[2023-03-18 08:17:18,478] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:17:18,478] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:17:18,478] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc9eec19-5f6f-4510-a764-4e1a5be743e7/dqc_reference
[2023-03-18 08:17:20,266] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:17:20,266] [INFO] Task started: Prodigal
[2023-03-18 08:17:20,266] [INFO] Running command: cat /var/lib/cwl/stg278b1224-40fd-4ade-b94a-477b9fed1844/OceanDNA-b6874.fa | prodigal -d OceanDNA-b6874/cds.fna -a OceanDNA-b6874/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:17:27,928] [INFO] Task succeeded: Prodigal
[2023-03-18 08:17:27,928] [INFO] Task started: HMMsearch
[2023-03-18 08:17:27,928] [INFO] Running command: hmmsearch --tblout OceanDNA-b6874/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc9eec19-5f6f-4510-a764-4e1a5be743e7/dqc_reference/reference_markers.hmm OceanDNA-b6874/protein.faa > /dev/null
[2023-03-18 08:17:28,079] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:17:28,080] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg278b1224-40fd-4ade-b94a-477b9fed1844/OceanDNA-b6874.fa]
[2023-03-18 08:17:28,089] [INFO] Query marker FASTA was written to OceanDNA-b6874/markers.fasta
[2023-03-18 08:17:28,089] [INFO] Task started: Blastn
[2023-03-18 08:17:28,089] [INFO] Running command: blastn -query OceanDNA-b6874/markers.fasta -db /var/lib/cwl/stgbc9eec19-5f6f-4510-a764-4e1a5be743e7/dqc_reference/reference_markers.fasta -out OceanDNA-b6874/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:17:28,590] [INFO] Task succeeded: Blastn
[2023-03-18 08:17:28,591] [INFO] Selected 25 target genomes.
[2023-03-18 08:17:28,591] [INFO] Target genome list was writen to OceanDNA-b6874/target_genomes.txt
[2023-03-18 08:17:28,603] [INFO] Task started: fastANI
[2023-03-18 08:17:28,603] [INFO] Running command: fastANI --query /var/lib/cwl/stg278b1224-40fd-4ade-b94a-477b9fed1844/OceanDNA-b6874.fa --refList OceanDNA-b6874/target_genomes.txt --output OceanDNA-b6874/fastani_result.tsv --threads 1
[2023-03-18 08:17:40,641] [INFO] Task succeeded: fastANI
[2023-03-18 08:17:40,641] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc9eec19-5f6f-4510-a764-4e1a5be743e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:17:40,642] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc9eec19-5f6f-4510-a764-4e1a5be743e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:17:40,642] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:17:40,642] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 08:17:40,642] [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
--------------------------------------------------------------------------------
[2023-03-18 08:17:40,642] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6874/tc_result.tsv
[2023-03-18 08:17:40,642] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:17:40,642] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:17:40,642] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc9eec19-5f6f-4510-a764-4e1a5be743e7/dqc_reference/checkm_data
[2023-03-18 08:17:40,645] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:17:40,648] [INFO] Task started: CheckM
[2023-03-18 08:17:40,648] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6874/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6874/checkm_input OceanDNA-b6874/checkm_result
[2023-03-18 08:18:04,715] [INFO] Task succeeded: CheckM
[2023-03-18 08:18:04,716] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:18:04,717] [INFO] ===== Completeness check finished =====
[2023-03-18 08:18:04,717] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:18:04,718] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6874/markers.fasta)
[2023-03-18 08:18:04,718] [INFO] Task started: Blastn
[2023-03-18 08:18:04,718] [INFO] Running command: blastn -query OceanDNA-b6874/markers.fasta -db /var/lib/cwl/stgbc9eec19-5f6f-4510-a764-4e1a5be743e7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6874/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:18:05,348] [INFO] Task succeeded: Blastn
[2023-03-18 08:18:05,349] [INFO] Selected 23 target genomes.
[2023-03-18 08:18:05,349] [INFO] Target genome list was writen to OceanDNA-b6874/target_genomes_gtdb.txt
[2023-03-18 08:18:05,533] [INFO] Task started: fastANI
[2023-03-18 08:18:05,533] [INFO] Running command: fastANI --query /var/lib/cwl/stg278b1224-40fd-4ade-b94a-477b9fed1844/OceanDNA-b6874.fa --refList OceanDNA-b6874/target_genomes_gtdb.txt --output OceanDNA-b6874/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:18:15,490] [INFO] Task succeeded: fastANI
[2023-03-18 08:18:15,495] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:18:15,495] [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_905182735.1	s__GCA-002723295 sp905182735	81.124	337	429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002723295	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002690805.1	s__GCA-002723295 sp002690805	79.2473	176	429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002723295	95.0	97.07	97.07	0.76	0.76	2	-
GCA_002711185.1	s__GCA-002723295 sp002711185	77.0026	105	429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002723295	95.0	98.54	98.54	0.83	0.83	2	-
GCA_002713495.1	s__GCA-002723295 sp002713495	76.9032	99	429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002723295	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721275.1	s__GCA-002723295 sp002721275	76.7757	96	429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002723295	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002719315.1	s__GCA-2719315 sp002719315	76.1013	72	429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2719315	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:18:15,495] [INFO] GTDB search result was written to OceanDNA-b6874/result_gtdb.tsv
[2023-03-18 08:18:15,496] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:18:15,496] [INFO] DFAST_QC result json was written to OceanDNA-b6874/dqc_result.json
[2023-03-18 08:18:15,496] [INFO] DFAST_QC completed!
[2023-03-18 08:18:15,496] [INFO] Total running time: 0h0m57s