[2023-03-15 21:32:41,292] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:32:41,292] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:32:41,292] [INFO] DQC Reference Directory: /var/lib/cwl/stge4fc6d06-ddca-4a5b-967c-fe3cc4f9fed9/dqc_reference
[2023-03-15 21:32:42,945] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:32:42,946] [INFO] Task started: Prodigal
[2023-03-15 21:32:42,946] [INFO] Running command: cat /var/lib/cwl/stg3c79e21c-d6b6-464e-a6b5-d6251ce7cd59/OceanDNA-b32692.fa | prodigal -d OceanDNA-b32692/cds.fna -a OceanDNA-b32692/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:33:06,281] [INFO] Task succeeded: Prodigal
[2023-03-15 21:33:06,282] [INFO] Task started: HMMsearch
[2023-03-15 21:33:06,282] [INFO] Running command: hmmsearch --tblout OceanDNA-b32692/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4fc6d06-ddca-4a5b-967c-fe3cc4f9fed9/dqc_reference/reference_markers.hmm OceanDNA-b32692/protein.faa > /dev/null
[2023-03-15 21:33:06,493] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:33:06,493] [INFO] Found 6/6 markers.
[2023-03-15 21:33:06,516] [INFO] Query marker FASTA was written to OceanDNA-b32692/markers.fasta
[2023-03-15 21:33:06,517] [INFO] Task started: Blastn
[2023-03-15 21:33:06,517] [INFO] Running command: blastn -query OceanDNA-b32692/markers.fasta -db /var/lib/cwl/stge4fc6d06-ddca-4a5b-967c-fe3cc4f9fed9/dqc_reference/reference_markers.fasta -out OceanDNA-b32692/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:33:07,162] [INFO] Task succeeded: Blastn
[2023-03-15 21:33:07,163] [INFO] Selected 29 target genomes.
[2023-03-15 21:33:07,163] [INFO] Target genome list was writen to OceanDNA-b32692/target_genomes.txt
[2023-03-15 21:33:07,247] [INFO] Task started: fastANI
[2023-03-15 21:33:07,247] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c79e21c-d6b6-464e-a6b5-d6251ce7cd59/OceanDNA-b32692.fa --refList OceanDNA-b32692/target_genomes.txt --output OceanDNA-b32692/fastani_result.tsv --threads 1
[2023-03-15 21:33:28,035] [INFO] Task succeeded: fastANI
[2023-03-15 21:33:28,035] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4fc6d06-ddca-4a5b-967c-fe3cc4f9fed9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:33:28,036] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4fc6d06-ddca-4a5b-967c-fe3cc4f9fed9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:33:28,039] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:33:28,039] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 21:33:28,039] [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
Oceanibacterium hippocampi	strain=CECT 7691	GCA_900172325.1	745714	745714	type	True	75.7217	55	1228	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:33:28,039] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32692/tc_result.tsv
[2023-03-15 21:33:28,039] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:33:28,039] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:33:28,039] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4fc6d06-ddca-4a5b-967c-fe3cc4f9fed9/dqc_reference/checkm_data
[2023-03-15 21:33:28,040] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:33:28,049] [INFO] Task started: CheckM
[2023-03-15 21:33:28,049] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32692/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32692/checkm_input OceanDNA-b32692/checkm_result
[2023-03-15 21:34:25,748] [INFO] Task succeeded: CheckM
[2023-03-15 21:34:25,748] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:34:25,888] [INFO] ===== Completeness check finished =====
[2023-03-15 21:34:25,888] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:34:25,889] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32692/markers.fasta)
[2023-03-15 21:34:25,889] [INFO] Task started: Blastn
[2023-03-15 21:34:25,889] [INFO] Running command: blastn -query OceanDNA-b32692/markers.fasta -db /var/lib/cwl/stge4fc6d06-ddca-4a5b-967c-fe3cc4f9fed9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32692/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:34:27,049] [INFO] Task succeeded: Blastn
[2023-03-15 21:34:27,062] [INFO] Selected 33 target genomes.
[2023-03-15 21:34:27,062] [INFO] Target genome list was writen to OceanDNA-b32692/target_genomes_gtdb.txt
[2023-03-15 21:34:28,458] [INFO] Task started: fastANI
[2023-03-15 21:34:28,458] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c79e21c-d6b6-464e-a6b5-d6251ce7cd59/OceanDNA-b32692.fa --refList OceanDNA-b32692/target_genomes_gtdb.txt --output OceanDNA-b32692/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:34:53,287] [INFO] Task succeeded: fastANI
[2023-03-15 21:34:53,290] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:34:53,290] [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_002348365.1	s__UBA2966 sp002348365	77.3532	344	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA2966;f__UBA2966;g__UBA2966	95.0	98.52	97.79	0.84	0.83	3	-
GCA_002690215.1	s__GCA-2690215 sp002690215	76.1578	55	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA2966;f__UBA2966;g__GCA-2690215	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576705.1	s__SYSU-D60015 sp003576705	75.3568	60	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__SYSU-D60015	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:34:53,292] [INFO] GTDB search result was written to OceanDNA-b32692/result_gtdb.tsv
[2023-03-15 21:34:53,293] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:34:53,293] [INFO] DFAST_QC result json was written to OceanDNA-b32692/dqc_result.json
[2023-03-15 21:34:53,294] [INFO] DFAST_QC completed!
[2023-03-15 21:34:53,294] [INFO] Total running time: 0h2m12s