[2023-03-18 05:35:37,305] [INFO] DFAST_QC pipeline started.
[2023-03-18 05:35:37,305] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 05:35:37,305] [INFO] DQC Reference Directory: /var/lib/cwl/stg3751b08d-25bd-44f5-920b-2252bb2dd4d7/dqc_reference
[2023-03-18 05:35:38,965] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 05:35:38,965] [INFO] Task started: Prodigal
[2023-03-18 05:35:38,965] [INFO] Running command: cat /var/lib/cwl/stg5f72841b-d4cb-4eb9-bc6d-0e7b93873000/OceanDNA-b16023.fa | prodigal -d OceanDNA-b16023/cds.fna -a OceanDNA-b16023/protein.faa -g 11 -q > /dev/null
[2023-03-18 05:36:04,542] [INFO] Task succeeded: Prodigal
[2023-03-18 05:36:04,542] [INFO] Task started: HMMsearch
[2023-03-18 05:36:04,542] [INFO] Running command: hmmsearch --tblout OceanDNA-b16023/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3751b08d-25bd-44f5-920b-2252bb2dd4d7/dqc_reference/reference_markers.hmm OceanDNA-b16023/protein.faa > /dev/null
[2023-03-18 05:36:04,796] [INFO] Task succeeded: HMMsearch
[2023-03-18 05:36:04,797] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5f72841b-d4cb-4eb9-bc6d-0e7b93873000/OceanDNA-b16023.fa]
[2023-03-18 05:36:04,828] [INFO] Query marker FASTA was written to OceanDNA-b16023/markers.fasta
[2023-03-18 05:36:04,829] [INFO] Task started: Blastn
[2023-03-18 05:36:04,830] [INFO] Running command: blastn -query OceanDNA-b16023/markers.fasta -db /var/lib/cwl/stg3751b08d-25bd-44f5-920b-2252bb2dd4d7/dqc_reference/reference_markers.fasta -out OceanDNA-b16023/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:36:05,347] [INFO] Task succeeded: Blastn
[2023-03-18 05:36:05,350] [INFO] Selected 22 target genomes.
[2023-03-18 05:36:05,350] [INFO] Target genome list was writen to OceanDNA-b16023/target_genomes.txt
[2023-03-18 05:36:05,362] [INFO] Task started: fastANI
[2023-03-18 05:36:05,362] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f72841b-d4cb-4eb9-bc6d-0e7b93873000/OceanDNA-b16023.fa --refList OceanDNA-b16023/target_genomes.txt --output OceanDNA-b16023/fastani_result.tsv --threads 1
[2023-03-18 05:36:20,777] [INFO] Task succeeded: fastANI
[2023-03-18 05:36:20,777] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3751b08d-25bd-44f5-920b-2252bb2dd4d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 05:36:20,778] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3751b08d-25bd-44f5-920b-2252bb2dd4d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 05:36:20,781] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 05:36:20,781] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 05:36:20,781] [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
Prochlorothrix hollandica	strain=PCC 9006	GCA_000332315.1	1223	1223	type	True	75.9892	62	1411	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 05:36:20,782] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16023/tc_result.tsv
[2023-03-18 05:36:20,782] [INFO] ===== Taxonomy check completed =====
[2023-03-18 05:36:20,782] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 05:36:20,782] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3751b08d-25bd-44f5-920b-2252bb2dd4d7/dqc_reference/checkm_data
[2023-03-18 05:36:20,783] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 05:36:20,790] [INFO] Task started: CheckM
[2023-03-18 05:36:20,790] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16023/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16023/checkm_input OceanDNA-b16023/checkm_result
[2023-03-18 05:37:23,112] [INFO] Task succeeded: CheckM
[2023-03-18 05:37:23,112] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 05:37:23,136] [INFO] ===== Completeness check finished =====
[2023-03-18 05:37:23,136] [INFO] ===== Start GTDB Search =====
[2023-03-18 05:37:23,136] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16023/markers.fasta)
[2023-03-18 05:37:23,138] [INFO] Task started: Blastn
[2023-03-18 05:37:23,138] [INFO] Running command: blastn -query OceanDNA-b16023/markers.fasta -db /var/lib/cwl/stg3751b08d-25bd-44f5-920b-2252bb2dd4d7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16023/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:37:23,842] [INFO] Task succeeded: Blastn
[2023-03-18 05:37:23,843] [INFO] Selected 28 target genomes.
[2023-03-18 05:37:23,843] [INFO] Target genome list was writen to OceanDNA-b16023/target_genomes_gtdb.txt
[2023-03-18 05:37:23,891] [INFO] Task started: fastANI
[2023-03-18 05:37:23,891] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f72841b-d4cb-4eb9-bc6d-0e7b93873000/OceanDNA-b16023.fa --refList OceanDNA-b16023/target_genomes_gtdb.txt --output OceanDNA-b16023/fastani_result_gtdb.tsv --threads 1
[2023-03-18 05:37:47,484] [INFO] Task succeeded: fastANI
[2023-03-18 05:37:47,491] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 05:37:47,491] [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_000332315.1	s__Prochlorothrix hollandica	75.9892	62	1411	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-9006;f__Prochlorotrichaceae;g__Prochlorothrix	95.0	99.78	99.78	0.95	0.95	2	-
GCA_001913845.2	s__CACIAM-69d sp001913845	75.9723	117	1411	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__CACIAM-69d;f__CACIAM-69d;g__CACIAM-69d	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016403105.1	s__Nodosilinea sp016403105	75.8251	51	1411	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002215035.1	s__Leptolyngbya_A ohadii	75.7692	53	1411	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__Leptolyngbya_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015272155.1	s__JACYME01 sp015272155	75.7609	51	1411	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__JACYME01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014698235.1	s__CACIAM-69d sp001698445	75.7097	116	1411	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__CACIAM-69d;f__CACIAM-69d;g__CACIAM-69d	95.0	98.17	97.78	0.95	0.92	7	-
GCF_014697375.1	s__Nodosilinea sp014697375	75.6158	63	1411	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000332095.2	s__PCC-6406 sp000332095	75.6157	53	1411	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__PCC-6406	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016888135.1	s__RECH01 sp016888135	75.5882	67	1411	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__RECH01	95.0	96.61	96.61	0.91	0.91	3	-
GCF_001548395.1	s__O-77 sp001548395	75.2419	70	1411	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__O-77	95.0	95.35	95.35	0.93	0.93	2	-
GCA_010672825.2	s__SIO1E4 sp010672825	75.118	51	1411	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__SIO1E4	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 05:37:47,491] [INFO] GTDB search result was written to OceanDNA-b16023/result_gtdb.tsv
[2023-03-18 05:37:47,493] [INFO] ===== GTDB Search completed =====
[2023-03-18 05:37:47,494] [INFO] DFAST_QC result json was written to OceanDNA-b16023/dqc_result.json
[2023-03-18 05:37:47,494] [INFO] DFAST_QC completed!
[2023-03-18 05:37:47,494] [INFO] Total running time: 0h2m10s