[2023-03-16 08:10:35,102] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:10:35,107] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:10:35,107] [INFO] DQC Reference Directory: /var/lib/cwl/stg75175388-b61e-41a3-84de-77fec7840d3f/dqc_reference
[2023-03-16 08:10:36,244] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:10:36,244] [INFO] Task started: Prodigal
[2023-03-16 08:10:36,245] [INFO] Running command: cat /var/lib/cwl/stg2fb3fc5a-102d-499d-82af-36d0313379bb/OceanDNA-b16709.fa | prodigal -d OceanDNA-b16709/cds.fna -a OceanDNA-b16709/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:10:50,855] [INFO] Task succeeded: Prodigal
[2023-03-16 08:10:50,856] [INFO] Task started: HMMsearch
[2023-03-16 08:10:50,856] [INFO] Running command: hmmsearch --tblout OceanDNA-b16709/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg75175388-b61e-41a3-84de-77fec7840d3f/dqc_reference/reference_markers.hmm OceanDNA-b16709/protein.faa > /dev/null
[2023-03-16 08:10:51,024] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:10:51,025] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2fb3fc5a-102d-499d-82af-36d0313379bb/OceanDNA-b16709.fa]
[2023-03-16 08:10:51,091] [INFO] Query marker FASTA was written to OceanDNA-b16709/markers.fasta
[2023-03-16 08:10:51,091] [INFO] Task started: Blastn
[2023-03-16 08:10:51,091] [INFO] Running command: blastn -query OceanDNA-b16709/markers.fasta -db /var/lib/cwl/stg75175388-b61e-41a3-84de-77fec7840d3f/dqc_reference/reference_markers.fasta -out OceanDNA-b16709/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:10:51,607] [INFO] Task succeeded: Blastn
[2023-03-16 08:10:51,617] [INFO] Selected 16 target genomes.
[2023-03-16 08:10:51,618] [INFO] Target genome list was writen to OceanDNA-b16709/target_genomes.txt
[2023-03-16 08:10:51,628] [INFO] Task started: fastANI
[2023-03-16 08:10:51,628] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fb3fc5a-102d-499d-82af-36d0313379bb/OceanDNA-b16709.fa --refList OceanDNA-b16709/target_genomes.txt --output OceanDNA-b16709/fastani_result.tsv --threads 1
[2023-03-16 08:10:59,424] [INFO] Task succeeded: fastANI
[2023-03-16 08:10:59,425] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg75175388-b61e-41a3-84de-77fec7840d3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:10:59,425] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg75175388-b61e-41a3-84de-77fec7840d3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:10:59,429] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 08:10:59,429] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 08:10:59,429] [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
Synechococcus lacustris	strain=Tous	GCA_003011125.1	2116544	2116544	suspected-type	True	97.8915	496	550	95	conclusive
Parasynechococcus marenigrum	strain=WH 8102	GCA_000195975.1	2881428	2881428	type	True	75.9787	66	550	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 08:10:59,434] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16709/tc_result.tsv
[2023-03-16 08:10:59,439] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:10:59,439] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:10:59,439] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg75175388-b61e-41a3-84de-77fec7840d3f/dqc_reference/checkm_data
[2023-03-16 08:10:59,440] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:10:59,448] [INFO] Task started: CheckM
[2023-03-16 08:10:59,448] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16709/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16709/checkm_input OceanDNA-b16709/checkm_result
[2023-03-16 08:11:39,504] [INFO] Task succeeded: CheckM
[2023-03-16 08:11:39,504] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 08:11:39,726] [INFO] ===== Completeness check finished =====
[2023-03-16 08:11:39,727] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:11:39,727] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16709/markers.fasta)
[2023-03-16 08:11:39,727] [INFO] Task started: Blastn
[2023-03-16 08:11:39,727] [INFO] Running command: blastn -query OceanDNA-b16709/markers.fasta -db /var/lib/cwl/stg75175388-b61e-41a3-84de-77fec7840d3f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16709/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:11:40,500] [INFO] Task succeeded: Blastn
[2023-03-16 08:11:40,520] [INFO] Selected 15 target genomes.
[2023-03-16 08:11:40,520] [INFO] Target genome list was writen to OceanDNA-b16709/target_genomes_gtdb.txt
[2023-03-16 08:11:40,564] [INFO] Task started: fastANI
[2023-03-16 08:11:40,564] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fb3fc5a-102d-499d-82af-36d0313379bb/OceanDNA-b16709.fa --refList OceanDNA-b16709/target_genomes_gtdb.txt --output OceanDNA-b16709/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:11:46,704] [INFO] Task succeeded: fastANI
[2023-03-16 08:11:46,713] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 08:11:46,713] [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_003011125.1	s__Synechococcus_D lacustris	97.8915	496	550	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_D	95.0	95.83	95.10	0.90	0.78	20	conclusive
GCA_009914645.1	s__Synechococcus_D sp009914645	79.6719	183	550	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_D	95.0	98.11	98.11	0.86	0.86	2	-
GCA_903943975.1	s__Synechococcus_D lacustris_A	78.0552	197	550	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_D	95.0	99.87	99.37	0.98	0.92	31	-
GCA_903855705.1	s__BAIKAL-G1 sp903855705	76.7906	86	550	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__BAIKAL-G1	95.0	98.86	98.32	0.88	0.87	5	-
GCA_002737305.1	s__BAIKAL-G1 sp002737305	76.681	74	550	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__BAIKAL-G1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014279595.1	s__Synechococcus_C sp000153065	76.6349	65	550	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	99.83	99.83	0.99	0.99	2	-
GCF_002252665.1	s__Cyanobium_A sp002252665	76.5486	90	550	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903862155.1	s__UBA5018 sp903862155	76.5326	60	550	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__UBA5018	95.0	99.05	99.00	0.85	0.80	5	-
GCF_002252635.1	s__MW101C3 sp002252635	76.467	85	550	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__MW101C3	95.0	97.20	97.20	0.89	0.89	2	-
GCA_016463595.1	s__BAIKAL-G1 sp016463595	76.341	93	550	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__BAIKAL-G1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010030955.1	s__Vulcanococcus sp010030955	76.3393	67	550	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	98.81	98.81	0.81	0.81	2	-
GCA_016882385.1	s__Cyanobium_A sp016882385	76.2811	70	550	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014191755.1	s__Cyanobium sp014191755	76.279	69	550	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000316515.1	s__Cyanobium gracile	76.2416	70	550	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002470305.1	s__RCC307 sp002470305	76.2371	90	550	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 08:11:46,717] [INFO] GTDB search result was written to OceanDNA-b16709/result_gtdb.tsv
[2023-03-16 08:11:46,720] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:11:46,724] [INFO] DFAST_QC result json was written to OceanDNA-b16709/dqc_result.json
[2023-03-16 08:11:46,724] [INFO] DFAST_QC completed!
[2023-03-16 08:11:46,724] [INFO] Total running time: 0h1m12s