[2023-03-16 21:45:13,531] [INFO] DFAST_QC pipeline started.
[2023-03-16 21:45:13,532] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 21:45:13,532] [INFO] DQC Reference Directory: /var/lib/cwl/stge4400de7-3a4d-4adb-9bb7-2bf81469e027/dqc_reference
[2023-03-16 21:45:15,326] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 21:45:15,327] [INFO] Task started: Prodigal
[2023-03-16 21:45:15,327] [INFO] Running command: cat /var/lib/cwl/stg12b318c0-6c66-4768-a01c-c0aff1a36191/OceanDNA-b16599.fa | prodigal -d OceanDNA-b16599/cds.fna -a OceanDNA-b16599/protein.faa -g 11 -q > /dev/null
[2023-03-16 21:45:25,064] [INFO] Task succeeded: Prodigal
[2023-03-16 21:45:25,064] [INFO] Task started: HMMsearch
[2023-03-16 21:45:25,064] [INFO] Running command: hmmsearch --tblout OceanDNA-b16599/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4400de7-3a4d-4adb-9bb7-2bf81469e027/dqc_reference/reference_markers.hmm OceanDNA-b16599/protein.faa > /dev/null
[2023-03-16 21:45:25,242] [INFO] Task succeeded: HMMsearch
[2023-03-16 21:45:25,243] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg12b318c0-6c66-4768-a01c-c0aff1a36191/OceanDNA-b16599.fa]
[2023-03-16 21:45:25,254] [INFO] Query marker FASTA was written to OceanDNA-b16599/markers.fasta
[2023-03-16 21:45:25,255] [INFO] Task started: Blastn
[2023-03-16 21:45:25,255] [INFO] Running command: blastn -query OceanDNA-b16599/markers.fasta -db /var/lib/cwl/stge4400de7-3a4d-4adb-9bb7-2bf81469e027/dqc_reference/reference_markers.fasta -out OceanDNA-b16599/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:45:25,794] [INFO] Task succeeded: Blastn
[2023-03-16 21:45:25,795] [INFO] Selected 25 target genomes.
[2023-03-16 21:45:25,796] [INFO] Target genome list was writen to OceanDNA-b16599/target_genomes.txt
[2023-03-16 21:45:25,810] [INFO] Task started: fastANI
[2023-03-16 21:45:25,810] [INFO] Running command: fastANI --query /var/lib/cwl/stg12b318c0-6c66-4768-a01c-c0aff1a36191/OceanDNA-b16599.fa --refList OceanDNA-b16599/target_genomes.txt --output OceanDNA-b16599/fastani_result.tsv --threads 1
[2023-03-16 21:45:43,827] [INFO] Task succeeded: fastANI
[2023-03-16 21:45:43,827] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4400de7-3a4d-4adb-9bb7-2bf81469e027/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 21:45:43,827] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4400de7-3a4d-4adb-9bb7-2bf81469e027/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 21:45:43,830] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 21:45:43,831] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 21:45:43,831] [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	98.252	245	248	95	conclusive
--------------------------------------------------------------------------------
[2023-03-16 21:45:43,831] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16599/tc_result.tsv
[2023-03-16 21:45:43,831] [INFO] ===== Taxonomy check completed =====
[2023-03-16 21:45:43,831] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 21:45:43,831] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4400de7-3a4d-4adb-9bb7-2bf81469e027/dqc_reference/checkm_data
[2023-03-16 21:45:43,832] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 21:45:43,835] [INFO] Task started: CheckM
[2023-03-16 21:45:43,835] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16599/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16599/checkm_input OceanDNA-b16599/checkm_result
[2023-03-16 21:46:13,988] [INFO] Task succeeded: CheckM
[2023-03-16 21:46:13,988] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 21:46:13,990] [INFO] ===== Completeness check finished =====
[2023-03-16 21:46:13,990] [INFO] ===== Start GTDB Search =====
[2023-03-16 21:46:13,990] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16599/markers.fasta)
[2023-03-16 21:46:13,990] [INFO] Task started: Blastn
[2023-03-16 21:46:13,990] [INFO] Running command: blastn -query OceanDNA-b16599/markers.fasta -db /var/lib/cwl/stge4400de7-3a4d-4adb-9bb7-2bf81469e027/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16599/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:46:14,783] [INFO] Task succeeded: Blastn
[2023-03-16 21:46:14,784] [INFO] Selected 11 target genomes.
[2023-03-16 21:46:14,784] [INFO] Target genome list was writen to OceanDNA-b16599/target_genomes_gtdb.txt
[2023-03-16 21:46:14,794] [INFO] Task started: fastANI
[2023-03-16 21:46:14,795] [INFO] Running command: fastANI --query /var/lib/cwl/stg12b318c0-6c66-4768-a01c-c0aff1a36191/OceanDNA-b16599.fa --refList OceanDNA-b16599/target_genomes_gtdb.txt --output OceanDNA-b16599/fastani_result_gtdb.tsv --threads 1
[2023-03-16 21:46:18,826] [INFO] Task succeeded: fastANI
[2023-03-16 21:46:18,833] [INFO] Found 11 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-16 21:46:18,833] [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
GCF_000195975.1	s__Synechococcus_E sp000195975	98.252	245	248	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	inconclusive
GCF_014280195.1	s__Synechococcus_E sp014280195	95.0255	246	248	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	inconclusive
GCF_014280175.1	s__Synechococcus_E sp004212765	87.3652	240	248	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_003211535.1	s__Synechococcus_E sp003211535	84.5546	182	248	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_000737575.1	s__Synechococcus_E sp000737575	80.9034	166	248	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	98.69	96.21	0.96	0.90	8	-
GCF_014279895.1	s__Synechococcus_E sp002724845	80.3172	162	248	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_002170825.1	s__Synechococcus_E sp002170825	80.2865	107	248	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_000161795.2	s__Synechococcus_E sp000161795	80.2069	154	248	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	79.9681	131	248	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_016779825.1	s__Synechococcus_E sp016779825	79.6453	133	248	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_002470305.1	s__RCC307 sp002470305	77.0277	66	248	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__RCC307	95.0	98.70	97.75	0.84	0.76	3	-
--------------------------------------------------------------------------------
[2023-03-16 21:46:18,833] [INFO] GTDB search result was written to OceanDNA-b16599/result_gtdb.tsv
[2023-03-16 21:46:18,833] [INFO] ===== GTDB Search completed =====
[2023-03-16 21:46:18,834] [INFO] DFAST_QC result json was written to OceanDNA-b16599/dqc_result.json
[2023-03-16 21:46:18,834] [INFO] DFAST_QC completed!
[2023-03-16 21:46:18,834] [INFO] Total running time: 0h1m5s