[2023-03-19 05:19:35,848] [INFO] DFAST_QC pipeline started.
[2023-03-19 05:19:35,848] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 05:19:35,848] [INFO] DQC Reference Directory: /var/lib/cwl/stg498ddaa8-b18e-496d-9da9-832dafea5f73/dqc_reference
[2023-03-19 05:19:37,002] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 05:19:37,002] [INFO] Task started: Prodigal
[2023-03-19 05:19:37,002] [INFO] Running command: cat /var/lib/cwl/stge75afd5b-8892-4b09-a259-eb43730991e7/OceanDNA-b41382.fa | prodigal -d OceanDNA-b41382/cds.fna -a OceanDNA-b41382/protein.faa -g 11 -q > /dev/null
[2023-03-19 05:19:55,367] [INFO] Task succeeded: Prodigal
[2023-03-19 05:19:55,367] [INFO] Task started: HMMsearch
[2023-03-19 05:19:55,368] [INFO] Running command: hmmsearch --tblout OceanDNA-b41382/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg498ddaa8-b18e-496d-9da9-832dafea5f73/dqc_reference/reference_markers.hmm OceanDNA-b41382/protein.faa > /dev/null
[2023-03-19 05:19:55,634] [INFO] Task succeeded: HMMsearch
[2023-03-19 05:19:55,634] [INFO] Found 6/6 markers.
[2023-03-19 05:19:55,656] [INFO] Query marker FASTA was written to OceanDNA-b41382/markers.fasta
[2023-03-19 05:19:55,656] [INFO] Task started: Blastn
[2023-03-19 05:19:55,656] [INFO] Running command: blastn -query OceanDNA-b41382/markers.fasta -db /var/lib/cwl/stg498ddaa8-b18e-496d-9da9-832dafea5f73/dqc_reference/reference_markers.fasta -out OceanDNA-b41382/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:19:56,330] [INFO] Task succeeded: Blastn
[2023-03-19 05:19:56,331] [INFO] Selected 25 target genomes.
[2023-03-19 05:19:56,331] [INFO] Target genome list was writen to OceanDNA-b41382/target_genomes.txt
[2023-03-19 05:19:56,344] [INFO] Task started: fastANI
[2023-03-19 05:19:56,344] [INFO] Running command: fastANI --query /var/lib/cwl/stge75afd5b-8892-4b09-a259-eb43730991e7/OceanDNA-b41382.fa --refList OceanDNA-b41382/target_genomes.txt --output OceanDNA-b41382/fastani_result.tsv --threads 1
[2023-03-19 05:20:12,564] [INFO] Task succeeded: fastANI
[2023-03-19 05:20:12,564] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg498ddaa8-b18e-496d-9da9-832dafea5f73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 05:20:12,564] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg498ddaa8-b18e-496d-9da9-832dafea5f73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 05:20:12,569] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 05:20:12,569] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 05:20:12,569] [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
Thalassolituus oleivorans	strain=MIL-1	GCA_000355675.1	187493	187493	type	True	79.0019	267	1062	95	below_threshold
Oleibacter marinus	strain=DSM 24913	GCA_900156675.1	484498	484498	type	True	78.3519	243	1062	95	below_threshold
Thalassolituus marinus	strain=IMCC1826	GCA_020320395.1	671053	671053	type	True	78.2684	141	1062	95	below_threshold
Oceanobacter kriegii	strain=DSM 6294	GCA_000422845.1	64972	64972	type	True	77.1619	95	1062	95	below_threshold
Bacterioplanes sanyensis	strain=KCTC 32220	GCA_014652515.1	1249553	1249553	type	True	77.0009	114	1062	95	below_threshold
Oceanobacter mangrovi	strain=SM2-42	GCA_019740315.1	2862510	2862510	type	True	76.9754	94	1062	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 05:20:12,570] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41382/tc_result.tsv
[2023-03-19 05:20:12,570] [INFO] ===== Taxonomy check completed =====
[2023-03-19 05:20:12,570] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 05:20:12,570] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg498ddaa8-b18e-496d-9da9-832dafea5f73/dqc_reference/checkm_data
[2023-03-19 05:20:12,571] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 05:20:12,627] [INFO] Task started: CheckM
[2023-03-19 05:20:12,628] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41382/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41382/checkm_input OceanDNA-b41382/checkm_result
[2023-03-19 05:21:00,271] [INFO] Task succeeded: CheckM
[2023-03-19 05:21:00,272] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 05:21:00,274] [INFO] ===== Completeness check finished =====
[2023-03-19 05:21:00,274] [INFO] ===== Start GTDB Search =====
[2023-03-19 05:21:00,274] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41382/markers.fasta)
[2023-03-19 05:21:00,274] [INFO] Task started: Blastn
[2023-03-19 05:21:00,275] [INFO] Running command: blastn -query OceanDNA-b41382/markers.fasta -db /var/lib/cwl/stg498ddaa8-b18e-496d-9da9-832dafea5f73/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41382/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:21:01,337] [INFO] Task succeeded: Blastn
[2023-03-19 05:21:01,338] [INFO] Selected 16 target genomes.
[2023-03-19 05:21:01,338] [INFO] Target genome list was writen to OceanDNA-b41382/target_genomes_gtdb.txt
[2023-03-19 05:21:01,392] [INFO] Task started: fastANI
[2023-03-19 05:21:01,392] [INFO] Running command: fastANI --query /var/lib/cwl/stge75afd5b-8892-4b09-a259-eb43730991e7/OceanDNA-b41382.fa --refList OceanDNA-b41382/target_genomes_gtdb.txt --output OceanDNA-b41382/fastani_result_gtdb.tsv --threads 1
[2023-03-19 05:21:10,652] [INFO] Task succeeded: fastANI
[2023-03-19 05:21:10,660] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 05:21:10,660] [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_002733645.1	s__Oleibacter sp002733645	97.6767	961	1062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	97.97	97.97	0.87	0.87	2	conclusive
GCF_000355675.1	s__Thalassolituus oleivorans	79.0019	267	1062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Thalassolituus	95.0	98.27	98.03	0.89	0.78	10	-
GCF_900156675.1	s__Oleibacter marinus	78.3528	243	1062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	98.96	98.96	0.99	0.99	2	-
GCA_002331105.1	s__Oleibacter sp002331105	77.8573	212	1062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	98.96	97.07	0.90	0.84	7	-
GCF_007785795.1	s__UBA2009 sp002335285	77.846	139	1062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	97.54	97.44	0.92	0.92	6	-
GCA_002733205.1	s__UBA2009 sp002733205	77.7378	132	1062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	96.83	96.83	0.84	0.84	2	-
GCA_002708475.1	s__Oleispira sp002708475	77.5249	60	1062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleispira	95.0	98.91	98.91	0.78	0.78	2	-
GCA_002298335.1	s__Oleibacter sp002298335	77.4655	123	1062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	99.94	99.90	0.96	0.95	5	-
GCA_014859445.1	s__Bacterioplanes sp014859445	77.243	111	1062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Bacterioplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422845.1	s__Oceanobacter kriegii	77.1338	94	1062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oceanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006212115.1	s__Oleibacter sp006212115	77.1113	168	1062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016132445.1	s__UBA2009 sp016132445	77.0279	120	1062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	97.98	97.98	0.94	0.94	2	-
GCF_014652515.1	s__Bacterioplanes sanyensis	77.0252	113	1062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Bacterioplanes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 05:21:10,660] [INFO] GTDB search result was written to OceanDNA-b41382/result_gtdb.tsv
[2023-03-19 05:21:10,661] [INFO] ===== GTDB Search completed =====
[2023-03-19 05:21:10,662] [INFO] DFAST_QC result json was written to OceanDNA-b41382/dqc_result.json
[2023-03-19 05:21:10,662] [INFO] DFAST_QC completed!
[2023-03-19 05:21:10,662] [INFO] Total running time: 0h1m35s