[2023-03-16 06:03:00,908] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:03:00,910] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:03:00,910] [INFO] DQC Reference Directory: /var/lib/cwl/stg893c268b-73a1-42a7-81ef-8b7a3e55ae52/dqc_reference
[2023-03-16 06:03:01,987] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:03:01,988] [INFO] Task started: Prodigal
[2023-03-16 06:03:01,988] [INFO] Running command: cat /var/lib/cwl/stga4a8af19-cb03-428f-b224-21040256e47c/OceanDNA-b42270.fa | prodigal -d OceanDNA-b42270/cds.fna -a OceanDNA-b42270/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:03:05,788] [INFO] Task succeeded: Prodigal
[2023-03-16 06:03:05,789] [INFO] Task started: HMMsearch
[2023-03-16 06:03:05,789] [INFO] Running command: hmmsearch --tblout OceanDNA-b42270/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg893c268b-73a1-42a7-81ef-8b7a3e55ae52/dqc_reference/reference_markers.hmm OceanDNA-b42270/protein.faa > /dev/null
[2023-03-16 06:03:05,933] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:03:05,934] [WARNING] Found 4/6 markers. [/var/lib/cwl/stga4a8af19-cb03-428f-b224-21040256e47c/OceanDNA-b42270.fa]
[2023-03-16 06:03:05,956] [INFO] Query marker FASTA was written to OceanDNA-b42270/markers.fasta
[2023-03-16 06:03:05,956] [INFO] Task started: Blastn
[2023-03-16 06:03:05,956] [INFO] Running command: blastn -query OceanDNA-b42270/markers.fasta -db /var/lib/cwl/stg893c268b-73a1-42a7-81ef-8b7a3e55ae52/dqc_reference/reference_markers.fasta -out OceanDNA-b42270/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:03:06,466] [INFO] Task succeeded: Blastn
[2023-03-16 06:03:06,474] [INFO] Selected 6 target genomes.
[2023-03-16 06:03:06,475] [INFO] Target genome list was writen to OceanDNA-b42270/target_genomes.txt
[2023-03-16 06:03:06,477] [INFO] Task started: fastANI
[2023-03-16 06:03:06,478] [INFO] Running command: fastANI --query /var/lib/cwl/stga4a8af19-cb03-428f-b224-21040256e47c/OceanDNA-b42270.fa --refList OceanDNA-b42270/target_genomes.txt --output OceanDNA-b42270/fastani_result.tsv --threads 1
[2023-03-16 06:03:09,364] [INFO] Task succeeded: fastANI
[2023-03-16 06:03:09,365] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg893c268b-73a1-42a7-81ef-8b7a3e55ae52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:03:09,365] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg893c268b-73a1-42a7-81ef-8b7a3e55ae52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:03:09,365] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:03:09,365] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 06:03:09,365] [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
--------------------------------------------------------------------------------
[2023-03-16 06:03:09,368] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42270/tc_result.tsv
[2023-03-16 06:03:09,370] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:03:09,370] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:03:09,370] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg893c268b-73a1-42a7-81ef-8b7a3e55ae52/dqc_reference/checkm_data
[2023-03-16 06:03:09,373] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:03:09,377] [INFO] Task started: CheckM
[2023-03-16 06:03:09,377] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42270/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42270/checkm_input OceanDNA-b42270/checkm_result
[2023-03-16 06:03:25,078] [INFO] Task succeeded: CheckM
[2023-03-16 06:03:25,079] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:03:25,091] [INFO] ===== Completeness check finished =====
[2023-03-16 06:03:25,091] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:03:25,091] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42270/markers.fasta)
[2023-03-16 06:03:25,093] [INFO] Task started: Blastn
[2023-03-16 06:03:25,093] [INFO] Running command: blastn -query OceanDNA-b42270/markers.fasta -db /var/lib/cwl/stg893c268b-73a1-42a7-81ef-8b7a3e55ae52/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42270/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:03:25,857] [INFO] Task succeeded: Blastn
[2023-03-16 06:03:25,861] [INFO] Selected 20 target genomes.
[2023-03-16 06:03:25,862] [INFO] Target genome list was writen to OceanDNA-b42270/target_genomes_gtdb.txt
[2023-03-16 06:03:25,889] [INFO] Task started: fastANI
[2023-03-16 06:03:25,890] [INFO] Running command: fastANI --query /var/lib/cwl/stga4a8af19-cb03-428f-b224-21040256e47c/OceanDNA-b42270.fa --refList OceanDNA-b42270/target_genomes_gtdb.txt --output OceanDNA-b42270/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:03:29,636] [INFO] Task succeeded: fastANI
[2023-03-16 06:03:29,647] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 06:03:29,647] [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_902582355.1	s__SAR86A sp902582355	99.2979	173	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	98.87	98.87	0.67	0.67	2	conclusive
GCA_902560315.1	s__SAR86A sp902560315	79.6809	124	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	95.47	95.47	0.82	0.82	2	-
GCA_902586925.1	s__SAR86A sp902586925	79.4276	126	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.82	96.82	0.89	0.89	2	-
GCA_902547295.1	s__SAR86A sp902547295	79.3512	104	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902516285.1	s__SAR86A sp902516285	79.225	75	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.51	96.51	0.92	0.92	2	-
GCA_004212975.1	s__SAR86A sp004212975	79.1953	101	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.30	95.02	0.85	0.76	8	-
GCA_902591925.1	s__SAR86A sp902591925	79.1489	139	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.32	97.27	0.90	0.89	3	-
GCA_902612915.1	s__SAR86A sp902612915	79.1293	118	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.80	95.61	0.84	0.75	10	-
GCA_902631785.1	s__SAR86A sp902631785	79.1011	110	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.84	96.84	0.79	0.79	2	-
GCA_902617045.1	s__SAR86A sp902617045	79.0993	125	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.06	95.32	0.86	0.86	4	-
GCA_902517505.1	s__SAR86A sp902517505	79.0585	119	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.73	97.59	0.82	0.80	3	-
GCA_902630885.1	s__SAR86A sp902630885	79.0429	104	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002690725.1	s__SAR86A sp002690725	78.7153	103	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	95.15	95.15	0.80	0.80	2	-
GCA_902528875.1	s__SAR86A sp902528875	78.5854	69	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902551185.1	s__SAR86A sp902551185	77.9478	84	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	99.17	99.17	0.78	0.78	2	-
GCA_902583575.1	s__SAR86A sp902583575	77.831	98	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902557965.1	s__SAR86A sp902557965	77.7385	79	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.42	97.04	0.73	0.71	3	-
GCA_002169105.1	s__SAR86A sp002169105	77.5286	58	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003213495.1	s__SAR86A sp003213495	77.484	102	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	98.20	96.41	0.97	0.94	3	-
--------------------------------------------------------------------------------
[2023-03-16 06:03:29,651] [INFO] GTDB search result was written to OceanDNA-b42270/result_gtdb.tsv
[2023-03-16 06:03:29,653] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:03:29,658] [INFO] DFAST_QC result json was written to OceanDNA-b42270/dqc_result.json
[2023-03-16 06:03:29,658] [INFO] DFAST_QC completed!
[2023-03-16 06:03:29,658] [INFO] Total running time: 0h0m29s