[2023-03-17 02:57:06,471] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:57:06,471] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:57:06,472] [INFO] DQC Reference Directory: /var/lib/cwl/stg19bace3c-83d2-40e4-b0d6-32cb3f1115ee/dqc_reference
[2023-03-17 02:57:08,637] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:57:08,637] [INFO] Task started: Prodigal
[2023-03-17 02:57:08,637] [INFO] Running command: cat /var/lib/cwl/stg76252432-01c5-47af-abdf-5fc8589142d1/OceanDNA-b24316.fa | prodigal -d OceanDNA-b24316/cds.fna -a OceanDNA-b24316/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:57:29,186] [INFO] Task succeeded: Prodigal
[2023-03-17 02:57:29,186] [INFO] Task started: HMMsearch
[2023-03-17 02:57:29,186] [INFO] Running command: hmmsearch --tblout OceanDNA-b24316/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19bace3c-83d2-40e4-b0d6-32cb3f1115ee/dqc_reference/reference_markers.hmm OceanDNA-b24316/protein.faa > /dev/null
[2023-03-17 02:57:29,391] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:57:29,392] [INFO] Found 6/6 markers.
[2023-03-17 02:57:29,418] [INFO] Query marker FASTA was written to OceanDNA-b24316/markers.fasta
[2023-03-17 02:57:29,419] [INFO] Task started: Blastn
[2023-03-17 02:57:29,419] [INFO] Running command: blastn -query OceanDNA-b24316/markers.fasta -db /var/lib/cwl/stg19bace3c-83d2-40e4-b0d6-32cb3f1115ee/dqc_reference/reference_markers.fasta -out OceanDNA-b24316/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:57:30,040] [INFO] Task succeeded: Blastn
[2023-03-17 02:57:30,040] [INFO] Selected 30 target genomes.
[2023-03-17 02:57:30,041] [INFO] Target genome list was writen to OceanDNA-b24316/target_genomes.txt
[2023-03-17 02:57:30,059] [INFO] Task started: fastANI
[2023-03-17 02:57:30,059] [INFO] Running command: fastANI --query /var/lib/cwl/stg76252432-01c5-47af-abdf-5fc8589142d1/OceanDNA-b24316.fa --refList OceanDNA-b24316/target_genomes.txt --output OceanDNA-b24316/fastani_result.tsv --threads 1
[2023-03-17 02:57:49,055] [INFO] Task succeeded: fastANI
[2023-03-17 02:57:49,055] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19bace3c-83d2-40e4-b0d6-32cb3f1115ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:57:49,056] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19bace3c-83d2-40e4-b0d6-32cb3f1115ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:57:49,062] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:57:49,062] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 02:57:49,062] [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
Ferrovibrio terrae	strain=K5	GCA_007197755.1	2594003	2594003	type	True	75.3073	50	1076	95	below_threshold
Skermanella rosea	strain=KEMB 2255-458	GCA_016806835.2	1817965	1817965	type	True	75.2805	59	1076	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	75.0609	53	1076	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	74.9639	56	1076	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 02:57:49,063] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24316/tc_result.tsv
[2023-03-17 02:57:49,063] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:57:49,063] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:57:49,063] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19bace3c-83d2-40e4-b0d6-32cb3f1115ee/dqc_reference/checkm_data
[2023-03-17 02:57:49,064] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:57:49,072] [INFO] Task started: CheckM
[2023-03-17 02:57:49,073] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24316/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24316/checkm_input OceanDNA-b24316/checkm_result
[2023-03-17 02:58:40,959] [INFO] Task succeeded: CheckM
[2023-03-17 02:58:40,959] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.07%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:58:40,962] [INFO] ===== Completeness check finished =====
[2023-03-17 02:58:40,962] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:58:40,963] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24316/markers.fasta)
[2023-03-17 02:58:40,963] [INFO] Task started: Blastn
[2023-03-17 02:58:40,964] [INFO] Running command: blastn -query OceanDNA-b24316/markers.fasta -db /var/lib/cwl/stg19bace3c-83d2-40e4-b0d6-32cb3f1115ee/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24316/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:58:41,935] [INFO] Task succeeded: Blastn
[2023-03-17 02:58:41,936] [INFO] Selected 14 target genomes.
[2023-03-17 02:58:41,936] [INFO] Target genome list was writen to OceanDNA-b24316/target_genomes_gtdb.txt
[2023-03-17 02:58:42,314] [INFO] Task started: fastANI
[2023-03-17 02:58:42,314] [INFO] Running command: fastANI --query /var/lib/cwl/stg76252432-01c5-47af-abdf-5fc8589142d1/OceanDNA-b24316.fa --refList OceanDNA-b24316/target_genomes_gtdb.txt --output OceanDNA-b24316/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:58:54,336] [INFO] Task succeeded: fastANI
[2023-03-17 02:58:54,343] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 02:58:54,343] [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_002731375.1	s__GCA-2731375 sp002731375	99.6127	1009	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	99.58	99.58	0.91	0.91	2	conclusive
GCA_018701215.1	s__GCA-2731375 sp018701215	85.1266	923	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	99.97	99.95	0.98	0.97	15	-
GCA_016776605.1	s__GCA-2731375 sp016776605	78.2998	546	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018667855.1	s__GCA-2731375 sp018667855	78.1864	500	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	99.62	99.58	0.85	0.84	3	-
GCA_018660265.1	s__GCA-2731375 sp018660265	77.6957	448	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	99.92	99.87	0.96	0.94	11	-
GCA_001657395.1	s__Pelagibius sp001657395	75.7851	52	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__Pelagibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016806835.1	s__Skermanella rosea	75.2854	59	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018823745.1	s__Oceanibaculum sp018823745	75.2488	53	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	99.98	99.98	1.00	1.00	4	-
GCF_016653635.2	s__Skermanella sp016653635	75.1157	65	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 02:58:54,343] [INFO] GTDB search result was written to OceanDNA-b24316/result_gtdb.tsv
[2023-03-17 02:58:54,343] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:58:54,344] [INFO] DFAST_QC result json was written to OceanDNA-b24316/dqc_result.json
[2023-03-17 02:58:54,345] [INFO] DFAST_QC completed!
[2023-03-17 02:58:54,345] [INFO] Total running time: 0h1m48s