[2023-03-15 16:37:12,222] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:37:12,223] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:37:12,223] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d6c340e-53c6-4cb6-bed2-d209ebc8b86f/dqc_reference
[2023-03-15 16:37:16,937] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:37:16,938] [INFO] Task started: Prodigal
[2023-03-15 16:37:16,938] [INFO] Running command: cat /var/lib/cwl/stgf4daf65a-2f36-4044-bbf3-a698e459b6b3/OceanDNA-b46717.fa | prodigal -d OceanDNA-b46717/cds.fna -a OceanDNA-b46717/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:37:59,602] [INFO] Task succeeded: Prodigal
[2023-03-15 16:37:59,603] [INFO] Task started: HMMsearch
[2023-03-15 16:37:59,603] [INFO] Running command: hmmsearch --tblout OceanDNA-b46717/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d6c340e-53c6-4cb6-bed2-d209ebc8b86f/dqc_reference/reference_markers.hmm OceanDNA-b46717/protein.faa > /dev/null
[2023-03-15 16:37:59,920] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:37:59,921] [INFO] Found 6/6 markers.
[2023-03-15 16:37:59,954] [INFO] Query marker FASTA was written to OceanDNA-b46717/markers.fasta
[2023-03-15 16:37:59,955] [INFO] Task started: Blastn
[2023-03-15 16:37:59,956] [INFO] Running command: blastn -query OceanDNA-b46717/markers.fasta -db /var/lib/cwl/stg3d6c340e-53c6-4cb6-bed2-d209ebc8b86f/dqc_reference/reference_markers.fasta -out OceanDNA-b46717/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:38:03,840] [INFO] Task succeeded: Blastn
[2023-03-15 16:38:03,842] [INFO] Selected 23 target genomes.
[2023-03-15 16:38:03,842] [INFO] Target genome list was writen to OceanDNA-b46717/target_genomes.txt
[2023-03-15 16:38:03,868] [INFO] Task started: fastANI
[2023-03-15 16:38:03,868] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4daf65a-2f36-4044-bbf3-a698e459b6b3/OceanDNA-b46717.fa --refList OceanDNA-b46717/target_genomes.txt --output OceanDNA-b46717/fastani_result.tsv --threads 1
[2023-03-15 16:38:18,399] [INFO] Task succeeded: fastANI
[2023-03-15 16:38:18,400] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d6c340e-53c6-4cb6-bed2-d209ebc8b86f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:38:18,400] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d6c340e-53c6-4cb6-bed2-d209ebc8b86f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:38:18,462] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:38:18,462] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 16:38:18,462] [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
Haloferula rosea	strain=KCTC 22201	GCA_016595525.1	490093	490093	type	True	76.0369	55	1592	95	below_threshold
Luteolibacter ambystomatis	strain=32A	GCA_018137965.1	2824561	2824561	type	True	75.7221	63	1592	95	below_threshold
Luteolibacter luteus	strain=G-1-1-1	GCA_012913485.1	2728835	2728835	type	True	75.5916	52	1592	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 16:38:18,463] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46717/tc_result.tsv
[2023-03-15 16:38:18,463] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:38:18,463] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:38:18,463] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d6c340e-53c6-4cb6-bed2-d209ebc8b86f/dqc_reference/checkm_data
[2023-03-15 16:38:18,464] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:38:18,534] [INFO] Task started: CheckM
[2023-03-15 16:38:18,534] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46717/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46717/checkm_input OceanDNA-b46717/checkm_result
[2023-03-15 16:40:07,294] [INFO] Task succeeded: CheckM
[2023-03-15 16:40:07,295] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 16:40:07,300] [INFO] ===== Completeness check finished =====
[2023-03-15 16:40:07,300] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:40:07,300] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46717/markers.fasta)
[2023-03-15 16:40:07,302] [INFO] Task started: Blastn
[2023-03-15 16:40:07,302] [INFO] Running command: blastn -query OceanDNA-b46717/markers.fasta -db /var/lib/cwl/stg3d6c340e-53c6-4cb6-bed2-d209ebc8b86f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46717/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:40:08,332] [INFO] Task succeeded: Blastn
[2023-03-15 16:40:08,334] [INFO] Selected 10 target genomes.
[2023-03-15 16:40:08,334] [INFO] Target genome list was writen to OceanDNA-b46717/target_genomes_gtdb.txt
[2023-03-15 16:40:08,343] [INFO] Task started: fastANI
[2023-03-15 16:40:08,343] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4daf65a-2f36-4044-bbf3-a698e459b6b3/OceanDNA-b46717.fa --refList OceanDNA-b46717/target_genomes_gtdb.txt --output OceanDNA-b46717/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:40:16,632] [INFO] Task succeeded: fastANI
[2023-03-15 16:40:16,638] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 16:40:16,638] [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_002501065.1	s__Roseibacillus_B sp002501065	99.7688	1436	1592	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	99.61	99.55	0.90	0.89	3	conclusive
GCA_003483645.1	s__Roseibacillus_B sp003483645	91.8493	632	1592	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014240355.1	s__Roseibacillus_B sp014240355	90.7804	739	1592	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002709395.1	s__Roseibacillus_B sp002709395	78.4251	505	1592	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	97.31	97.31	0.76	0.76	2	-
GCA_002721695.1	s__Roseibacillus_B sp002721695	77.8708	435	1592	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001695.1	s__Roseibacillus_B sp013001695	76.8135	204	1592	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002715825.1	s__Roseibacillus_B sp002715825	76.6877	173	1592	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	99.08	98.76	0.87	0.85	4	-
--------------------------------------------------------------------------------
[2023-03-15 16:40:16,639] [INFO] GTDB search result was written to OceanDNA-b46717/result_gtdb.tsv
[2023-03-15 16:40:16,641] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:40:16,643] [INFO] DFAST_QC result json was written to OceanDNA-b46717/dqc_result.json
[2023-03-15 16:40:16,644] [INFO] DFAST_QC completed!
[2023-03-15 16:40:16,644] [INFO] Total running time: 0h3m4s