[2023-03-15 14:06:11,260] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:06:11,260] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:06:11,260] [INFO] DQC Reference Directory: /var/lib/cwl/stg46f1f2ab-1fff-4959-a35d-3fc47dcea3f3/dqc_reference
[2023-03-15 14:06:12,345] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:06:12,346] [INFO] Task started: Prodigal
[2023-03-15 14:06:12,346] [INFO] Running command: cat /var/lib/cwl/stge0e3bbc3-c989-4292-9a54-17d797e07e61/OceanDNA-b16525.fa | prodigal -d OceanDNA-b16525/cds.fna -a OceanDNA-b16525/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:06:22,361] [INFO] Task succeeded: Prodigal
[2023-03-15 14:06:22,362] [INFO] Task started: HMMsearch
[2023-03-15 14:06:22,362] [INFO] Running command: hmmsearch --tblout OceanDNA-b16525/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46f1f2ab-1fff-4959-a35d-3fc47dcea3f3/dqc_reference/reference_markers.hmm OceanDNA-b16525/protein.faa > /dev/null
[2023-03-15 14:06:22,500] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:06:22,501] [WARNING] Found 3/6 markers. [/var/lib/cwl/stge0e3bbc3-c989-4292-9a54-17d797e07e61/OceanDNA-b16525.fa]
[2023-03-15 14:06:22,513] [INFO] Query marker FASTA was written to OceanDNA-b16525/markers.fasta
[2023-03-15 14:06:22,514] [INFO] Task started: Blastn
[2023-03-15 14:06:22,514] [INFO] Running command: blastn -query OceanDNA-b16525/markers.fasta -db /var/lib/cwl/stg46f1f2ab-1fff-4959-a35d-3fc47dcea3f3/dqc_reference/reference_markers.fasta -out OceanDNA-b16525/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:06:23,012] [INFO] Task succeeded: Blastn
[2023-03-15 14:06:23,014] [INFO] Selected 20 target genomes.
[2023-03-15 14:06:23,014] [INFO] Target genome list was writen to OceanDNA-b16525/target_genomes.txt
[2023-03-15 14:06:23,027] [INFO] Task started: fastANI
[2023-03-15 14:06:23,027] [INFO] Running command: fastANI --query /var/lib/cwl/stge0e3bbc3-c989-4292-9a54-17d797e07e61/OceanDNA-b16525.fa --refList OceanDNA-b16525/target_genomes.txt --output OceanDNA-b16525/fastani_result.tsv --threads 1
[2023-03-15 14:06:36,412] [INFO] Task succeeded: fastANI
[2023-03-15 14:06:36,413] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46f1f2ab-1fff-4959-a35d-3fc47dcea3f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:06:36,413] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46f1f2ab-1fff-4959-a35d-3fc47dcea3f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:06:36,416] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 14:06:36,416] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 14:06:36,416] [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	77.9865	108	216	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 14:06:36,417] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16525/tc_result.tsv
[2023-03-15 14:06:36,418] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:06:36,419] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:06:36,419] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46f1f2ab-1fff-4959-a35d-3fc47dcea3f3/dqc_reference/checkm_data
[2023-03-15 14:06:36,419] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:06:36,565] [INFO] Task started: CheckM
[2023-03-15 14:06:36,565] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16525/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16525/checkm_input OceanDNA-b16525/checkm_result
[2023-03-15 14:07:08,608] [INFO] Task succeeded: CheckM
[2023-03-15 14:07:08,609] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.19%
Contamintation: 6.25%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 14:07:08,617] [INFO] ===== Completeness check finished =====
[2023-03-15 14:07:08,617] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:07:08,617] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16525/markers.fasta)
[2023-03-15 14:07:08,618] [INFO] Task started: Blastn
[2023-03-15 14:07:08,618] [INFO] Running command: blastn -query OceanDNA-b16525/markers.fasta -db /var/lib/cwl/stg46f1f2ab-1fff-4959-a35d-3fc47dcea3f3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16525/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:07:09,283] [INFO] Task succeeded: Blastn
[2023-03-15 14:07:09,285] [INFO] Selected 16 target genomes.
[2023-03-15 14:07:09,285] [INFO] Target genome list was writen to OceanDNA-b16525/target_genomes_gtdb.txt
[2023-03-15 14:07:09,300] [INFO] Task started: fastANI
[2023-03-15 14:07:09,301] [INFO] Running command: fastANI --query /var/lib/cwl/stge0e3bbc3-c989-4292-9a54-17d797e07e61/OceanDNA-b16525.fa --refList OceanDNA-b16525/target_genomes_gtdb.txt --output OceanDNA-b16525/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:07:15,268] [INFO] Task succeeded: fastANI
[2023-03-15 14:07:15,277] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 14:07:15,278] [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_003210735.1	s__Synechococcus_E sp003210735	83.7415	162	216	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	95.42	95.39	0.68	0.68	3	-
GCA_003210795.1	s__Synechococcus_E sp003210795	83.4685	159	216	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_003211235.1	s__Synechococcus_E sp003211235	83.2124	117	216	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	-
GCF_014279895.1	s__Synechococcus_E sp002724845	78.3392	104	216	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	96.37	95.03	0.93	0.89	13	-
GCA_016779825.1	s__Synechococcus_E sp016779825	78.2164	78	216	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	-
GCF_000012625.1	s__Synechococcus_E sp000012625	78.2054	94	216	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	95.15	95.15	0.92	0.92	2	-
GCF_000737595.1	s__Synechococcus_E sp000737595	78.0751	93	216	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_013911515.1	s__Synechococcus_E sp013911515	78.0237	82	216	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	-
GCF_014280195.1	s__Synechococcus_E sp014280195	78.002	107	216	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	-
GCF_000195975.1	s__Synechococcus_E sp000195975	77.9865	108	216	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	98.37	97.74	0.92	0.91	7	-
GCF_000737575.1	s__Synechococcus_E sp000737575	77.8062	109	216	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	98.69	96.21	0.96	0.90	8	-
GCF_014279755.1	s__Synechococcus_E sp014279755	77.6871	88	216	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	-
GCF_000515235.1	s__Synechococcus_E sp000515235	77.4618	64	216	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	97.70	97.70	0.82	0.82	2	-
GCA_002170825.1	s__Synechococcus_E sp002170825	77.4247	60	216	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	98.06	98.06	0.77	0.77	2	-
GCF_000737535.1	s__Synechococcus_E sp000737535	77.3673	77	216	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	-
GCF_000155635.1	s__NIES-981 sp000155635	76.6388	53	216	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	-
--------------------------------------------------------------------------------
[2023-03-15 14:07:15,279] [INFO] GTDB search result was written to OceanDNA-b16525/result_gtdb.tsv
[2023-03-15 14:07:15,279] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:07:15,281] [INFO] DFAST_QC result json was written to OceanDNA-b16525/dqc_result.json
[2023-03-15 14:07:15,281] [INFO] DFAST_QC completed!
[2023-03-15 14:07:15,281] [INFO] Total running time: 0h1m4s