[2023-03-18 00:05:54,520] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:05:54,520] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:05:54,520] [INFO] DQC Reference Directory: /var/lib/cwl/stgd562a88a-726e-4b6b-b54f-08aa70487a7c/dqc_reference
[2023-03-18 00:05:55,631] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:05:55,631] [INFO] Task started: Prodigal
[2023-03-18 00:05:55,631] [INFO] Running command: cat /var/lib/cwl/stg94ab1b1f-689c-4e95-8d6b-e403d4ca38ff/OceanDNA-b16664.fa | prodigal -d OceanDNA-b16664/cds.fna -a OceanDNA-b16664/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:06:09,503] [INFO] Task succeeded: Prodigal
[2023-03-18 00:06:09,504] [INFO] Task started: HMMsearch
[2023-03-18 00:06:09,504] [INFO] Running command: hmmsearch --tblout OceanDNA-b16664/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd562a88a-726e-4b6b-b54f-08aa70487a7c/dqc_reference/reference_markers.hmm OceanDNA-b16664/protein.faa > /dev/null
[2023-03-18 00:06:09,650] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:06:09,650] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg94ab1b1f-689c-4e95-8d6b-e403d4ca38ff/OceanDNA-b16664.fa]
[2023-03-18 00:06:09,663] [INFO] Query marker FASTA was written to OceanDNA-b16664/markers.fasta
[2023-03-18 00:06:09,663] [INFO] Task started: Blastn
[2023-03-18 00:06:09,664] [INFO] Running command: blastn -query OceanDNA-b16664/markers.fasta -db /var/lib/cwl/stgd562a88a-726e-4b6b-b54f-08aa70487a7c/dqc_reference/reference_markers.fasta -out OceanDNA-b16664/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:06:10,167] [INFO] Task succeeded: Blastn
[2023-03-18 00:06:10,167] [INFO] Selected 19 target genomes.
[2023-03-18 00:06:10,168] [INFO] Target genome list was writen to OceanDNA-b16664/target_genomes.txt
[2023-03-18 00:06:10,178] [INFO] Task started: fastANI
[2023-03-18 00:06:10,178] [INFO] Running command: fastANI --query /var/lib/cwl/stg94ab1b1f-689c-4e95-8d6b-e403d4ca38ff/OceanDNA-b16664.fa --refList OceanDNA-b16664/target_genomes.txt --output OceanDNA-b16664/fastani_result.tsv --threads 1
[2023-03-18 00:06:19,921] [INFO] Task succeeded: fastANI
[2023-03-18 00:06:19,922] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd562a88a-726e-4b6b-b54f-08aa70487a7c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:06:19,922] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd562a88a-726e-4b6b-b54f-08aa70487a7c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:06:19,925] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:06:19,925] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:06:19,925] [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	79.6343	257	486	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:06:19,925] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16664/tc_result.tsv
[2023-03-18 00:06:19,926] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:06:19,926] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:06:19,926] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd562a88a-726e-4b6b-b54f-08aa70487a7c/dqc_reference/checkm_data
[2023-03-18 00:06:19,927] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:06:19,930] [INFO] Task started: CheckM
[2023-03-18 00:06:19,931] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16664/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16664/checkm_input OceanDNA-b16664/checkm_result
[2023-03-18 00:06:59,824] [INFO] Task succeeded: CheckM
[2023-03-18 00:06:59,824] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.89%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 00:06:59,865] [INFO] ===== Completeness check finished =====
[2023-03-18 00:06:59,865] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:06:59,865] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16664/markers.fasta)
[2023-03-18 00:06:59,866] [INFO] Task started: Blastn
[2023-03-18 00:06:59,866] [INFO] Running command: blastn -query OceanDNA-b16664/markers.fasta -db /var/lib/cwl/stgd562a88a-726e-4b6b-b54f-08aa70487a7c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16664/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:07:00,553] [INFO] Task succeeded: Blastn
[2023-03-18 00:07:00,561] [INFO] Selected 12 target genomes.
[2023-03-18 00:07:00,561] [INFO] Target genome list was writen to OceanDNA-b16664/target_genomes_gtdb.txt
[2023-03-18 00:07:00,575] [INFO] Task started: fastANI
[2023-03-18 00:07:00,575] [INFO] Running command: fastANI --query /var/lib/cwl/stg94ab1b1f-689c-4e95-8d6b-e403d4ca38ff/OceanDNA-b16664.fa --refList OceanDNA-b16664/target_genomes_gtdb.txt --output OceanDNA-b16664/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:07:05,163] [INFO] Task succeeded: fastANI
[2023-03-18 00:07:05,170] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:07:05,171] [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_002691345.1	s__Synechococcus_E sp002691345	98.8108	418	486	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	conclusive
GCF_014279895.1	s__Synechococcus_E sp002724845	80.4286	297	486	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	-
GCF_000161795.2	s__Synechococcus_E sp000161795	79.9863	275	486	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_013911515.1	s__Synechococcus_E sp013911515	79.9587	262	486	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_014279755.1	s__Synechococcus_E sp014279755	79.905	315	486	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_900474185.1	s__Synechococcus_E sp900474185	79.9027	300	486	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	95.68	95.24	0.90	0.90	3	-
GCF_000012625.1	s__Synechococcus_E sp000012625	79.708	313	486	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	79.6838	249	486	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_000737595.1	s__Synechococcus_E sp000737595	79.6799	318	486	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_014280195.1	s__Synechococcus_E sp014280195	79.2686	258	486	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	79.2607	271	486	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	-
GCA_002170825.1	s__Synechococcus_E sp002170825	78.8406	161	486	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	-
--------------------------------------------------------------------------------
[2023-03-18 00:07:05,175] [INFO] GTDB search result was written to OceanDNA-b16664/result_gtdb.tsv
[2023-03-18 00:07:05,189] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:07:05,192] [INFO] DFAST_QC result json was written to OceanDNA-b16664/dqc_result.json
[2023-03-18 00:07:05,192] [INFO] DFAST_QC completed!
[2023-03-18 00:07:05,192] [INFO] Total running time: 0h1m11s