[2023-03-19 02:40:15,890] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:40:15,891] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:40:15,891] [INFO] DQC Reference Directory: /var/lib/cwl/stgc55546c6-9e06-4fd7-a429-ad10280c18c4/dqc_reference
[2023-03-19 02:40:16,981] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:40:16,982] [INFO] Task started: Prodigal
[2023-03-19 02:40:16,982] [INFO] Running command: cat /var/lib/cwl/stgddec65d9-add1-4e15-8a8a-4d41853a3209/OceanDNA-b16540.fa | prodigal -d OceanDNA-b16540/cds.fna -a OceanDNA-b16540/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:40:25,345] [INFO] Task succeeded: Prodigal
[2023-03-19 02:40:25,345] [INFO] Task started: HMMsearch
[2023-03-19 02:40:25,345] [INFO] Running command: hmmsearch --tblout OceanDNA-b16540/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc55546c6-9e06-4fd7-a429-ad10280c18c4/dqc_reference/reference_markers.hmm OceanDNA-b16540/protein.faa > /dev/null
[2023-03-19 02:40:25,475] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:40:25,476] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgddec65d9-add1-4e15-8a8a-4d41853a3209/OceanDNA-b16540.fa]
[2023-03-19 02:40:25,491] [INFO] Query marker FASTA was written to OceanDNA-b16540/markers.fasta
[2023-03-19 02:40:25,492] [INFO] Task started: Blastn
[2023-03-19 02:40:25,492] [INFO] Running command: blastn -query OceanDNA-b16540/markers.fasta -db /var/lib/cwl/stgc55546c6-9e06-4fd7-a429-ad10280c18c4/dqc_reference/reference_markers.fasta -out OceanDNA-b16540/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:40:25,939] [INFO] Task succeeded: Blastn
[2023-03-19 02:40:25,942] [INFO] Selected 20 target genomes.
[2023-03-19 02:40:25,943] [INFO] Target genome list was writen to OceanDNA-b16540/target_genomes.txt
[2023-03-19 02:40:25,956] [INFO] Task started: fastANI
[2023-03-19 02:40:25,956] [INFO] Running command: fastANI --query /var/lib/cwl/stgddec65d9-add1-4e15-8a8a-4d41853a3209/OceanDNA-b16540.fa --refList OceanDNA-b16540/target_genomes.txt --output OceanDNA-b16540/fastani_result.tsv --threads 1
[2023-03-19 02:40:38,563] [INFO] Task succeeded: fastANI
[2023-03-19 02:40:38,563] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc55546c6-9e06-4fd7-a429-ad10280c18c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:40:38,564] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc55546c6-9e06-4fd7-a429-ad10280c18c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:40:38,566] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:40:38,567] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 02:40:38,567] [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
Parasynechococcus marenigrum	strain=WH 8102	GCA_000195975.1	2881428	2881428	type	True	85.2342	225	242	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 02:40:38,568] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16540/tc_result.tsv
[2023-03-19 02:40:38,570] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:40:38,570] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:40:38,570] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc55546c6-9e06-4fd7-a429-ad10280c18c4/dqc_reference/checkm_data
[2023-03-19 02:40:38,571] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:40:38,576] [INFO] Task started: CheckM
[2023-03-19 02:40:38,576] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16540/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16540/checkm_input OceanDNA-b16540/checkm_result
[2023-03-19 02:41:05,621] [INFO] Task succeeded: CheckM
[2023-03-19 02:41:05,622] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.38%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:41:05,638] [INFO] ===== Completeness check finished =====
[2023-03-19 02:41:05,638] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:41:05,638] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16540/markers.fasta)
[2023-03-19 02:41:05,639] [INFO] Task started: Blastn
[2023-03-19 02:41:05,639] [INFO] Running command: blastn -query OceanDNA-b16540/markers.fasta -db /var/lib/cwl/stgc55546c6-9e06-4fd7-a429-ad10280c18c4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16540/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:41:06,137] [INFO] Task succeeded: Blastn
[2023-03-19 02:41:06,141] [INFO] Selected 11 target genomes.
[2023-03-19 02:41:06,141] [INFO] Target genome list was writen to OceanDNA-b16540/target_genomes_gtdb.txt
[2023-03-19 02:41:06,152] [INFO] Task started: fastANI
[2023-03-19 02:41:06,152] [INFO] Running command: fastANI --query /var/lib/cwl/stgddec65d9-add1-4e15-8a8a-4d41853a3209/OceanDNA-b16540.fa --refList OceanDNA-b16540/target_genomes_gtdb.txt --output OceanDNA-b16540/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:41:09,856] [INFO] Task succeeded: fastANI
[2023-03-19 02:41:09,862] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:41:09,863] [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_003211535.1	s__Synechococcus_E sp003211535	88.2962	188	242	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014280175.1	s__Synechococcus_E sp004212765	87.2449	231	242	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	98.21	96.96	0.98	0.97	4	-
GCF_000195975.1	s__Synechococcus_E sp000195975	85.2342	225	242	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	98.37	97.74	0.92	0.91	7	-
GCF_014280195.1	s__Synechococcus_E sp014280195	85.0736	230	242	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002170825.1	s__Synechococcus_E sp002170825	79.5745	100	242	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	98.06	98.06	0.77	0.77	2	-
GCF_014279895.1	s__Synechococcus_E sp002724845	79.0292	125	242	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	96.37	95.03	0.93	0.89	13	-
GCA_013911515.1	s__Synechococcus_E sp013911515	78.8843	112	242	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012625.1	s__Synechococcus_E sp000012625	78.7399	126	242	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	95.15	95.15	0.92	0.92	2	-
GCA_016779825.1	s__Synechococcus_E sp016779825	78.721	106	242	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000161795.2	s__Synechococcus_E sp000161795	78.6022	115	242	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002691345.1	s__Synechococcus_E sp002691345	78.0874	100	242	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	100.00	100.00	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-19 02:41:09,864] [INFO] GTDB search result was written to OceanDNA-b16540/result_gtdb.tsv
[2023-03-19 02:41:09,865] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:41:09,867] [INFO] DFAST_QC result json was written to OceanDNA-b16540/dqc_result.json
[2023-03-19 02:41:09,868] [INFO] DFAST_QC completed!
[2023-03-19 02:41:09,868] [INFO] Total running time: 0h0m54s