[2023-03-15 21:16:33,628] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:16:33,628] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:16:33,628] [INFO] DQC Reference Directory: /var/lib/cwl/stg05daabcd-0578-4a27-9155-7b635af013a7/dqc_reference
[2023-03-15 21:16:35,472] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:16:35,472] [INFO] Task started: Prodigal
[2023-03-15 21:16:35,472] [INFO] Running command: cat /var/lib/cwl/stg2f0a95ee-0ac5-4a68-a1db-0d9bf64bfab3/OceanDNA-b22827.fa | prodigal -d OceanDNA-b22827/cds.fna -a OceanDNA-b22827/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:17:17,567] [INFO] Task succeeded: Prodigal
[2023-03-15 21:17:17,567] [INFO] Task started: HMMsearch
[2023-03-15 21:17:17,567] [INFO] Running command: hmmsearch --tblout OceanDNA-b22827/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05daabcd-0578-4a27-9155-7b635af013a7/dqc_reference/reference_markers.hmm OceanDNA-b22827/protein.faa > /dev/null
[2023-03-15 21:17:17,847] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:17:17,847] [INFO] Found 6/6 markers.
[2023-03-15 21:17:17,887] [INFO] Query marker FASTA was written to OceanDNA-b22827/markers.fasta
[2023-03-15 21:17:17,889] [INFO] Task started: Blastn
[2023-03-15 21:17:17,889] [INFO] Running command: blastn -query OceanDNA-b22827/markers.fasta -db /var/lib/cwl/stg05daabcd-0578-4a27-9155-7b635af013a7/dqc_reference/reference_markers.fasta -out OceanDNA-b22827/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:17:18,419] [INFO] Task succeeded: Blastn
[2023-03-15 21:17:18,420] [INFO] Selected 30 target genomes.
[2023-03-15 21:17:18,420] [INFO] Target genome list was writen to OceanDNA-b22827/target_genomes.txt
[2023-03-15 21:17:18,453] [INFO] Task started: fastANI
[2023-03-15 21:17:18,453] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f0a95ee-0ac5-4a68-a1db-0d9bf64bfab3/OceanDNA-b22827.fa --refList OceanDNA-b22827/target_genomes.txt --output OceanDNA-b22827/fastani_result.tsv --threads 1
[2023-03-15 21:17:44,770] [INFO] Task succeeded: fastANI
[2023-03-15 21:17:44,771] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05daabcd-0578-4a27-9155-7b635af013a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:17:44,771] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05daabcd-0578-4a27-9155-7b635af013a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:17:44,776] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:17:44,776] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 21:17:44,776] [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
Thalassoroseus pseudoceratinae	strain=JC658	GCA_011634775.1	2713176	2713176	type	True	75.5048	53	2146	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	75.3441	51	2146	95	below_threshold
Planctomicrobium piriforme	strain=DSM 26348	GCA_900113665.1	1576369	1576369	type	True	75.3406	53	2146	95	below_threshold
Lacipirellula parvula	strain=PX69	GCA_009177095.1	2650471	2650471	type	True	75.2871	58	2146	95	below_threshold
Rubinisphaera margarita	strain=ICM_H10	GCA_022267515.1	2909586	2909586	type	True	75.092	62	2146	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:17:44,777] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22827/tc_result.tsv
[2023-03-15 21:17:44,777] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:17:44,777] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:17:44,777] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05daabcd-0578-4a27-9155-7b635af013a7/dqc_reference/checkm_data
[2023-03-15 21:17:44,778] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:17:45,152] [INFO] Task started: CheckM
[2023-03-15 21:17:45,152] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22827/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22827/checkm_input OceanDNA-b22827/checkm_result
[2023-03-15 21:19:25,535] [INFO] Task succeeded: CheckM
[2023-03-15 21:19:25,536] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:19:25,540] [INFO] ===== Completeness check finished =====
[2023-03-15 21:19:25,540] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:19:25,540] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22827/markers.fasta)
[2023-03-15 21:19:25,542] [INFO] Task started: Blastn
[2023-03-15 21:19:25,542] [INFO] Running command: blastn -query OceanDNA-b22827/markers.fasta -db /var/lib/cwl/stg05daabcd-0578-4a27-9155-7b635af013a7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22827/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:19:26,273] [INFO] Task succeeded: Blastn
[2023-03-15 21:19:26,274] [INFO] Selected 31 target genomes.
[2023-03-15 21:19:26,274] [INFO] Target genome list was writen to OceanDNA-b22827/target_genomes_gtdb.txt
[2023-03-15 21:19:27,254] [INFO] Task started: fastANI
[2023-03-15 21:19:27,254] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f0a95ee-0ac5-4a68-a1db-0d9bf64bfab3/OceanDNA-b22827.fa --refList OceanDNA-b22827/target_genomes_gtdb.txt --output OceanDNA-b22827/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:20:00,335] [INFO] Task succeeded: fastANI
[2023-03-15 21:20:00,344] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:20:00,344] [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_018699955.1	s__JABISG01 sp018699955	88.7261	1699	2146	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABISG01	95.0	99.95	99.95	0.96	0.96	3	-
GCA_002722955.1	s__GCA-2722955 sp002722955	75.7262	68	2146	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__GCA-2722955	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009691905.1	s__SIAF01 sp009691905	75.5862	99	2146	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__UBA10511;g__SIAF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124895.1	s__JABMPE01 sp016124895	75.5313	104	2146	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABMPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011634775.1	s__JC658 sp011634775	75.5048	53	2146	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JC658	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007748155.1	s__Gimesia panareensis	75.4733	66	2146	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	96.61	95.86	0.91	0.90	3	-
GCA_003669125.1	s__SXKJ01 sp003669125	75.4309	83	2146	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXKJ01	95.0	99.07	98.94	0.92	0.91	3	-
GCF_007859765.1	s__Posidoniimonas corsicana	75.3441	51	2146	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Posidoniimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872645.1	s__SXKJ01 sp016872645	75.2949	84	2146	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXKJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113665.1	s__Planctomicrobium piriforme	75.2854	51	2146	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Planctomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005798445.1	s__SXKJ01 sp005798445	75.2454	90	2146	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXKJ01	95.0	99.80	99.80	0.90	0.90	2	-
GCA_016235885.1	s__JACRIH01 sp016235885	75.132	89	2146	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__UBA10511;g__JACRIH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001610835.1	s__Planctomyces_A sp001610835	74.9723	61	2146	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Planctomyces_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898385.1	s__Paludisphaera sp001898385	74.9549	55	2146	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903840265.1	s__Schlesneria sp903840265	74.8961	63	2146	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Schlesneria	95.0	99.98	99.98	0.97	0.97	3	-
--------------------------------------------------------------------------------
[2023-03-15 21:20:00,344] [INFO] GTDB search result was written to OceanDNA-b22827/result_gtdb.tsv
[2023-03-15 21:20:00,344] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:20:00,346] [INFO] DFAST_QC result json was written to OceanDNA-b22827/dqc_result.json
[2023-03-15 21:20:00,346] [INFO] DFAST_QC completed!
[2023-03-15 21:20:00,346] [INFO] Total running time: 0h3m27s