[2023-03-18 08:17:20,575] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:17:20,575] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:17:20,575] [INFO] DQC Reference Directory: /var/lib/cwl/stg2bf4c65e-13d1-4418-95b8-8d7edeae3b89/dqc_reference
[2023-03-18 08:17:21,786] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:17:21,786] [INFO] Task started: Prodigal
[2023-03-18 08:17:21,786] [INFO] Running command: cat /var/lib/cwl/stg85f75c4c-7cf6-48be-8807-8da57012dc3f/OceanDNA-b45436.fa | prodigal -d OceanDNA-b45436/cds.fna -a OceanDNA-b45436/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:17:43,436] [INFO] Task succeeded: Prodigal
[2023-03-18 08:17:43,437] [INFO] Task started: HMMsearch
[2023-03-18 08:17:43,437] [INFO] Running command: hmmsearch --tblout OceanDNA-b45436/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2bf4c65e-13d1-4418-95b8-8d7edeae3b89/dqc_reference/reference_markers.hmm OceanDNA-b45436/protein.faa > /dev/null
[2023-03-18 08:17:43,674] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:17:43,675] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg85f75c4c-7cf6-48be-8807-8da57012dc3f/OceanDNA-b45436.fa]
[2023-03-18 08:17:43,695] [INFO] Query marker FASTA was written to OceanDNA-b45436/markers.fasta
[2023-03-18 08:17:43,695] [INFO] Task started: Blastn
[2023-03-18 08:17:43,695] [INFO] Running command: blastn -query OceanDNA-b45436/markers.fasta -db /var/lib/cwl/stg2bf4c65e-13d1-4418-95b8-8d7edeae3b89/dqc_reference/reference_markers.fasta -out OceanDNA-b45436/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:17:44,288] [INFO] Task succeeded: Blastn
[2023-03-18 08:17:44,289] [INFO] Selected 23 target genomes.
[2023-03-18 08:17:44,289] [INFO] Target genome list was writen to OceanDNA-b45436/target_genomes.txt
[2023-03-18 08:17:44,316] [INFO] Task started: fastANI
[2023-03-18 08:17:44,316] [INFO] Running command: fastANI --query /var/lib/cwl/stg85f75c4c-7cf6-48be-8807-8da57012dc3f/OceanDNA-b45436.fa --refList OceanDNA-b45436/target_genomes.txt --output OceanDNA-b45436/fastani_result.tsv --threads 1
[2023-03-18 08:18:00,927] [INFO] Task succeeded: fastANI
[2023-03-18 08:18:00,928] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2bf4c65e-13d1-4418-95b8-8d7edeae3b89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:18:00,928] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2bf4c65e-13d1-4418-95b8-8d7edeae3b89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:18:00,931] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:18:00,931] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:18:00,931] [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
Ruficoccus amylovorans	strain=JCM31066	GCA_014230085.1	1804625	1804625	type	True	76.5163	51	634	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:18:00,931] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45436/tc_result.tsv
[2023-03-18 08:18:00,931] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:18:00,931] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:18:00,931] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2bf4c65e-13d1-4418-95b8-8d7edeae3b89/dqc_reference/checkm_data
[2023-03-18 08:18:00,932] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:18:00,936] [INFO] Task started: CheckM
[2023-03-18 08:18:00,936] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45436/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45436/checkm_input OceanDNA-b45436/checkm_result
[2023-03-18 08:18:54,361] [INFO] Task succeeded: CheckM
[2023-03-18 08:18:54,361] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.87%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 08:18:54,364] [INFO] ===== Completeness check finished =====
[2023-03-18 08:18:54,364] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:18:54,364] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45436/markers.fasta)
[2023-03-18 08:18:54,364] [INFO] Task started: Blastn
[2023-03-18 08:18:54,364] [INFO] Running command: blastn -query OceanDNA-b45436/markers.fasta -db /var/lib/cwl/stg2bf4c65e-13d1-4418-95b8-8d7edeae3b89/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45436/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:18:55,232] [INFO] Task succeeded: Blastn
[2023-03-18 08:18:55,233] [INFO] Selected 24 target genomes.
[2023-03-18 08:18:55,233] [INFO] Target genome list was writen to OceanDNA-b45436/target_genomes_gtdb.txt
[2023-03-18 08:18:55,436] [INFO] Task started: fastANI
[2023-03-18 08:18:55,436] [INFO] Running command: fastANI --query /var/lib/cwl/stg85f75c4c-7cf6-48be-8807-8da57012dc3f/OceanDNA-b45436.fa --refList OceanDNA-b45436/target_genomes_gtdb.txt --output OceanDNA-b45436/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:19:07,699] [INFO] Task succeeded: fastANI
[2023-03-18 08:19:07,703] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:19:07,703] [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
GCF_014230085.1	s__Ruficoccus amylovorans	76.5163	51	634	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__KCTC-12870;g__Ruficoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903830425.1	s__Opi-474 sp903830425	76.1484	53	634	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.49	99.28	0.91	0.87	25	-
GCA_001650175.1	s__Ereboglobus sp001650175	76.1306	78	634	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Ereboglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002288455.1	s__ER46 sp002288455	75.9305	53	634	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:19:07,703] [INFO] GTDB search result was written to OceanDNA-b45436/result_gtdb.tsv
[2023-03-18 08:19:07,703] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:19:07,704] [INFO] DFAST_QC result json was written to OceanDNA-b45436/dqc_result.json
[2023-03-18 08:19:07,704] [INFO] DFAST_QC completed!
[2023-03-18 08:19:07,704] [INFO] Total running time: 0h1m47s