[2023-03-19 04:11:06,925] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:11:06,925] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:11:06,925] [INFO] DQC Reference Directory: /var/lib/cwl/stg60d5c398-e681-4994-90d7-17ae891c22b6/dqc_reference
[2023-03-19 04:11:08,543] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:11:08,544] [INFO] Task started: Prodigal
[2023-03-19 04:11:08,544] [INFO] Running command: cat /var/lib/cwl/stg9eb2316e-036b-411a-b547-fb9ac24ea99f/OceanDNA-b17764.fa | prodigal -d OceanDNA-b17764/cds.fna -a OceanDNA-b17764/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:11:37,961] [INFO] Task succeeded: Prodigal
[2023-03-19 04:11:37,961] [INFO] Task started: HMMsearch
[2023-03-19 04:11:37,961] [INFO] Running command: hmmsearch --tblout OceanDNA-b17764/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60d5c398-e681-4994-90d7-17ae891c22b6/dqc_reference/reference_markers.hmm OceanDNA-b17764/protein.faa > /dev/null
[2023-03-19 04:11:38,198] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:11:38,199] [INFO] Found 6/6 markers.
[2023-03-19 04:11:38,235] [INFO] Query marker FASTA was written to OceanDNA-b17764/markers.fasta
[2023-03-19 04:11:38,235] [INFO] Task started: Blastn
[2023-03-19 04:11:38,235] [INFO] Running command: blastn -query OceanDNA-b17764/markers.fasta -db /var/lib/cwl/stg60d5c398-e681-4994-90d7-17ae891c22b6/dqc_reference/reference_markers.fasta -out OceanDNA-b17764/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:11:38,774] [INFO] Task succeeded: Blastn
[2023-03-19 04:11:38,775] [INFO] Selected 30 target genomes.
[2023-03-19 04:11:38,776] [INFO] Target genome list was writen to OceanDNA-b17764/target_genomes.txt
[2023-03-19 04:11:38,790] [INFO] Task started: fastANI
[2023-03-19 04:11:38,790] [INFO] Running command: fastANI --query /var/lib/cwl/stg9eb2316e-036b-411a-b547-fb9ac24ea99f/OceanDNA-b17764.fa --refList OceanDNA-b17764/target_genomes.txt --output OceanDNA-b17764/fastani_result.tsv --threads 1
[2023-03-19 04:12:02,460] [INFO] Task succeeded: fastANI
[2023-03-19 04:12:02,461] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60d5c398-e681-4994-90d7-17ae891c22b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:12:02,461] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60d5c398-e681-4994-90d7-17ae891c22b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:12:02,464] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:12:02,464] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:12:02,464] [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
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	74.6476	61	1483	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:12:02,464] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17764/tc_result.tsv
[2023-03-19 04:12:02,464] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:12:02,464] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:12:02,464] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60d5c398-e681-4994-90d7-17ae891c22b6/dqc_reference/checkm_data
[2023-03-19 04:12:02,465] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:12:02,472] [INFO] Task started: CheckM
[2023-03-19 04:12:02,472] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17764/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17764/checkm_input OceanDNA-b17764/checkm_result
[2023-03-19 04:13:16,088] [INFO] Task succeeded: CheckM
[2023-03-19 04:13:16,088] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.19%
Contamintation: 2.55%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-19 04:13:16,092] [INFO] ===== Completeness check finished =====
[2023-03-19 04:13:16,092] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:13:16,092] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17764/markers.fasta)
[2023-03-19 04:13:16,092] [INFO] Task started: Blastn
[2023-03-19 04:13:16,092] [INFO] Running command: blastn -query OceanDNA-b17764/markers.fasta -db /var/lib/cwl/stg60d5c398-e681-4994-90d7-17ae891c22b6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17764/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:13:16,868] [INFO] Task succeeded: Blastn
[2023-03-19 04:13:16,869] [INFO] Selected 27 target genomes.
[2023-03-19 04:13:16,869] [INFO] Target genome list was writen to OceanDNA-b17764/target_genomes_gtdb.txt
[2023-03-19 04:13:17,146] [INFO] Task started: fastANI
[2023-03-19 04:13:17,146] [INFO] Running command: fastANI --query /var/lib/cwl/stg9eb2316e-036b-411a-b547-fb9ac24ea99f/OceanDNA-b17764.fa --refList OceanDNA-b17764/target_genomes_gtdb.txt --output OceanDNA-b17764/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:13:35,215] [INFO] Task succeeded: fastANI
[2023-03-19 04:13:35,220] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:13:35,220] [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_002726335.1	s__UBA8231 sp002726335	77.5797	441	1483	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__UBA8231	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018673255.1	s__UBA12574 sp018673255	76.3734	194	1483	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__UBA12574	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018660835.1	s__UBA12574 sp018660835	75.9724	135	1483	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__UBA12574	95.0	99.93	99.91	0.98	0.97	7	-
GCA_002712305.1	s__UBA12574 sp002712305	75.9566	95	1483	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__UBA12574	95.0	98.27	97.81	0.83	0.79	3	-
GCA_016867395.1	s__SICG01 sp016867395	75.788	66	1483	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__SICG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016187725.1	s__SICG01 sp016187725	75.654	77	1483	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__SICG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903893785.1	s__CAITNQ01 sp903893785	75.3942	71	1483	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__CAITNQ01	95.0	99.57	99.57	0.93	0.93	2	-
GCA_018672475.1	s__GCA-2724215 sp018672475	75.3806	57	1483	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	99.78	99.75	0.95	0.94	9	-
--------------------------------------------------------------------------------
[2023-03-19 04:13:35,220] [INFO] GTDB search result was written to OceanDNA-b17764/result_gtdb.tsv
[2023-03-19 04:13:35,221] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:13:35,221] [INFO] DFAST_QC result json was written to OceanDNA-b17764/dqc_result.json
[2023-03-19 04:13:35,221] [INFO] DFAST_QC completed!
[2023-03-19 04:13:35,221] [INFO] Total running time: 0h2m28s