[2023-03-14 11:14:12,758] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:14:12,764] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:14:12,764] [INFO] DQC Reference Directory: /var/lib/cwl/stg78c12d0e-4b45-4d01-8756-eff86939ba43/dqc_reference
[2023-03-14 11:14:14,203] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:14:14,203] [INFO] Task started: Prodigal
[2023-03-14 11:14:14,204] [INFO] Running command: cat /var/lib/cwl/stg57970622-4b11-46f2-9163-2b4be35600fb/OceanDNA-b24146.fa | prodigal -d OceanDNA-b24146/cds.fna -a OceanDNA-b24146/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:14:26,540] [INFO] Task succeeded: Prodigal
[2023-03-14 11:14:26,540] [INFO] Task started: HMMsearch
[2023-03-14 11:14:26,540] [INFO] Running command: hmmsearch --tblout OceanDNA-b24146/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78c12d0e-4b45-4d01-8756-eff86939ba43/dqc_reference/reference_markers.hmm OceanDNA-b24146/protein.faa > /dev/null
[2023-03-14 11:14:26,829] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:14:26,830] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg57970622-4b11-46f2-9163-2b4be35600fb/OceanDNA-b24146.fa]
[2023-03-14 11:14:26,857] [INFO] Query marker FASTA was written to OceanDNA-b24146/markers.fasta
[2023-03-14 11:14:26,857] [INFO] Task started: Blastn
[2023-03-14 11:14:26,857] [INFO] Running command: blastn -query OceanDNA-b24146/markers.fasta -db /var/lib/cwl/stg78c12d0e-4b45-4d01-8756-eff86939ba43/dqc_reference/reference_markers.fasta -out OceanDNA-b24146/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:14:27,508] [INFO] Task succeeded: Blastn
[2023-03-14 11:14:27,509] [INFO] Selected 28 target genomes.
[2023-03-14 11:14:27,509] [INFO] Target genome list was writen to OceanDNA-b24146/target_genomes.txt
[2023-03-14 11:14:27,530] [INFO] Task started: fastANI
[2023-03-14 11:14:27,530] [INFO] Running command: fastANI --query /var/lib/cwl/stg57970622-4b11-46f2-9163-2b4be35600fb/OceanDNA-b24146.fa --refList OceanDNA-b24146/target_genomes.txt --output OceanDNA-b24146/fastani_result.tsv --threads 1
[2023-03-14 11:14:48,300] [INFO] Task succeeded: fastANI
[2023-03-14 11:14:48,300] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78c12d0e-4b45-4d01-8756-eff86939ba43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:14:48,300] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78c12d0e-4b45-4d01-8756-eff86939ba43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:14:48,306] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:14:48,306] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 11:14:48,306] [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
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	75.8128	50	638	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	75.7906	53	638	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	75.7689	56	638	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	75.5261	51	638	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.2861	67	638	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	75.1836	58	638	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:14:48,306] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24146/tc_result.tsv
[2023-03-14 11:14:48,306] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:14:48,306] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:14:48,306] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78c12d0e-4b45-4d01-8756-eff86939ba43/dqc_reference/checkm_data
[2023-03-14 11:14:48,307] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:14:48,357] [INFO] Task started: CheckM
[2023-03-14 11:14:48,357] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24146/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24146/checkm_input OceanDNA-b24146/checkm_result
[2023-03-14 11:15:22,873] [INFO] Task succeeded: CheckM
[2023-03-14 11:15:22,873] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:15:22,875] [INFO] ===== Completeness check finished =====
[2023-03-14 11:15:22,875] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:15:22,876] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24146/markers.fasta)
[2023-03-14 11:15:22,876] [INFO] Task started: Blastn
[2023-03-14 11:15:22,876] [INFO] Running command: blastn -query OceanDNA-b24146/markers.fasta -db /var/lib/cwl/stg78c12d0e-4b45-4d01-8756-eff86939ba43/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24146/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:15:23,971] [INFO] Task succeeded: Blastn
[2023-03-14 11:15:23,972] [INFO] Selected 26 target genomes.
[2023-03-14 11:15:23,972] [INFO] Target genome list was writen to OceanDNA-b24146/target_genomes_gtdb.txt
[2023-03-14 11:15:24,005] [INFO] Task started: fastANI
[2023-03-14 11:15:24,005] [INFO] Running command: fastANI --query /var/lib/cwl/stg57970622-4b11-46f2-9163-2b4be35600fb/OceanDNA-b24146.fa --refList OceanDNA-b24146/target_genomes_gtdb.txt --output OceanDNA-b24146/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:15:41,727] [INFO] Task succeeded: fastANI
[2023-03-14 11:15:41,733] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:15:41,733] [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_002471575.1	s__UBA830 sp002471575	78.7046	339	638	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	97.90	95.90	0.91	0.84	7	-
GCA_905181725.1	s__UBA830 sp905181725	77.6577	223	638	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479125.1	s__UBA830 sp905479125	77.4331	217	638	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	98.22	98.19	0.84	0.83	3	-
GCA_002937455.1	s__UBA830 sp002937455	76.4735	62	638	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	99.94	99.90	0.94	0.84	5	-
GCA_009377375.1	s__WHUE01 sp009377375	76.2972	94	638	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__WHUE01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001618175.1	s__Oceanibaculum pacificum	75.8128	50	638	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423185.1	s__Inquilinus limosus	75.7689	56	638	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__Inquilinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904705.1	s__Nisaea sp014904705	75.5261	51	638	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008039615.1	s__SYSU-D60007 sp008039615	75.2861	67	638	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__SYSU-D60007	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:15:41,733] [INFO] GTDB search result was written to OceanDNA-b24146/result_gtdb.tsv
[2023-03-14 11:15:41,733] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:15:41,734] [INFO] DFAST_QC result json was written to OceanDNA-b24146/dqc_result.json
[2023-03-14 11:15:41,734] [INFO] DFAST_QC completed!
[2023-03-14 11:15:41,734] [INFO] Total running time: 0h1m29s