[2023-06-30 07:19:44,197] [INFO] DFAST_QC pipeline started.
[2023-06-30 07:19:44,199] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 07:19:44,199] [INFO] DQC Reference Directory: /var/lib/cwl/stg49b3753a-2feb-4153-903d-5f2b4cc47337/dqc_reference
[2023-06-30 07:19:45,512] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 07:19:45,513] [INFO] Task started: Prodigal
[2023-06-30 07:19:45,513] [INFO] Running command: gunzip -c /var/lib/cwl/stg32d90983-cd79-4586-b861-e990d27a24cd/GCA_903908445.1_freshwater_MAG_---_Erken-D5_bin-0316_genomic.fna.gz | prodigal -d GCA_903908445.1_freshwater_MAG_---_Erken-D5_bin-0316_genomic.fna/cds.fna -a GCA_903908445.1_freshwater_MAG_---_Erken-D5_bin-0316_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 07:19:56,058] [INFO] Task succeeded: Prodigal
[2023-06-30 07:19:56,059] [INFO] Task started: HMMsearch
[2023-06-30 07:19:56,059] [INFO] Running command: hmmsearch --tblout GCA_903908445.1_freshwater_MAG_---_Erken-D5_bin-0316_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg49b3753a-2feb-4153-903d-5f2b4cc47337/dqc_reference/reference_markers.hmm GCA_903908445.1_freshwater_MAG_---_Erken-D5_bin-0316_genomic.fna/protein.faa > /dev/null
[2023-06-30 07:19:56,278] [INFO] Task succeeded: HMMsearch
[2023-06-30 07:19:56,280] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg32d90983-cd79-4586-b861-e990d27a24cd/GCA_903908445.1_freshwater_MAG_---_Erken-D5_bin-0316_genomic.fna.gz]
[2023-06-30 07:19:56,306] [INFO] Query marker FASTA was written to GCA_903908445.1_freshwater_MAG_---_Erken-D5_bin-0316_genomic.fna/markers.fasta
[2023-06-30 07:19:56,306] [INFO] Task started: Blastn
[2023-06-30 07:19:56,306] [INFO] Running command: blastn -query GCA_903908445.1_freshwater_MAG_---_Erken-D5_bin-0316_genomic.fna/markers.fasta -db /var/lib/cwl/stg49b3753a-2feb-4153-903d-5f2b4cc47337/dqc_reference/reference_markers.fasta -out GCA_903908445.1_freshwater_MAG_---_Erken-D5_bin-0316_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 07:19:56,906] [INFO] Task succeeded: Blastn
[2023-06-30 07:19:56,910] [INFO] Selected 23 target genomes.
[2023-06-30 07:19:56,910] [INFO] Target genome list was writen to GCA_903908445.1_freshwater_MAG_---_Erken-D5_bin-0316_genomic.fna/target_genomes.txt
[2023-06-30 07:19:56,912] [INFO] Task started: fastANI
[2023-06-30 07:19:56,912] [INFO] Running command: fastANI --query /var/lib/cwl/stg32d90983-cd79-4586-b861-e990d27a24cd/GCA_903908445.1_freshwater_MAG_---_Erken-D5_bin-0316_genomic.fna.gz --refList GCA_903908445.1_freshwater_MAG_---_Erken-D5_bin-0316_genomic.fna/target_genomes.txt --output GCA_903908445.1_freshwater_MAG_---_Erken-D5_bin-0316_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 07:20:10,201] [INFO] Task succeeded: fastANI
[2023-06-30 07:20:10,202] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg49b3753a-2feb-4153-903d-5f2b4cc47337/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 07:20:10,203] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg49b3753a-2feb-4153-903d-5f2b4cc47337/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 07:20:10,209] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 07:20:10,209] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 07:20:10,209] [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	77.4897	59	205	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 07:20:10,212] [INFO] DFAST Taxonomy check result was written to GCA_903908445.1_freshwater_MAG_---_Erken-D5_bin-0316_genomic.fna/tc_result.tsv
[2023-06-30 07:20:10,212] [INFO] ===== Taxonomy check completed =====
[2023-06-30 07:20:10,212] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 07:20:10,212] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg49b3753a-2feb-4153-903d-5f2b4cc47337/dqc_reference/checkm_data
[2023-06-30 07:20:10,214] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 07:20:10,241] [INFO] Task started: CheckM
[2023-06-30 07:20:10,241] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903908445.1_freshwater_MAG_---_Erken-D5_bin-0316_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903908445.1_freshwater_MAG_---_Erken-D5_bin-0316_genomic.fna/checkm_input GCA_903908445.1_freshwater_MAG_---_Erken-D5_bin-0316_genomic.fna/checkm_result
[2023-06-30 07:20:44,096] [INFO] Task succeeded: CheckM
[2023-06-30 07:20:44,098] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.69%
Contamintation: 2.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 07:20:44,120] [INFO] ===== Completeness check finished =====
[2023-06-30 07:20:44,121] [INFO] ===== Start GTDB Search =====
[2023-06-30 07:20:44,121] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903908445.1_freshwater_MAG_---_Erken-D5_bin-0316_genomic.fna/markers.fasta)
[2023-06-30 07:20:44,121] [INFO] Task started: Blastn
[2023-06-30 07:20:44,122] [INFO] Running command: blastn -query GCA_903908445.1_freshwater_MAG_---_Erken-D5_bin-0316_genomic.fna/markers.fasta -db /var/lib/cwl/stg49b3753a-2feb-4153-903d-5f2b4cc47337/dqc_reference/reference_markers_gtdb.fasta -out GCA_903908445.1_freshwater_MAG_---_Erken-D5_bin-0316_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 07:20:45,001] [INFO] Task succeeded: Blastn
[2023-06-30 07:20:45,010] [INFO] Selected 21 target genomes.
[2023-06-30 07:20:45,010] [INFO] Target genome list was writen to GCA_903908445.1_freshwater_MAG_---_Erken-D5_bin-0316_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 07:20:45,014] [INFO] Task started: fastANI
[2023-06-30 07:20:45,014] [INFO] Running command: fastANI --query /var/lib/cwl/stg32d90983-cd79-4586-b861-e990d27a24cd/GCA_903908445.1_freshwater_MAG_---_Erken-D5_bin-0316_genomic.fna.gz --refList GCA_903908445.1_freshwater_MAG_---_Erken-D5_bin-0316_genomic.fna/target_genomes_gtdb.txt --output GCA_903908445.1_freshwater_MAG_---_Erken-D5_bin-0316_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 07:20:53,790] [INFO] Task succeeded: fastANI
[2023-06-30 07:20:53,811] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 07:20:53,811] [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_002396505.1	s__UBA5018 sp002396505	94.8583	161	205	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__UBA5018	95.0	99.77	99.77	0.86	0.86	2	-
GCA_018399015.1	s__NIES-981 sp018399015	79.8847	122	205	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903862155.1	s__UBA5018 sp903862155	79.8607	105	205	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_001039265.1	s__NIES-981 sp001039265	79.8433	81	205	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014280235.1	s__NIES-981 sp014280235	79.7611	111	205	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981	95.0	97.33	97.33	0.87	0.87	2	-
GCA_010029175.1	s__Vulcanococcus sp010029175	79.5681	87	205	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002252675.1	s__Cyanobium sp002252675	79.4123	115	205	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	97.52	95.99	0.91	0.88	5	-
GCF_014698445.1	s__Cyanobium elabens	79.4058	119	205	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_016882525.1	s__NIES-981 sp016882525	79.3784	107	205	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900088535.1	s__NIES-981 sp900088535	79.2872	110	205	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009926195.1	s__Vulcanococcus sp009926195	79.2138	80	205	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016882385.1	s__Cyanobium_A sp016882385	79.2075	95	205	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_903823115.1	s__Cyanobium sp903823115	79.1099	103	205	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	99.94	99.88	0.97	0.96	6	-
GCF_019104765.1	s__Vulcanococcus sp019104765	79.0796	90	205	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010030955.1	s__Vulcanococcus sp010030955	78.9953	90	205	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_018400215.1	s__NIES-981 sp018400215	78.9879	76	205	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981	95.0	99.01	99.01	0.86	0.86	2	-
GCF_015840915.1	s__CBW1002 sp015840915	78.9602	110	205	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__CBW1002	95.0	98.61	98.61	0.83	0.83	2	-
GCF_015840715.1	s__Cyanobium sp015840715	78.7618	93	205	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_903882285.1	s__Cyanobium sp903882285	78.741	91	205	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	99.61	99.61	0.88	0.88	2	-
GCF_018502385.1	s__Vulcanococcus sp018502385	78.6584	81	205	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903917565.1	s__Cyanobium sp903917565	78.6054	108	205	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	100.00	99.99	0.99	0.98	6	-
--------------------------------------------------------------------------------
[2023-06-30 07:20:53,814] [INFO] GTDB search result was written to GCA_903908445.1_freshwater_MAG_---_Erken-D5_bin-0316_genomic.fna/result_gtdb.tsv
[2023-06-30 07:20:53,814] [INFO] ===== GTDB Search completed =====
[2023-06-30 07:20:53,818] [INFO] DFAST_QC result json was written to GCA_903908445.1_freshwater_MAG_---_Erken-D5_bin-0316_genomic.fna/dqc_result.json
[2023-06-30 07:20:53,818] [INFO] DFAST_QC completed!
[2023-06-30 07:20:53,818] [INFO] Total running time: 0h1m10s