[2023-03-14 13:16:07,188] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:16:07,188] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:16:07,188] [INFO] DQC Reference Directory: /var/lib/cwl/stg14a2ec7b-4318-417b-b7e5-4ad244622f31/dqc_reference
[2023-03-14 13:16:08,293] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:16:08,293] [INFO] Task started: Prodigal
[2023-03-14 13:16:08,294] [INFO] Running command: cat /var/lib/cwl/stg63064280-c813-4170-89d4-d527f894dc7c/OceanDNA-b28109.fa | prodigal -d OceanDNA-b28109/cds.fna -a OceanDNA-b28109/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:16:33,614] [INFO] Task succeeded: Prodigal
[2023-03-14 13:16:33,614] [INFO] Task started: HMMsearch
[2023-03-14 13:16:33,615] [INFO] Running command: hmmsearch --tblout OceanDNA-b28109/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg14a2ec7b-4318-417b-b7e5-4ad244622f31/dqc_reference/reference_markers.hmm OceanDNA-b28109/protein.faa > /dev/null
[2023-03-14 13:16:33,818] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:16:33,818] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg63064280-c813-4170-89d4-d527f894dc7c/OceanDNA-b28109.fa]
[2023-03-14 13:16:33,911] [INFO] Query marker FASTA was written to OceanDNA-b28109/markers.fasta
[2023-03-14 13:16:33,912] [INFO] Task started: Blastn
[2023-03-14 13:16:33,912] [INFO] Running command: blastn -query OceanDNA-b28109/markers.fasta -db /var/lib/cwl/stg14a2ec7b-4318-417b-b7e5-4ad244622f31/dqc_reference/reference_markers.fasta -out OceanDNA-b28109/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:16:34,520] [INFO] Task succeeded: Blastn
[2023-03-14 13:16:34,521] [INFO] Selected 15 target genomes.
[2023-03-14 13:16:34,521] [INFO] Target genome list was writen to OceanDNA-b28109/target_genomes.txt
[2023-03-14 13:16:34,533] [INFO] Task started: fastANI
[2023-03-14 13:16:34,533] [INFO] Running command: fastANI --query /var/lib/cwl/stg63064280-c813-4170-89d4-d527f894dc7c/OceanDNA-b28109.fa --refList OceanDNA-b28109/target_genomes.txt --output OceanDNA-b28109/fastani_result.tsv --threads 1
[2023-03-14 13:16:44,815] [INFO] Task succeeded: fastANI
[2023-03-14 13:16:44,815] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg14a2ec7b-4318-417b-b7e5-4ad244622f31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:16:44,816] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg14a2ec7b-4318-417b-b7e5-4ad244622f31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:16:44,825] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:16:44,825] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 13:16:44,825] [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
Celeribacter baekdonensis	strain=DSM 27375	GCA_900102315.1	875171	875171	type	True	94.088	1130	1268	95	below_threshold
Celeribacter ethanolicus	strain=NH195	GCA_001550095.1	1758178	1758178	type	True	79.3083	644	1268	95	below_threshold
Celeribacter neptunius	strain=DSM 26471	GCA_900113955.1	588602	588602	type	True	79.2676	633	1268	95	below_threshold
Celeribacter halophilus	strain=DSM 26270	GCA_003254175.1	576117	576117	type	True	79.0841	510	1268	95	below_threshold
Celeribacter halophilus	strain=ZXM137	GCA_001550085.1	576117	576117	type	True	79.0632	508	1268	95	below_threshold
Celeribacter halophilus	strain=CGMCC 1.8891	GCA_900114135.1	576117	576117	type	True	79.0586	500	1268	95	below_threshold
Celeribacter persicus	strain=DSM 100434	GCA_003050785.1	1651082	1651082	type	True	78.9894	588	1268	95	below_threshold
Celeribacter marinus	strain=DSM 100036	GCA_900114275.1	1397108	1397108	type	True	77.8168	300	1268	95	below_threshold
Celeribacter marinus	strain=IMCC12053	GCA_001308265.1	1397108	1397108	type	True	77.8066	307	1268	95	below_threshold
Pseudoprimorskyibacter insulae	strain=CECT 8871	GCA_900302505.1	1695997	1695997	type	True	76.8	205	1268	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	76.2883	146	1268	95	below_threshold
Pseudogemmobacter hezensis	strain=D13-10-4-6	GCA_013155295.1	2737662	2737662	type	True	76.1048	137	1268	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	76.068	114	1268	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.0584	140	1268	95	below_threshold
Pseudogemmobacter bohemicus	strain=Cd-10	GCA_003290025.1	2250708	2250708	type	True	76.0509	143	1268	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 13:16:44,825] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28109/tc_result.tsv
[2023-03-14 13:16:44,825] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:16:44,826] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:16:44,826] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg14a2ec7b-4318-417b-b7e5-4ad244622f31/dqc_reference/checkm_data
[2023-03-14 13:16:44,826] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:16:44,983] [INFO] Task started: CheckM
[2023-03-14 13:16:44,983] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28109/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28109/checkm_input OceanDNA-b28109/checkm_result
[2023-03-14 13:18:11,086] [INFO] Task succeeded: CheckM
[2023-03-14 13:18:11,086] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 13:18:11,089] [INFO] ===== Completeness check finished =====
[2023-03-14 13:18:11,089] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:18:11,089] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28109/markers.fasta)
[2023-03-14 13:18:11,091] [INFO] Task started: Blastn
[2023-03-14 13:18:11,091] [INFO] Running command: blastn -query OceanDNA-b28109/markers.fasta -db /var/lib/cwl/stg14a2ec7b-4318-417b-b7e5-4ad244622f31/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28109/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:18:12,132] [INFO] Task succeeded: Blastn
[2023-03-14 13:18:12,133] [INFO] Selected 9 target genomes.
[2023-03-14 13:18:12,133] [INFO] Target genome list was writen to OceanDNA-b28109/target_genomes_gtdb.txt
[2023-03-14 13:18:12,145] [INFO] Task started: fastANI
[2023-03-14 13:18:12,145] [INFO] Running command: fastANI --query /var/lib/cwl/stg63064280-c813-4170-89d4-d527f894dc7c/OceanDNA-b28109.fa --refList OceanDNA-b28109/target_genomes_gtdb.txt --output OceanDNA-b28109/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:18:20,108] [INFO] Task succeeded: fastANI
[2023-03-14 13:18:20,114] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 13:18:20,114] [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
GCF_000299875.1	s__Celeribacter baekdonensis_A	99.144	1231	1268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	99.07	99.01	0.95	0.93	3	conclusive
GCF_900102315.1	s__Celeribacter baekdonensis	94.0803	1131	1268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	97.81	97.75	0.91	0.89	8	-
GCF_003047105.1	s__Celeribacter baekdonensis_B	90.8156	1049	1268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011806455.1	s__Celeribacter sp011806455	80.0006	668	1268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	97.95	97.95	0.96	0.96	2	-
GCF_001550095.1	s__Celeribacter ethanolicus	79.3158	643	1268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	98.17	98.15	0.91	0.89	3	-
GCF_900113955.1	s__Celeribacter neptunius	79.2676	633	1268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114135.1	s__Celeribacter halophilus	79.0633	499	1268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	98.37	95.14	0.95	0.87	4	-
GCF_003050785.1	s__Celeribacter persicus	78.982	589	1268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001308265.1	s__Celeribacter_A marinus	77.8066	307	1268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter_A	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-14 13:18:20,114] [INFO] GTDB search result was written to OceanDNA-b28109/result_gtdb.tsv
[2023-03-14 13:18:20,114] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:18:20,116] [INFO] DFAST_QC result json was written to OceanDNA-b28109/dqc_result.json
[2023-03-14 13:18:20,116] [INFO] DFAST_QC completed!
[2023-03-14 13:18:20,116] [INFO] Total running time: 0h2m13s