[2023-03-16 09:43:37,169] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:43:37,169] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:43:37,169] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f85bb45-5db1-4d11-a0a2-13d731686405/dqc_reference
[2023-03-16 09:43:39,241] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:43:39,241] [INFO] Task started: Prodigal
[2023-03-16 09:43:39,241] [INFO] Running command: cat /var/lib/cwl/stgb0cdf16b-97d7-44c6-b3cc-fa05ae83657f/OceanDNA-b21428.fa | prodigal -d OceanDNA-b21428/cds.fna -a OceanDNA-b21428/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:43:45,920] [INFO] Task succeeded: Prodigal
[2023-03-16 09:43:45,921] [INFO] Task started: HMMsearch
[2023-03-16 09:43:45,921] [INFO] Running command: hmmsearch --tblout OceanDNA-b21428/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f85bb45-5db1-4d11-a0a2-13d731686405/dqc_reference/reference_markers.hmm OceanDNA-b21428/protein.faa > /dev/null
[2023-03-16 09:43:46,073] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:43:46,074] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgb0cdf16b-97d7-44c6-b3cc-fa05ae83657f/OceanDNA-b21428.fa]
[2023-03-16 09:43:46,081] [INFO] Query marker FASTA was written to OceanDNA-b21428/markers.fasta
[2023-03-16 09:43:46,081] [INFO] Task started: Blastn
[2023-03-16 09:43:46,081] [INFO] Running command: blastn -query OceanDNA-b21428/markers.fasta -db /var/lib/cwl/stg5f85bb45-5db1-4d11-a0a2-13d731686405/dqc_reference/reference_markers.fasta -out OceanDNA-b21428/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:43:46,564] [INFO] Task succeeded: Blastn
[2023-03-16 09:43:46,565] [INFO] Selected 5 target genomes.
[2023-03-16 09:43:46,565] [INFO] Target genome list was writen to OceanDNA-b21428/target_genomes.txt
[2023-03-16 09:43:46,611] [INFO] Task started: fastANI
[2023-03-16 09:43:46,611] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0cdf16b-97d7-44c6-b3cc-fa05ae83657f/OceanDNA-b21428.fa --refList OceanDNA-b21428/target_genomes.txt --output OceanDNA-b21428/fastani_result.tsv --threads 1
[2023-03-16 09:43:48,583] [INFO] Task succeeded: fastANI
[2023-03-16 09:43:48,584] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f85bb45-5db1-4d11-a0a2-13d731686405/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:43:48,584] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f85bb45-5db1-4d11-a0a2-13d731686405/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:43:48,584] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:43:48,584] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 09:43:48,584] [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 09:43:48,584] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21428/tc_result.tsv
[2023-03-16 09:43:48,584] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:43:48,585] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:43:48,585] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f85bb45-5db1-4d11-a0a2-13d731686405/dqc_reference/checkm_data
[2023-03-16 09:43:48,587] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:43:48,590] [INFO] Task started: CheckM
[2023-03-16 09:43:48,590] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21428/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21428/checkm_input OceanDNA-b21428/checkm_result
[2023-03-16 09:44:14,060] [INFO] Task succeeded: CheckM
[2023-03-16 09:44:14,060] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.87%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:44:14,062] [INFO] ===== Completeness check finished =====
[2023-03-16 09:44:14,062] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:44:14,062] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21428/markers.fasta)
[2023-03-16 09:44:14,062] [INFO] Task started: Blastn
[2023-03-16 09:44:14,062] [INFO] Running command: blastn -query OceanDNA-b21428/markers.fasta -db /var/lib/cwl/stg5f85bb45-5db1-4d11-a0a2-13d731686405/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21428/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:44:15,118] [INFO] Task succeeded: Blastn
[2023-03-16 09:44:15,118] [INFO] Selected 10 target genomes.
[2023-03-16 09:44:15,118] [INFO] Target genome list was writen to OceanDNA-b21428/target_genomes_gtdb.txt
[2023-03-16 09:44:15,244] [INFO] Task started: fastANI
[2023-03-16 09:44:15,244] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0cdf16b-97d7-44c6-b3cc-fa05ae83657f/OceanDNA-b21428.fa --refList OceanDNA-b21428/target_genomes_gtdb.txt --output OceanDNA-b21428/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:44:17,742] [INFO] Task succeeded: fastANI
[2023-03-16 09:44:17,744] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 09:44:17,744] [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_002716765.1	s__GCA-2716765 sp002716765	99.8955	241	290	d__Bacteria;p__Patescibacteria;c__ABY1;o__Magasanikbacterales;f__UBA922;g__GCA-2716765	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018661775.1	s__GCA-2716765 sp018661775	81.0467	109	290	d__Bacteria;p__Patescibacteria;c__ABY1;o__Magasanikbacterales;f__UBA922;g__GCA-2716765	95.0	99.74	99.72	0.91	0.91	3	-
--------------------------------------------------------------------------------
[2023-03-16 09:44:17,744] [INFO] GTDB search result was written to OceanDNA-b21428/result_gtdb.tsv
[2023-03-16 09:44:17,745] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:44:17,745] [INFO] DFAST_QC result json was written to OceanDNA-b21428/dqc_result.json
[2023-03-16 09:44:17,745] [INFO] DFAST_QC completed!
[2023-03-16 09:44:17,745] [INFO] Total running time: 0h0m41s