[2023-06-30 16:54:38,624] [INFO] DFAST_QC pipeline started.
[2023-06-30 16:54:38,635] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 16:54:38,635] [INFO] DQC Reference Directory: /var/lib/cwl/stgb8aeaca2-bef0-49cd-996d-95ccaabc05dd/dqc_reference
[2023-06-30 16:54:40,963] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 16:54:40,964] [INFO] Task started: Prodigal
[2023-06-30 16:54:40,965] [INFO] Running command: gunzip -c /var/lib/cwl/stg48ddbe66-eeca-444d-ad49-0f609ee59c70/GCA_903949385.1_freshwater_MAG_---_Loc090519-4m_bin-515_genomic.fna.gz | prodigal -d GCA_903949385.1_freshwater_MAG_---_Loc090519-4m_bin-515_genomic.fna/cds.fna -a GCA_903949385.1_freshwater_MAG_---_Loc090519-4m_bin-515_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 16:54:56,475] [INFO] Task succeeded: Prodigal
[2023-06-30 16:54:56,475] [INFO] Task started: HMMsearch
[2023-06-30 16:54:56,476] [INFO] Running command: hmmsearch --tblout GCA_903949385.1_freshwater_MAG_---_Loc090519-4m_bin-515_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb8aeaca2-bef0-49cd-996d-95ccaabc05dd/dqc_reference/reference_markers.hmm GCA_903949385.1_freshwater_MAG_---_Loc090519-4m_bin-515_genomic.fna/protein.faa > /dev/null
[2023-06-30 16:54:56,730] [INFO] Task succeeded: HMMsearch
[2023-06-30 16:54:56,731] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg48ddbe66-eeca-444d-ad49-0f609ee59c70/GCA_903949385.1_freshwater_MAG_---_Loc090519-4m_bin-515_genomic.fna.gz]
[2023-06-30 16:54:56,762] [INFO] Query marker FASTA was written to GCA_903949385.1_freshwater_MAG_---_Loc090519-4m_bin-515_genomic.fna/markers.fasta
[2023-06-30 16:54:56,762] [INFO] Task started: Blastn
[2023-06-30 16:54:56,762] [INFO] Running command: blastn -query GCA_903949385.1_freshwater_MAG_---_Loc090519-4m_bin-515_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8aeaca2-bef0-49cd-996d-95ccaabc05dd/dqc_reference/reference_markers.fasta -out GCA_903949385.1_freshwater_MAG_---_Loc090519-4m_bin-515_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 16:54:57,416] [INFO] Task succeeded: Blastn
[2023-06-30 16:54:57,421] [INFO] Selected 22 target genomes.
[2023-06-30 16:54:57,421] [INFO] Target genome list was writen to GCA_903949385.1_freshwater_MAG_---_Loc090519-4m_bin-515_genomic.fna/target_genomes.txt
[2023-06-30 16:54:57,422] [INFO] Task started: fastANI
[2023-06-30 16:54:57,423] [INFO] Running command: fastANI --query /var/lib/cwl/stg48ddbe66-eeca-444d-ad49-0f609ee59c70/GCA_903949385.1_freshwater_MAG_---_Loc090519-4m_bin-515_genomic.fna.gz --refList GCA_903949385.1_freshwater_MAG_---_Loc090519-4m_bin-515_genomic.fna/target_genomes.txt --output GCA_903949385.1_freshwater_MAG_---_Loc090519-4m_bin-515_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 16:55:10,057] [INFO] Task succeeded: fastANI
[2023-06-30 16:55:10,058] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb8aeaca2-bef0-49cd-996d-95ccaabc05dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 16:55:10,059] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb8aeaca2-bef0-49cd-996d-95ccaabc05dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 16:55:10,065] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 16:55:10,065] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 16:55:10,066] [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	78.3472	210	818	95	below_threshold
Parasynechococcus marenigrum	strain=WH 8102	GCA_000195975.1	2881428	2881428	type	True	77.6065	186	818	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 16:55:10,069] [INFO] DFAST Taxonomy check result was written to GCA_903949385.1_freshwater_MAG_---_Loc090519-4m_bin-515_genomic.fna/tc_result.tsv
[2023-06-30 16:55:10,069] [INFO] ===== Taxonomy check completed =====
[2023-06-30 16:55:10,069] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 16:55:10,070] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb8aeaca2-bef0-49cd-996d-95ccaabc05dd/dqc_reference/checkm_data
[2023-06-30 16:55:10,070] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 16:55:10,108] [INFO] Task started: CheckM
[2023-06-30 16:55:10,109] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903949385.1_freshwater_MAG_---_Loc090519-4m_bin-515_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903949385.1_freshwater_MAG_---_Loc090519-4m_bin-515_genomic.fna/checkm_input GCA_903949385.1_freshwater_MAG_---_Loc090519-4m_bin-515_genomic.fna/checkm_result
[2023-06-30 16:55:54,531] [INFO] Task succeeded: CheckM
[2023-06-30 16:55:54,532] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 16:55:54,560] [INFO] ===== Completeness check finished =====
[2023-06-30 16:55:54,561] [INFO] ===== Start GTDB Search =====
[2023-06-30 16:55:54,561] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903949385.1_freshwater_MAG_---_Loc090519-4m_bin-515_genomic.fna/markers.fasta)
[2023-06-30 16:55:54,562] [INFO] Task started: Blastn
[2023-06-30 16:55:54,562] [INFO] Running command: blastn -query GCA_903949385.1_freshwater_MAG_---_Loc090519-4m_bin-515_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8aeaca2-bef0-49cd-996d-95ccaabc05dd/dqc_reference/reference_markers_gtdb.fasta -out GCA_903949385.1_freshwater_MAG_---_Loc090519-4m_bin-515_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 16:55:55,643] [INFO] Task succeeded: Blastn
[2023-06-30 16:55:55,660] [INFO] Selected 22 target genomes.
[2023-06-30 16:55:55,661] [INFO] Target genome list was writen to GCA_903949385.1_freshwater_MAG_---_Loc090519-4m_bin-515_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 16:55:55,663] [INFO] Task started: fastANI
[2023-06-30 16:55:55,663] [INFO] Running command: fastANI --query /var/lib/cwl/stg48ddbe66-eeca-444d-ad49-0f609ee59c70/GCA_903949385.1_freshwater_MAG_---_Loc090519-4m_bin-515_genomic.fna.gz --refList GCA_903949385.1_freshwater_MAG_---_Loc090519-4m_bin-515_genomic.fna/target_genomes_gtdb.txt --output GCA_903949385.1_freshwater_MAG_---_Loc090519-4m_bin-515_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 16:56:06,302] [INFO] Task succeeded: fastANI
[2023-06-30 16:56:06,325] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 16:56:06,325] [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_903943975.1	s__Synechococcus_D lacustris_A	99.9992	808	818	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	conclusive
GCF_003003925.1	s__Cyanobium minutissimum	78.9299	332	818	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	95.57	95.57	0.88	0.88	2	-
GCF_014697415.1	s__Cyanobium_A sp014697415	78.9274	333	818	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_016463595.1	s__BAIKAL-G1 sp016463595	78.7806	279	818	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_903871775.1	s__CAIQIA01 sp903871775	78.7543	369	818	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__CAIQIA01	95.0	99.96	99.90	0.96	0.88	7	-
GCF_000316515.1	s__Cyanobium gracile	78.6809	325	818	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_014280235.1	s__NIES-981 sp014280235	78.6722	329	818	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	-
GCF_019104765.1	s__Vulcanococcus sp019104765	78.6572	308	818	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_019038415.1	s__Cyanobium sp019038415	78.6423	323	818	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_002252675.1	s__Cyanobium sp002252675	78.6158	343	818	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_900088535.1	s__NIES-981 sp900088535	78.6026	334	818	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_016882315.1	s__Cyanobium sp016882315	78.5784	342	818	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	78.5261	305	818	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	-
GCF_015841355.1	s__WH-5701 sp015841355	78.4592	309	818	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_000063525.1	s__RCC307 sp000063525	78.3486	301	818	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__RCC307	95.0	98.48	97.86	0.96	0.93	5	-
GCA_000708525.1	s__Cyanobium sp000708525	78.3023	292	818	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_014191755.1	s__Cyanobium sp014191755	78.1738	316	818	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	78.1109	226	818	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_903934375.1	s__Vulcanococcus sp903934375	78.088	273	818	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	98.96	98.94	0.87	0.87	3	-
GCA_018623875.1	s__Vulcanococcus sp018623875	77.8727	157	818	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_014217875.1	s__Vulcanococcus sp014217875	77.8093	212	818	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_014217855.1	s__Synechococcus_C sp004332415	77.6526	172	818	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	97.38	96.99	0.88	0.86	3	-
--------------------------------------------------------------------------------
[2023-06-30 16:56:06,333] [INFO] GTDB search result was written to GCA_903949385.1_freshwater_MAG_---_Loc090519-4m_bin-515_genomic.fna/result_gtdb.tsv
[2023-06-30 16:56:06,334] [INFO] ===== GTDB Search completed =====
[2023-06-30 16:56:06,338] [INFO] DFAST_QC result json was written to GCA_903949385.1_freshwater_MAG_---_Loc090519-4m_bin-515_genomic.fna/dqc_result.json
[2023-06-30 16:56:06,338] [INFO] DFAST_QC completed!
[2023-06-30 16:56:06,338] [INFO] Total running time: 0h1m28s