[2023-03-15 10:49:28,631] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:49:28,632] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:49:28,632] [INFO] DQC Reference Directory: /var/lib/cwl/stg75a3dc9d-3f87-43e0-848d-ddd77593df44/dqc_reference
[2023-03-15 10:49:29,735] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:49:29,735] [INFO] Task started: Prodigal
[2023-03-15 10:49:29,735] [INFO] Running command: cat /var/lib/cwl/stg1a1b144d-d73c-44a6-9105-ecc12e04d718/OceanDNA-b1783.fa | prodigal -d OceanDNA-b1783/cds.fna -a OceanDNA-b1783/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:49:39,477] [INFO] Task succeeded: Prodigal
[2023-03-15 10:49:39,477] [INFO] Task started: HMMsearch
[2023-03-15 10:49:39,477] [INFO] Running command: hmmsearch --tblout OceanDNA-b1783/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg75a3dc9d-3f87-43e0-848d-ddd77593df44/dqc_reference/reference_markers.hmm OceanDNA-b1783/protein.faa > /dev/null
[2023-03-15 10:49:39,664] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:49:39,664] [INFO] Found 6/6 markers.
[2023-03-15 10:49:39,680] [INFO] Query marker FASTA was written to OceanDNA-b1783/markers.fasta
[2023-03-15 10:49:39,681] [INFO] Task started: Blastn
[2023-03-15 10:49:39,681] [INFO] Running command: blastn -query OceanDNA-b1783/markers.fasta -db /var/lib/cwl/stg75a3dc9d-3f87-43e0-848d-ddd77593df44/dqc_reference/reference_markers.fasta -out OceanDNA-b1783/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:49:40,280] [INFO] Task succeeded: Blastn
[2023-03-15 10:49:40,281] [INFO] Selected 33 target genomes.
[2023-03-15 10:49:40,281] [INFO] Target genome list was writen to OceanDNA-b1783/target_genomes.txt
[2023-03-15 10:49:40,300] [INFO] Task started: fastANI
[2023-03-15 10:49:40,300] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a1b144d-d73c-44a6-9105-ecc12e04d718/OceanDNA-b1783.fa --refList OceanDNA-b1783/target_genomes.txt --output OceanDNA-b1783/fastani_result.tsv --threads 1
[2023-03-15 10:50:02,957] [INFO] Task succeeded: fastANI
[2023-03-15 10:50:02,958] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg75a3dc9d-3f87-43e0-848d-ddd77593df44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:50:02,958] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg75a3dc9d-3f87-43e0-848d-ddd77593df44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:50:02,962] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:50:02,962] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 10:50:02,962] [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
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.1682	63	476	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	75.6222	59	476	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 10:50:02,962] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1783/tc_result.tsv
[2023-03-15 10:50:02,963] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:50:02,963] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:50:02,963] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg75a3dc9d-3f87-43e0-848d-ddd77593df44/dqc_reference/checkm_data
[2023-03-15 10:50:02,964] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:50:02,967] [INFO] Task started: CheckM
[2023-03-15 10:50:02,967] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1783/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1783/checkm_input OceanDNA-b1783/checkm_result
[2023-03-15 10:50:31,640] [INFO] Task succeeded: CheckM
[2023-03-15 10:50:31,640] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.64%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:50:31,643] [INFO] ===== Completeness check finished =====
[2023-03-15 10:50:31,643] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:50:31,643] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1783/markers.fasta)
[2023-03-15 10:50:31,645] [INFO] Task started: Blastn
[2023-03-15 10:50:31,645] [INFO] Running command: blastn -query OceanDNA-b1783/markers.fasta -db /var/lib/cwl/stg75a3dc9d-3f87-43e0-848d-ddd77593df44/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1783/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:50:32,571] [INFO] Task succeeded: Blastn
[2023-03-15 10:50:32,573] [INFO] Selected 20 target genomes.
[2023-03-15 10:50:32,573] [INFO] Target genome list was writen to OceanDNA-b1783/target_genomes_gtdb.txt
[2023-03-15 10:50:32,596] [INFO] Task started: fastANI
[2023-03-15 10:50:32,596] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a1b144d-d73c-44a6-9105-ecc12e04d718/OceanDNA-b1783.fa --refList OceanDNA-b1783/target_genomes_gtdb.txt --output OceanDNA-b1783/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:50:43,298] [INFO] Task succeeded: fastANI
[2023-03-15 10:50:43,304] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 10:50:43,304] [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_905480195.1	s__UBA11606 sp905480195	99.5613	449	476	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002694825.1	s__UBA11606 sp002694825	78.6316	167	476	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	97.28	96.77	0.84	0.81	7	-
GCA_002729125.1	s__UBA11606 sp002729125	78.165	163	476	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	99.78	99.78	0.92	0.92	2	-
GCA_002699625.1	s__UBA11606 sp002699625	78.1241	151	476	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845585.1	s__UBA11606 sp016845585	77.6536	154	476	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018699415.1	s__UBA11606 sp018699415	76.9703	77	476	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	99.44	99.44	0.86	0.85	3	-
GCA_009937405.1	s__UBA11606 sp009937405	76.8814	80	476	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	99.36	99.36	0.86	0.86	2	-
GCA_003697065.1	s__J010 sp003697065	76.7369	56	476	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__J010	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003231645.1	s__SZUA-87 sp003231645	76.4986	71	476	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__SZUA-87	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009844405.1	s__VYCW01 sp009844405	76.2219	54	476	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__VYCW01	95.0	99.44	99.17	0.93	0.90	7	-
--------------------------------------------------------------------------------
[2023-03-15 10:50:43,305] [INFO] GTDB search result was written to OceanDNA-b1783/result_gtdb.tsv
[2023-03-15 10:50:43,305] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:50:43,307] [INFO] DFAST_QC result json was written to OceanDNA-b1783/dqc_result.json
[2023-03-15 10:50:43,307] [INFO] DFAST_QC completed!
[2023-03-15 10:50:43,307] [INFO] Total running time: 0h1m15s