers.fasta -db /var/lib/cwl/stg15406e30-dfc7-4d9e-9e1d-364b06365480/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22548/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:36:24,030] [INFO] Task succeeded: Blastn
[2023-03-16 07:36:24,035] [INFO] Selected 21 target genomes.
[2023-03-16 07:36:24,035] [INFO] Target genome list was writen to OceanDNA-b22548/target_genomes_gtdb.txt
[2023-03-16 07:36:24,425] [INFO] Task started: fastANI
[2023-03-16 07:36:24,425] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ce44b52-f9bf-4e23-8af0-5d83e27c98ae/OceanDNA-b22548.fa --refList OceanDNA-b22548/target_genomes_gtdb.txt --output OceanDNA-b22548/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:36:42,937] [INFO] Task succeeded: fastANI
[2023-03-16 07:36:42,942] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 07:36:42,942] [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_002348315.1	s__UBA721 sp002348315	99.5568	1188	1372	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA721	95.0	99.57	99.57	0.92	0.92	2	conclusive
GCA_002717145.1	s__UBA721 sp002717145	78.601	224	1372	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA721	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701385.1	s__UBA721 sp002701385	78.2684	359	1372	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA721	95.0	97.70	97.13	0.90	0.85	6	-
GCA_002709045.1	s__UBA721 sp002709045	78.2478	312	1372	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA721	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698965.1	s__UBA721 sp002698965	77.5774	258	1372	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA721	95.0	99.68	99.68	0.87	0.87	2	-
GCA_002705165.1	s__UBA721 sp002705165	77.4494	182	1372	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA721	95.0	97.82	97.82	0.67	0.67	2	-
--------------------------------------------------------------------------------
[2023-03-16 07:36:42,942] [INFO] GTDB search result was written to OceanDNA-b22548/result_gtdb.tsv
[2023-03-16 07:36:42,942] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:36:42,943] [INFO] DFAST_QC result json was written to OceanDNA-b22548/dqc_result.json
[2023-03-16 07:36:42,943] [INFO] DFAST_QC completed!
[2023-03-16 07:36:42,943] [INFO] Total running time: 0h2m2s