[2023-03-15 21:01:44,342] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:01:44,342] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:01:44,342] [INFO] DQC Reference Directory: /var/lib/cwl/stg194c6e8b-144a-4dce-8072-92aeb90f9e75/dqc_reference
[2023-03-15 21:01:45,597] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:01:45,597] [INFO] Task started: Prodigal
[2023-03-15 21:01:45,597] [INFO] Running command: cat /var/lib/cwl/stg206fd7d1-2da2-431c-82e9-03cde6dfe3ec/OceanDNA-b10500.fa | prodigal -d OceanDNA-b10500/cds.fna -a OceanDNA-b10500/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:02:02,868] [INFO] Task succeeded: Prodigal
[2023-03-15 21:02:02,868] [INFO] Task started: HMMsearch
[2023-03-15 21:02:02,868] [INFO] Running command: hmmsearch --tblout OceanDNA-b10500/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg194c6e8b-144a-4dce-8072-92aeb90f9e75/dqc_reference/reference_markers.hmm OceanDNA-b10500/protein.faa > /dev/null
[2023-03-15 21:02:03,011] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:02:03,012] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg206fd7d1-2da2-431c-82e9-03cde6dfe3ec/OceanDNA-b10500.fa]
[2023-03-15 21:02:03,027] [INFO] Query marker FASTA was written to OceanDNA-b10500/markers.fasta
[2023-03-15 21:02:03,027] [INFO] Task started: Blastn
[2023-03-15 21:02:03,027] [INFO] Running command: blastn -query OceanDNA-b10500/markers.fasta -db /var/lib/cwl/stg194c6e8b-144a-4dce-8072-92aeb90f9e75/dqc_reference/reference_markers.fasta -out OceanDNA-b10500/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:02:03,458] [INFO] Task succeeded: Blastn
[2023-03-15 21:02:03,458] [INFO] Selected 14 target genomes.
[2023-03-15 21:02:03,459] [INFO] Target genome list was writen to OceanDNA-b10500/target_genomes.txt
[2023-03-15 21:02:03,469] [INFO] Task started: fastANI
[2023-03-15 21:02:03,469] [INFO] Running command: fastANI --query /var/lib/cwl/stg206fd7d1-2da2-431c-82e9-03cde6dfe3ec/OceanDNA-b10500.fa --refList OceanDNA-b10500/target_genomes.txt --output OceanDNA-b10500/fastani_result.tsv --threads 1
[2023-03-15 21:02:11,119] [INFO] Task succeeded: fastANI
[2023-03-15 21:02:11,119] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg194c6e8b-144a-4dce-8072-92aeb90f9e75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:02:11,119] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg194c6e8b-144a-4dce-8072-92aeb90f9e75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:02:11,122] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:02:11,122] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 21:02:11,122] [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
Marinirhabdus gelatinilytica	strain=DSM 101478	GCA_003353425.1	1703343	1703343	type	True	80.341	112	713	95	below_threshold
Aequorivita sublithincola	strain=DSM 14238	GCA_000265385.1	101385	101385	type	True	78.0708	60	713	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:02:11,123] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10500/tc_result.tsv
[2023-03-15 21:02:11,123] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:02:11,123] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:02:11,123] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg194c6e8b-144a-4dce-8072-92aeb90f9e75/dqc_reference/checkm_data
[2023-03-15 21:02:11,124] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:02:11,129] [INFO] Task started: CheckM
[2023-03-15 21:02:11,129] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10500/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10500/checkm_input OceanDNA-b10500/checkm_result
[2023-03-15 21:02:56,199] [INFO] Task succeeded: CheckM
[2023-03-15 21:02:56,199] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:02:56,201] [INFO] ===== Completeness check finished =====
[2023-03-15 21:02:56,201] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:02:56,202] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10500/markers.fasta)
[2023-03-15 21:02:56,203] [INFO] Task started: Blastn
[2023-03-15 21:02:56,203] [INFO] Running command: blastn -query OceanDNA-b10500/markers.fasta -db /var/lib/cwl/stg194c6e8b-144a-4dce-8072-92aeb90f9e75/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10500/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:02:56,614] [INFO] Task succeeded: Blastn
[2023-03-15 21:02:56,615] [INFO] Selected 16 target genomes.
[2023-03-15 21:02:56,615] [INFO] Target genome list was writen to OceanDNA-b10500/target_genomes_gtdb.txt
[2023-03-15 21:02:56,930] [INFO] Task started: fastANI
[2023-03-15 21:02:56,930] [INFO] Running command: fastANI --query /var/lib/cwl/stg206fd7d1-2da2-431c-82e9-03cde6dfe3ec/OceanDNA-b10500.fa --refList OceanDNA-b10500/target_genomes_gtdb.txt --output OceanDNA-b10500/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:03:05,404] [INFO] Task succeeded: fastANI
[2023-03-15 21:03:05,408] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 21:03:05,408] [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_002693605.1	s__Marixanthomonas sp002693605	99.4859	329	713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003353425.1	s__Marinirhabdus gelatinilytica	80.3398	112	713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002375695.1	s__Aequorivita sp002375695	79.4706	52	713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.99	99.99	0.99	0.99	2	-
GCA_011044175.1	s__Marinirhabdus sp011044175	79.0032	74	713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:03:05,408] [INFO] GTDB search result was written to OceanDNA-b10500/result_gtdb.tsv
[2023-03-15 21:03:05,408] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:03:05,409] [INFO] DFAST_QC result json was written to OceanDNA-b10500/dqc_result.json
[2023-03-15 21:03:05,409] [INFO] DFAST_QC completed!
[2023-03-15 21:03:05,409] [INFO] Total running time: 0h1m21s