[2023-06-28 16:34:31,205] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:34:31,207] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:34:31,207] [INFO] DQC Reference Directory: /var/lib/cwl/stgb805b656-ca99-4dbd-8a15-ac60d6ea0baf/dqc_reference
[2023-06-28 16:34:32,340] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:34:32,341] [INFO] Task started: Prodigal
[2023-06-28 16:34:32,341] [INFO] Running command: gunzip -c /var/lib/cwl/stga224155c-dd59-46ef-8c0e-23f8e83e5da2/GCA_913048995.1_ERR599100_bin.95_MetaBAT_v2.12.1_MAG_genomic.fna.gz | prodigal -d GCA_913048995.1_ERR599100_bin.95_MetaBAT_v2.12.1_MAG_genomic.fna/cds.fna -a GCA_913048995.1_ERR599100_bin.95_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:34:41,084] [INFO] Task succeeded: Prodigal
[2023-06-28 16:34:41,085] [INFO] Task started: HMMsearch
[2023-06-28 16:34:41,085] [INFO] Running command: hmmsearch --tblout GCA_913048995.1_ERR599100_bin.95_MetaBAT_v2.12.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb805b656-ca99-4dbd-8a15-ac60d6ea0baf/dqc_reference/reference_markers.hmm GCA_913048995.1_ERR599100_bin.95_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:34:41,271] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:34:41,272] [WARNING] Found 4/6 markers. [/var/lib/cwl/stga224155c-dd59-46ef-8c0e-23f8e83e5da2/GCA_913048995.1_ERR599100_bin.95_MetaBAT_v2.12.1_MAG_genomic.fna.gz]
[2023-06-28 16:34:41,290] [INFO] Query marker FASTA was written to GCA_913048995.1_ERR599100_bin.95_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta
[2023-06-28 16:34:41,290] [INFO] Task started: Blastn
[2023-06-28 16:34:41,290] [INFO] Running command: blastn -query GCA_913048995.1_ERR599100_bin.95_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb805b656-ca99-4dbd-8a15-ac60d6ea0baf/dqc_reference/reference_markers.fasta -out GCA_913048995.1_ERR599100_bin.95_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:34:41,814] [INFO] Task succeeded: Blastn
[2023-06-28 16:34:41,817] [INFO] Selected 21 target genomes.
[2023-06-28 16:34:41,817] [INFO] Target genome list was writen to GCA_913048995.1_ERR599100_bin.95_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt
[2023-06-28 16:34:41,818] [INFO] Task started: fastANI
[2023-06-28 16:34:41,818] [INFO] Running command: fastANI --query /var/lib/cwl/stga224155c-dd59-46ef-8c0e-23f8e83e5da2/GCA_913048995.1_ERR599100_bin.95_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913048995.1_ERR599100_bin.95_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt --output GCA_913048995.1_ERR599100_bin.95_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:34:54,249] [INFO] Task succeeded: fastANI
[2023-06-28 16:34:54,250] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb805b656-ca99-4dbd-8a15-ac60d6ea0baf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:34:54,250] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb805b656-ca99-4dbd-8a15-ac60d6ea0baf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:34:54,252] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:34:54,252] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 16:34:54,252] [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
--------------------------------------------------------------------------------
[2023-06-28 16:34:54,254] [INFO] DFAST Taxonomy check result was written to GCA_913048995.1_ERR599100_bin.95_MetaBAT_v2.12.1_MAG_genomic.fna/tc_result.tsv
[2023-06-28 16:34:54,255] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:34:54,255] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:34:54,255] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb805b656-ca99-4dbd-8a15-ac60d6ea0baf/dqc_reference/checkm_data
[2023-06-28 16:34:54,257] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:34:54,279] [INFO] Task started: CheckM
[2023-06-28 16:34:54,279] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913048995.1_ERR599100_bin.95_MetaBAT_v2.12.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913048995.1_ERR599100_bin.95_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_input GCA_913048995.1_ERR599100_bin.95_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_result
[2023-06-28 16:35:23,566] [INFO] Task succeeded: CheckM
[2023-06-28 16:35:23,567] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.62%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 16:35:23,588] [INFO] ===== Completeness check finished =====
[2023-06-28 16:35:23,588] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:35:23,589] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913048995.1_ERR599100_bin.95_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta)
[2023-06-28 16:35:23,589] [INFO] Task started: Blastn
[2023-06-28 16:35:23,589] [INFO] Running command: blastn -query GCA_913048995.1_ERR599100_bin.95_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb805b656-ca99-4dbd-8a15-ac60d6ea0baf/dqc_reference/reference_markers_gtdb.fasta -out GCA_913048995.1_ERR599100_bin.95_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:35:24,373] [INFO] Task succeeded: Blastn
[2023-06-28 16:35:24,376] [INFO] Selected 16 target genomes.
[2023-06-28 16:35:24,376] [INFO] Target genome list was writen to GCA_913048995.1_ERR599100_bin.95_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:35:24,379] [INFO] Task started: fastANI
[2023-06-28 16:35:24,379] [INFO] Running command: fastANI --query /var/lib/cwl/stga224155c-dd59-46ef-8c0e-23f8e83e5da2/GCA_913048995.1_ERR599100_bin.95_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913048995.1_ERR599100_bin.95_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_913048995.1_ERR599100_bin.95_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:35:31,185] [INFO] Task succeeded: fastANI
[2023-06-28 16:35:31,195] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 16:35:31,195] [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_002168155.1	s__RCC307 sp002168155	90.5254	481	537	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__RCC307	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002470305.1	s__RCC307 sp002470305	81.7374	355	537	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_000063525.1	s__RCC307 sp000063525	78.6516	260	537	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_012270465.1	s__RCC307 sp012270465	78.3519	194	537	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__RCC307	95.0	98.23	98.23	0.84	0.84	2	-
GCA_016882415.1	s__Vulcanococcus sp016882415	77.6805	97	537	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_014191535.1	s__Vulcanococcus sp014191535	77.5904	115	537	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_903862155.1	s__UBA5018 sp903862155	77.3727	107	537	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_000161795.2	s__Synechococcus_E sp000161795	77.3372	122	537	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_903871775.1	s__CAIQIA01 sp903871775	77.2654	160	537	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_903943975.1	s__Synechococcus_D lacustris_A	77.2372	166	537	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_003003925.1	s__Cyanobium minutissimum	76.9911	154	537	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_000316515.1	s__Cyanobium gracile	76.921	143	537	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_014698445.1	s__Cyanobium elabens	76.7287	141	537	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_004768415.1	s__Aphanocapsa_A feldmannii	76.2348	77	537	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Aphanocapsa_A	95.0	99.25	99.04	0.95	0.95	3	-
--------------------------------------------------------------------------------
[2023-06-28 16:35:31,197] [INFO] GTDB search result was written to GCA_913048995.1_ERR599100_bin.95_MetaBAT_v2.12.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 16:35:31,197] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:35:31,200] [INFO] DFAST_QC result json was written to GCA_913048995.1_ERR599100_bin.95_MetaBAT_v2.12.1_MAG_genomic.fna/dqc_result.json
[2023-06-28 16:35:31,200] [INFO] DFAST_QC completed!
[2023-06-28 16:35:31,200] [INFO] Total running time: 0h0m60s