[2023-06-05 10:22:52,089] [INFO] DFAST_QC pipeline started.
[2023-06-05 10:22:52,102] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 10:22:52,103] [INFO] DQC Reference Directory: /var/lib/cwl/stg34907258-4bc9-4188-8d33-96960a4dc0b5/dqc_reference
[2023-06-05 10:22:54,381] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 10:22:54,382] [INFO] Task started: Prodigal
[2023-06-05 10:22:54,382] [INFO] Running command: gunzip -c /var/lib/cwl/stgd9f9bfef-2ebe-4b44-9243-f38b3fc4462a/GCA_010026945.1_ASM1002694v1_genomic.fna.gz | prodigal -d GCA_010026945.1_ASM1002694v1_genomic.fna/cds.fna -a GCA_010026945.1_ASM1002694v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 10:23:04,267] [INFO] Task succeeded: Prodigal
[2023-06-05 10:23:04,267] [INFO] Task started: HMMsearch
[2023-06-05 10:23:04,268] [INFO] Running command: hmmsearch --tblout GCA_010026945.1_ASM1002694v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34907258-4bc9-4188-8d33-96960a4dc0b5/dqc_reference/reference_markers.hmm GCA_010026945.1_ASM1002694v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 10:23:04,498] [INFO] Task succeeded: HMMsearch
[2023-06-05 10:23:04,500] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd9f9bfef-2ebe-4b44-9243-f38b3fc4462a/GCA_010026945.1_ASM1002694v1_genomic.fna.gz]
[2023-06-05 10:23:04,527] [INFO] Query marker FASTA was written to GCA_010026945.1_ASM1002694v1_genomic.fna/markers.fasta
[2023-06-05 10:23:04,528] [INFO] Task started: Blastn
[2023-06-05 10:23:04,528] [INFO] Running command: blastn -query GCA_010026945.1_ASM1002694v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34907258-4bc9-4188-8d33-96960a4dc0b5/dqc_reference/reference_markers.fasta -out GCA_010026945.1_ASM1002694v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:23:05,066] [INFO] Task succeeded: Blastn
[2023-06-05 10:23:05,071] [INFO] Selected 16 target genomes.
[2023-06-05 10:23:05,071] [INFO] Target genome list was writen to GCA_010026945.1_ASM1002694v1_genomic.fna/target_genomes.txt
[2023-06-05 10:23:05,076] [INFO] Task started: fastANI
[2023-06-05 10:23:05,076] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9f9bfef-2ebe-4b44-9243-f38b3fc4462a/GCA_010026945.1_ASM1002694v1_genomic.fna.gz --refList GCA_010026945.1_ASM1002694v1_genomic.fna/target_genomes.txt --output GCA_010026945.1_ASM1002694v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 10:23:12,902] [INFO] Task succeeded: fastANI
[2023-06-05 10:23:12,902] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34907258-4bc9-4188-8d33-96960a4dc0b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 10:23:12,903] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34907258-4bc9-4188-8d33-96960a4dc0b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 10:23:12,908] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2023-06-05 10:23:12,909] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-05 10:23:12,909] [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	95.5303	436	484	95	conclusive
--------------------------------------------------------------------------------
[2023-06-05 10:23:12,911] [INFO] DFAST Taxonomy check result was written to GCA_010026945.1_ASM1002694v1_genomic.fna/tc_result.tsv
[2023-06-05 10:23:12,912] [INFO] ===== Taxonomy check completed =====
[2023-06-05 10:23:12,912] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 10:23:12,912] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34907258-4bc9-4188-8d33-96960a4dc0b5/dqc_reference/checkm_data
[2023-06-05 10:23:12,913] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 10:23:12,936] [INFO] Task started: CheckM
[2023-06-05 10:23:12,937] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_010026945.1_ASM1002694v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_010026945.1_ASM1002694v1_genomic.fna/checkm_input GCA_010026945.1_ASM1002694v1_genomic.fna/checkm_result
[2023-06-05 10:23:45,696] [INFO] Task succeeded: CheckM
[2023-06-05 10:23:45,697] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-05 10:23:45,737] [INFO] ===== Completeness check finished =====
[2023-06-05 10:23:45,738] [INFO] ===== Start GTDB Search =====
[2023-06-05 10:23:45,738] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_010026945.1_ASM1002694v1_genomic.fna/markers.fasta)
[2023-06-05 10:23:45,739] [INFO] Task started: Blastn
[2023-06-05 10:23:45,739] [INFO] Running command: blastn -query GCA_010026945.1_ASM1002694v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34907258-4bc9-4188-8d33-96960a4dc0b5/dqc_reference/reference_markers_gtdb.fasta -out GCA_010026945.1_ASM1002694v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:23:46,440] [INFO] Task succeeded: Blastn
[2023-06-05 10:23:46,448] [INFO] Selected 20 target genomes.
[2023-06-05 10:23:46,448] [INFO] Target genome list was writen to GCA_010026945.1_ASM1002694v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 10:23:46,462] [INFO] Task started: fastANI
[2023-06-05 10:23:46,463] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9f9bfef-2ebe-4b44-9243-f38b3fc4462a/GCA_010026945.1_ASM1002694v1_genomic.fna.gz --refList GCA_010026945.1_ASM1002694v1_genomic.fna/target_genomes_gtdb.txt --output GCA_010026945.1_ASM1002694v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 10:23:53,924] [INFO] Task succeeded: fastANI
[2023-06-05 10:23:53,943] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 10:23:53,944] [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	95.5456	435	484	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	79.8556	149	484	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	77.9228	181	484	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	-
GCF_002252625.1	s__WH-5701 sp002252625	77.0028	68	484	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__WH-5701	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010030955.1	s__Vulcanococcus sp010030955	76.8571	51	484	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_003249115.1	s__QBMD01 sp003249115	76.7972	57	484	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__QBMD01	95.0	98.24	98.24	0.84	0.84	2	-
GCA_903871775.1	s__CAIQIA01 sp903871775	76.759	76	484	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__CAIQIA01	95.0	99.96	99.90	0.96	0.88	7	-
GCA_903862155.1	s__UBA5018 sp903862155	76.7314	51	484	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__UBA5018	95.0	99.05	99.00	0.85	0.80	5	-
GCA_002737305.1	s__BAIKAL-G1 sp002737305	76.6976	59	484	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_016882525.1	s__NIES-981 sp016882525	76.6315	51	484	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_019038415.1	s__Cyanobium sp019038415	76.5756	58	484	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_903855705.1	s__BAIKAL-G1 sp903855705	76.5237	79	484	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_014191755.1	s__Cyanobium sp014191755	76.4269	73	484	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_000179235.2	s__Vulcanococcus sp000179235	76.35	83	484	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_002470305.1	s__RCC307 sp002470305	76.3321	77	484	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__RCC307	95.0	98.70	97.75	0.84	0.76	3	-
GCA_016882415.1	s__Vulcanococcus sp016882415	76.2715	50	484	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_002252635.1	s__MW101C3 sp002252635	76.2238	77	484	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__MW101C3	95.0	97.20	97.20	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-06-05 10:23:53,946] [INFO] GTDB search result was written to GCA_010026945.1_ASM1002694v1_genomic.fna/result_gtdb.tsv
[2023-06-05 10:23:53,946] [INFO] ===== GTDB Search completed =====
[2023-06-05 10:23:53,950] [INFO] DFAST_QC result json was written to GCA_010026945.1_ASM1002694v1_genomic.fna/dqc_result.json
[2023-06-05 10:23:53,950] [INFO] DFAST_QC completed!
[2023-06-05 10:23:53,951] [INFO] Total running time: 0h1m2s