[2023-03-18 23:27:53,696] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:27:53,696] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:27:53,697] [INFO] DQC Reference Directory: /var/lib/cwl/stg13717ece-ee58-4dd3-b147-a11291799d1b/dqc_reference
[2023-03-18 23:27:55,547] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:27:55,548] [INFO] Task started: Prodigal
[2023-03-18 23:27:55,548] [INFO] Running command: cat /var/lib/cwl/stg7cd5ef67-efc7-4437-9627-11c4adeadcba/OceanDNA-b45848.fa | prodigal -d OceanDNA-b45848/cds.fna -a OceanDNA-b45848/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:28:28,013] [INFO] Task succeeded: Prodigal
[2023-03-18 23:28:28,013] [INFO] Task started: HMMsearch
[2023-03-18 23:28:28,013] [INFO] Running command: hmmsearch --tblout OceanDNA-b45848/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13717ece-ee58-4dd3-b147-a11291799d1b/dqc_reference/reference_markers.hmm OceanDNA-b45848/protein.faa > /dev/null
[2023-03-18 23:28:28,283] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:28:28,284] [INFO] Found 6/6 markers.
[2023-03-18 23:28:28,309] [INFO] Query marker FASTA was written to OceanDNA-b45848/markers.fasta
[2023-03-18 23:28:28,310] [INFO] Task started: Blastn
[2023-03-18 23:28:28,310] [INFO] Running command: blastn -query OceanDNA-b45848/markers.fasta -db /var/lib/cwl/stg13717ece-ee58-4dd3-b147-a11291799d1b/dqc_reference/reference_markers.fasta -out OceanDNA-b45848/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:28:28,922] [INFO] Task succeeded: Blastn
[2023-03-18 23:28:28,923] [INFO] Selected 15 target genomes.
[2023-03-18 23:28:28,923] [INFO] Target genome list was writen to OceanDNA-b45848/target_genomes.txt
[2023-03-18 23:28:28,934] [INFO] Task started: fastANI
[2023-03-18 23:28:28,934] [INFO] Running command: fastANI --query /var/lib/cwl/stg7cd5ef67-efc7-4437-9627-11c4adeadcba/OceanDNA-b45848.fa --refList OceanDNA-b45848/target_genomes.txt --output OceanDNA-b45848/fastani_result.tsv --threads 1
[2023-03-18 23:28:39,623] [INFO] Task succeeded: fastANI
[2023-03-18 23:28:39,624] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13717ece-ee58-4dd3-b147-a11291799d1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:28:39,624] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13717ece-ee58-4dd3-b147-a11291799d1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:28:39,630] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:28:39,630] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:28:39,630] [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
Rariglobus hedericola	strain=53C-WASEF	GCA_007559335.1	2597822	2597822	type	True	76.8336	82	1252	95	below_threshold
Nibricoccus aquaticus	strain=HZ-65	GCA_002310495.1	2576891	2576891	type	True	76.192	79	1252	95	below_threshold
Geminisphaera colitermitum	strain=TAV2	GCA_000171235.2	1148786	1148786	type	True	75.9986	51	1252	95	below_threshold
Opitutus terrae	strain=PB90-1	GCA_000019965.1	107709	107709	type	True	75.8673	57	1252	95	below_threshold
Ereboglobus luteus	strain=Ho45	GCA_003096195.1	1796921	1796921	type	True	75.5962	55	1252	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:28:39,630] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45848/tc_result.tsv
[2023-03-18 23:28:39,630] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:28:39,630] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:28:39,630] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13717ece-ee58-4dd3-b147-a11291799d1b/dqc_reference/checkm_data
[2023-03-18 23:28:39,631] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:28:39,671] [INFO] Task started: CheckM
[2023-03-18 23:28:39,671] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45848/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45848/checkm_input OceanDNA-b45848/checkm_result
[2023-03-18 23:29:59,071] [INFO] Task succeeded: CheckM
[2023-03-18 23:29:59,072] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:29:59,076] [INFO] ===== Completeness check finished =====
[2023-03-18 23:29:59,076] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:29:59,076] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45848/markers.fasta)
[2023-03-18 23:29:59,078] [INFO] Task started: Blastn
[2023-03-18 23:29:59,078] [INFO] Running command: blastn -query OceanDNA-b45848/markers.fasta -db /var/lib/cwl/stg13717ece-ee58-4dd3-b147-a11291799d1b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45848/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:30:00,127] [INFO] Task succeeded: Blastn
[2023-03-18 23:30:00,128] [INFO] Selected 18 target genomes.
[2023-03-18 23:30:00,128] [INFO] Target genome list was writen to OceanDNA-b45848/target_genomes_gtdb.txt
[2023-03-18 23:30:00,148] [INFO] Task started: fastANI
[2023-03-18 23:30:00,148] [INFO] Running command: fastANI --query /var/lib/cwl/stg7cd5ef67-efc7-4437-9627-11c4adeadcba/OceanDNA-b45848.fa --refList OceanDNA-b45848/target_genomes_gtdb.txt --output OceanDNA-b45848/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:30:12,413] [INFO] Task succeeded: fastANI
[2023-03-18 23:30:12,422] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:30:12,422] [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_018667915.1	s__M30B9 sp018667915	79.9919	583	1252	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__M30B9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402455.1	s__M30B9 sp018402455	77.125	223	1252	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__M30B9	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007559335.1	s__Rariglobus hedericola	76.8336	82	1252	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Rariglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001746835.1	s__Lacunisphaera limnophila	76.4967	66	1252	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016187945.1	s__Didemnitutus sp016187945	76.4668	56	1252	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Didemnitutus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004118375.1	s__Lacunisphaera lenta	76.2998	66	1252	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903876795.1	s__Rariglobus sp903876795	76.2837	75	1252	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Rariglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002304445.1	s__Tous-C4FEB sp002304445	76.2251	63	1252	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Tous-C4FEB	95.0	98.22	97.15	0.85	0.81	4	-
GCA_000242935.3	s__Geminisphaera sp000242935	76.222	66	1252	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Geminisphaera	95.0	96.61	96.61	0.73	0.73	2	-
GCA_016235555.1	s__ER46 sp016235555	76.1875	79	1252	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795565.1	s__Lacunisphaera sp016795565	76.097	60	1252	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000171235.2	s__Geminisphaera colitermitum	75.9986	51	1252	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Geminisphaera	95.0	97.34	97.31	0.79	0.79	3	-
GCA_903862595.1	s__UBA6669 sp903862595	75.7299	58	1252	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA6669	95.0	99.22	99.13	0.81	0.80	3	-
GCF_003096195.1	s__Ereboglobus luteus	75.5933	55	1252	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Ereboglobus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:30:12,422] [INFO] GTDB search result was written to OceanDNA-b45848/result_gtdb.tsv
[2023-03-18 23:30:12,422] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:30:12,423] [INFO] DFAST_QC result json was written to OceanDNA-b45848/dqc_result.json
[2023-03-18 23:30:12,424] [INFO] DFAST_QC completed!
[2023-03-18 23:30:12,424] [INFO] Total running time: 0h2m19s