[2023-03-19 03:50:07,821] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:50:07,821] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:50:07,821] [INFO] DQC Reference Directory: /var/lib/cwl/stg32f69d26-3843-43a9-b5e4-382e6a1d045f/dqc_reference
[2023-03-19 03:50:09,593] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:50:09,593] [INFO] Task started: Prodigal
[2023-03-19 03:50:09,594] [INFO] Running command: cat /var/lib/cwl/stg2015d709-71d9-4657-8772-04161273d17f/OceanDNA-b42016.fa | prodigal -d OceanDNA-b42016/cds.fna -a OceanDNA-b42016/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:50:14,976] [INFO] Task succeeded: Prodigal
[2023-03-19 03:50:14,976] [INFO] Task started: HMMsearch
[2023-03-19 03:50:14,976] [INFO] Running command: hmmsearch --tblout OceanDNA-b42016/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32f69d26-3843-43a9-b5e4-382e6a1d045f/dqc_reference/reference_markers.hmm OceanDNA-b42016/protein.faa > /dev/null
[2023-03-19 03:50:15,127] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:50:15,128] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2015d709-71d9-4657-8772-04161273d17f/OceanDNA-b42016.fa]
[2023-03-19 03:50:15,137] [INFO] Query marker FASTA was written to OceanDNA-b42016/markers.fasta
[2023-03-19 03:50:15,137] [INFO] Task started: Blastn
[2023-03-19 03:50:15,137] [INFO] Running command: blastn -query OceanDNA-b42016/markers.fasta -db /var/lib/cwl/stg32f69d26-3843-43a9-b5e4-382e6a1d045f/dqc_reference/reference_markers.fasta -out OceanDNA-b42016/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:50:15,851] [INFO] Task succeeded: Blastn
[2023-03-19 03:50:15,851] [INFO] Selected 17 target genomes.
[2023-03-19 03:50:15,852] [INFO] Target genome list was writen to OceanDNA-b42016/target_genomes.txt
[2023-03-19 03:50:15,860] [INFO] Task started: fastANI
[2023-03-19 03:50:15,860] [INFO] Running command: fastANI --query /var/lib/cwl/stg2015d709-71d9-4657-8772-04161273d17f/OceanDNA-b42016.fa --refList OceanDNA-b42016/target_genomes.txt --output OceanDNA-b42016/fastani_result.tsv --threads 1
[2023-03-19 03:50:22,275] [INFO] Task succeeded: fastANI
[2023-03-19 03:50:22,275] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32f69d26-3843-43a9-b5e4-382e6a1d045f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:50:22,275] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32f69d26-3843-43a9-b5e4-382e6a1d045f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:50:22,276] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:50:22,276] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 03:50:22,276] [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
--------------------------------------------------------------------------------
[2023-03-19 03:50:22,276] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42016/tc_result.tsv
[2023-03-19 03:50:22,276] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:50:22,276] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:50:22,276] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32f69d26-3843-43a9-b5e4-382e6a1d045f/dqc_reference/checkm_data
[2023-03-19 03:50:22,279] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:50:22,281] [INFO] Task started: CheckM
[2023-03-19 03:50:22,281] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42016/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42016/checkm_input OceanDNA-b42016/checkm_result
[2023-03-19 03:50:41,472] [INFO] Task succeeded: CheckM
[2023-03-19 03:50:41,472] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.56%
Contamintation: 4.69%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 03:50:41,474] [INFO] ===== Completeness check finished =====
[2023-03-19 03:50:41,474] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:50:41,474] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42016/markers.fasta)
[2023-03-19 03:50:41,474] [INFO] Task started: Blastn
[2023-03-19 03:50:41,474] [INFO] Running command: blastn -query OceanDNA-b42016/markers.fasta -db /var/lib/cwl/stg32f69d26-3843-43a9-b5e4-382e6a1d045f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42016/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:50:42,261] [INFO] Task succeeded: Blastn
[2023-03-19 03:50:42,262] [INFO] Selected 22 target genomes.
[2023-03-19 03:50:42,262] [INFO] Target genome list was writen to OceanDNA-b42016/target_genomes_gtdb.txt
[2023-03-19 03:50:42,292] [INFO] Task started: fastANI
[2023-03-19 03:50:42,292] [INFO] Running command: fastANI --query /var/lib/cwl/stg2015d709-71d9-4657-8772-04161273d17f/OceanDNA-b42016.fa --refList OceanDNA-b42016/target_genomes_gtdb.txt --output OceanDNA-b42016/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:50:46,366] [INFO] Task succeeded: fastANI
[2023-03-19 03:50:46,378] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 03:50:46,378] [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_902557705.1	s__SCGC-AAA076-P13 sp902557705	77.4051	66	353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902558375.1	s__SCGC-AAA076-P13 sp902558375	77.2706	74	353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902556355.1	s__SCGC-AAA076-P13 sp902556355	77.08	74	353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902610905.1	s__SCGC-AAA076-P13 sp902610905	77.0599	86	353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902547295.1	s__SAR86A sp902547295	77.0415	50	353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000385055.1	s__SCGC-AAA076-P13 sp000385055	77.017	95	353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	98.19	98.19	0.89	0.89	2	-
GCA_902591665.1	s__SCGC-AAA076-P13 sp902591665	76.9818	98	353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	99.81	99.81	0.85	0.85	2	-
GCA_902558395.1	s__SCGC-AAA076-P13 sp902558395	76.9741	102	353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	97.77	97.77	0.94	0.94	2	-
GCA_905478035.1	s__SCGC-AAA076-P13 sp905478035	76.8632	95	353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010024215.1	s__SCGC-AAA076-P13 sp010024215	76.8564	59	353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	98.04	96.58	0.74	0.68	5	-
GCA_000384935.1	s__SCGC-AAA076-P13 sp000384935	76.8046	85	353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902591565.1	s__SCGC-AAA076-P13 sp902591565	76.8043	67	353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902560315.1	s__SAR86A sp902560315	76.7838	65	353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	95.47	95.47	0.82	0.82	2	-
GCA_902617045.1	s__SAR86A sp902617045	76.7709	66	353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.06	95.32	0.86	0.86	4	-
GCA_902612915.1	s__SAR86A sp902612915	76.746	59	353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.80	95.61	0.84	0.75	10	-
GCA_902541175.1	s__SAR86A sp902541175	76.6989	65	353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.65	95.31	0.89	0.85	3	-
GCA_902558095.1	s__SAR86A sp902558095	76.6236	69	353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902591925.1	s__SAR86A sp902591925	76.5876	67	353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.32	97.27	0.90	0.89	3	-
GCA_902559885.1	s__CACEJU01 sp902559885	76.4821	68	353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__CACEJU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902515155.1	s__SCGC-AAA076-P13 sp902515155	76.4231	56	353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 03:50:46,378] [INFO] GTDB search result was written to OceanDNA-b42016/result_gtdb.tsv
[2023-03-19 03:50:46,378] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:50:46,380] [INFO] DFAST_QC result json was written to OceanDNA-b42016/dqc_result.json
[2023-03-19 03:50:46,380] [INFO] DFAST_QC completed!
[2023-03-19 03:50:46,380] [INFO] Total running time: 0h0m39s