[2023-03-15 03:56:21,756] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:56:21,756] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:56:21,756] [INFO] DQC Reference Directory: /var/lib/cwl/stg4268aec7-9519-4ff6-8f60-22fef430aabe/dqc_reference
[2023-03-15 03:56:23,405] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:56:23,406] [INFO] Task started: Prodigal
[2023-03-15 03:56:23,406] [INFO] Running command: cat /var/lib/cwl/stgc9c60845-cdea-42e3-af64-f46ae17fb3db/OceanDNA-b22842.fa | prodigal -d OceanDNA-b22842/cds.fna -a OceanDNA-b22842/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:57:08,530] [INFO] Task succeeded: Prodigal
[2023-03-15 03:57:08,531] [INFO] Task started: HMMsearch
[2023-03-15 03:57:08,531] [INFO] Running command: hmmsearch --tblout OceanDNA-b22842/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4268aec7-9519-4ff6-8f60-22fef430aabe/dqc_reference/reference_markers.hmm OceanDNA-b22842/protein.faa > /dev/null
[2023-03-15 03:57:08,845] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:57:08,845] [INFO] Found 6/6 markers.
[2023-03-15 03:57:08,888] [INFO] Query marker FASTA was written to OceanDNA-b22842/markers.fasta
[2023-03-15 03:57:08,890] [INFO] Task started: Blastn
[2023-03-15 03:57:08,890] [INFO] Running command: blastn -query OceanDNA-b22842/markers.fasta -db /var/lib/cwl/stg4268aec7-9519-4ff6-8f60-22fef430aabe/dqc_reference/reference_markers.fasta -out OceanDNA-b22842/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:57:09,424] [INFO] Task succeeded: Blastn
[2023-03-15 03:57:09,425] [INFO] Selected 26 target genomes.
[2023-03-15 03:57:09,426] [INFO] Target genome list was writen to OceanDNA-b22842/target_genomes.txt
[2023-03-15 03:57:09,444] [INFO] Task started: fastANI
[2023-03-15 03:57:09,445] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9c60845-cdea-42e3-af64-f46ae17fb3db/OceanDNA-b22842.fa --refList OceanDNA-b22842/target_genomes.txt --output OceanDNA-b22842/fastani_result.tsv --threads 1
[2023-03-15 03:57:32,870] [INFO] Task succeeded: fastANI
[2023-03-15 03:57:32,871] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4268aec7-9519-4ff6-8f60-22fef430aabe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:57:32,871] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4268aec7-9519-4ff6-8f60-22fef430aabe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:57:32,876] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:57:32,876] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 03:57:32,876] [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
Rubinisphaera margarita	strain=ICM_H10	GCA_022267515.1	2909586	2909586	type	True	75.4605	71	2443	95	below_threshold
Fuerstiella marisgermanici	strain=NH11	GCA_001983935.1	1891926	1891926	type	True	75.3489	77	2443	95	below_threshold
Maioricimonas rarisocia	strain=Mal4	GCA_007747795.1	2528026	2528026	type	True	75.2652	107	2443	95	below_threshold
Gimesia panareensis	strain=Enr10	GCA_007748155.1	2527978	2527978	type	True	74.9553	63	2443	95	below_threshold
Lacipirellula parvula	strain=PX69	GCA_009177095.1	2650471	2650471	type	True	74.8923	56	2443	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 03:57:32,877] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22842/tc_result.tsv
[2023-03-15 03:57:32,877] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:57:32,877] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:57:32,877] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4268aec7-9519-4ff6-8f60-22fef430aabe/dqc_reference/checkm_data
[2023-03-15 03:57:32,878] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:57:32,909] [INFO] Task started: CheckM
[2023-03-15 03:57:32,909] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22842/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22842/checkm_input OceanDNA-b22842/checkm_result
[2023-03-15 03:59:19,010] [INFO] Task succeeded: CheckM
[2023-03-15 03:59:19,010] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.29%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:59:19,015] [INFO] ===== Completeness check finished =====
[2023-03-15 03:59:19,015] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:59:19,015] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22842/markers.fasta)
[2023-03-15 03:59:19,017] [INFO] Task started: Blastn
[2023-03-15 03:59:19,017] [INFO] Running command: blastn -query OceanDNA-b22842/markers.fasta -db /var/lib/cwl/stg4268aec7-9519-4ff6-8f60-22fef430aabe/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22842/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:59:19,728] [INFO] Task succeeded: Blastn
[2023-03-15 03:59:19,729] [INFO] Selected 21 target genomes.
[2023-03-15 03:59:19,729] [INFO] Target genome list was writen to OceanDNA-b22842/target_genomes_gtdb.txt
[2023-03-15 03:59:19,749] [INFO] Task started: fastANI
[2023-03-15 03:59:19,750] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9c60845-cdea-42e3-af64-f46ae17fb3db/OceanDNA-b22842.fa --refList OceanDNA-b22842/target_genomes_gtdb.txt --output OceanDNA-b22842/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:59:40,516] [INFO] Task succeeded: fastANI
[2023-03-15 03:59:40,524] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 03:59:40,524] [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_016779365.1	s__JABMPE01 sp016779365	80.247	631	2443	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABMPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013203845.1	s__JABMPE01 sp013203845	79.8133	1173	2443	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABMPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124895.1	s__JABMPE01 sp016124895	76.2091	325	2443	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABMPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003669125.1	s__SXKJ01 sp003669125	75.6091	94	2443	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXKJ01	95.0	99.07	98.94	0.92	0.91	3	-
GCA_903840265.1	s__Schlesneria sp903840265	75.3957	53	2443	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Schlesneria	95.0	99.98	99.98	0.97	0.97	3	-
GCF_000165715.2	s__Rubinisphaera brasiliensis	75.3421	60	2443	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Rubinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900299185.1	s__AM-0621 sp900299185	75.3295	86	2443	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__AM-0621	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007747795.1	s__Maioricimonas rarisocia	75.2888	104	2443	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Maioricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003388505.1	s__MB-PLM-1 sp003388505	75.1108	89	2443	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__MB-PLM-1	95.0	99.82	99.66	0.97	0.95	4	-
GCF_007748155.1	s__Gimesia panareensis	74.9637	62	2443	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	96.61	95.86	0.91	0.90	3	-
GCF_009177095.1	s__Lacipirellula parvula	74.9001	55	2443	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 03:59:40,524] [INFO] GTDB search result was written to OceanDNA-b22842/result_gtdb.tsv
[2023-03-15 03:59:40,524] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:59:40,525] [INFO] DFAST_QC result json was written to OceanDNA-b22842/dqc_result.json
[2023-03-15 03:59:40,525] [INFO] DFAST_QC completed!
[2023-03-15 03:59:40,525] [INFO] Total running time: 0h3m19s