[2023-03-19 04:52:18,304] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:52:18,305] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:52:18,305] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c67c68d-8bf4-4002-a770-d48361587ab6/dqc_reference
[2023-03-19 04:52:19,374] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:52:19,374] [INFO] Task started: Prodigal
[2023-03-19 04:52:19,374] [INFO] Running command: cat /var/lib/cwl/stg16ceeaf6-e5fc-4751-a341-a8b9fc1d031c/OceanDNA-b16118.fa | prodigal -d OceanDNA-b16118/cds.fna -a OceanDNA-b16118/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:52:45,027] [INFO] Task succeeded: Prodigal
[2023-03-19 04:52:45,027] [INFO] Task started: HMMsearch
[2023-03-19 04:52:45,027] [INFO] Running command: hmmsearch --tblout OceanDNA-b16118/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c67c68d-8bf4-4002-a770-d48361587ab6/dqc_reference/reference_markers.hmm OceanDNA-b16118/protein.faa > /dev/null
[2023-03-19 04:52:45,281] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:52:45,282] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg16ceeaf6-e5fc-4751-a341-a8b9fc1d031c/OceanDNA-b16118.fa]
[2023-03-19 04:52:45,311] [INFO] Query marker FASTA was written to OceanDNA-b16118/markers.fasta
[2023-03-19 04:52:45,312] [INFO] Task started: Blastn
[2023-03-19 04:52:45,313] [INFO] Running command: blastn -query OceanDNA-b16118/markers.fasta -db /var/lib/cwl/stg8c67c68d-8bf4-4002-a770-d48361587ab6/dqc_reference/reference_markers.fasta -out OceanDNA-b16118/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:52:45,821] [INFO] Task succeeded: Blastn
[2023-03-19 04:52:45,824] [INFO] Selected 17 target genomes.
[2023-03-19 04:52:45,824] [INFO] Target genome list was writen to OceanDNA-b16118/target_genomes.txt
[2023-03-19 04:52:45,859] [INFO] Task started: fastANI
[2023-03-19 04:52:45,859] [INFO] Running command: fastANI --query /var/lib/cwl/stg16ceeaf6-e5fc-4751-a341-a8b9fc1d031c/OceanDNA-b16118.fa --refList OceanDNA-b16118/target_genomes.txt --output OceanDNA-b16118/fastani_result.tsv --threads 1
[2023-03-19 04:53:00,526] [INFO] Task succeeded: fastANI
[2023-03-19 04:53:00,526] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c67c68d-8bf4-4002-a770-d48361587ab6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:53:00,527] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c67c68d-8bf4-4002-a770-d48361587ab6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:53:00,533] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:53:00,533] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:53:00,533] [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
Stanieria cyanosphaera	strain=PCC 7437	GCA_000317575.1	102116	102116	type	True	76.1048	99	1623	95	below_threshold
Allocoleopsis franciscana	strain=PCC 7113	GCA_000317515.1	2886352	2886352	type	True	75.7341	69	1623	95	below_threshold
Crocosphaera subtropica	strain=ATCC 51142	GCA_000017845.1	2546360	2546360	type	True	75.6761	58	1623	95	below_threshold
Crocosphaera chwakensis	strain=CCY0110	GCA_000169335.1	2546361	2546361	type	True	75.4236	66	1623	95	below_threshold
Scytonema hofmannii	strain=PCC 7110	GCA_000346485.2	34078	34078	type	True	75.1388	60	1623	95	below_threshold
Nostoc punctiforme	strain=ATCC 29133; PCC 73102	GCA_000020025.1	272131	272131	type	True	75.1107	67	1623	95	below_threshold
Nostoc favosum	strain=CHAB 5714	GCA_020829495.1	2907819	2907819	type	True	75.0963	57	1623	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:53:00,535] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16118/tc_result.tsv
[2023-03-19 04:53:00,535] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:53:00,535] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:53:00,535] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c67c68d-8bf4-4002-a770-d48361587ab6/dqc_reference/checkm_data
[2023-03-19 04:53:00,536] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:53:00,543] [INFO] Task started: CheckM
[2023-03-19 04:53:00,543] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16118/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16118/checkm_input OceanDNA-b16118/checkm_result
[2023-03-19 04:54:03,654] [INFO] Task succeeded: CheckM
[2023-03-19 04:54:03,654] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:54:03,755] [INFO] ===== Completeness check finished =====
[2023-03-19 04:54:03,755] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:54:03,755] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16118/markers.fasta)
[2023-03-19 04:54:03,756] [INFO] Task started: Blastn
[2023-03-19 04:54:03,756] [INFO] Running command: blastn -query OceanDNA-b16118/markers.fasta -db /var/lib/cwl/stg8c67c68d-8bf4-4002-a770-d48361587ab6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16118/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:54:04,442] [INFO] Task succeeded: Blastn
[2023-03-19 04:54:04,445] [INFO] Selected 30 target genomes.
[2023-03-19 04:54:04,445] [INFO] Target genome list was writen to OceanDNA-b16118/target_genomes_gtdb.txt
[2023-03-19 04:54:04,535] [INFO] Task started: fastANI
[2023-03-19 04:54:04,535] [INFO] Running command: fastANI --query /var/lib/cwl/stg16ceeaf6-e5fc-4751-a341-a8b9fc1d031c/OceanDNA-b16118.fa --refList OceanDNA-b16118/target_genomes_gtdb.txt --output OceanDNA-b16118/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:54:33,600] [INFO] Task succeeded: fastANI
[2023-03-19 04:54:33,613] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:54:33,613] [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_001767235.1	s__Moorea producens_A	76.4475	108	1623	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Coleofasciculaceae;g__Moorea	95.0	96.04	96.04	0.84	0.84	2	-
GCA_010692325.1	s__Moorea sp010692325	76.066	84	1623	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Coleofasciculaceae;g__Moorea	95.0	97.88	97.68	0.88	0.86	3	-
GCA_002110465.1	s__Rippkaea sp002110465	75.9515	57	1623	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Rippkaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003448685.1	s__Rippkaea sp003448685	75.9347	58	1623	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Rippkaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355455.1	s__Stanieria sp002355455	75.9061	89	1623	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Stanieria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317515.1	s__PCC7113 sp000317515	75.7341	69	1623	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Coleofasciculaceae;g__PCC7113	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015207375.1	s__LEGE-07092 sp015207375	75.7215	56	1623	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Coleofasciculaceae;g__LEGE-07092	95.0	99.97	99.97	0.97	0.97	2	-
GCA_002172675.1	s__Crocosphaera sp002172675	75.6856	55	1623	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Crocosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017845.1	s__Crocosphaera subtropica	75.6761	58	1623	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Crocosphaera	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000317495.1	s__Crinalium epipsammum	75.5667	67	1623	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Chamaesiphonaceae;g__Crinalium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015207425.1	s__Lusitaniella coriacea	75.53	60	1623	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Spirulinaceae;g__Lusitaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015207735.1	s__Phormidium_B sp015207735	75.5293	55	1623	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Phormidiaceae_A;g__Phormidium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390955.1	s__Planktothricoides sp011390955	75.4536	63	1623	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Oscillatoriaceae;g__Planktothricoides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002949735.1	s__Nostoc sp002949735	75.4362	53	1623	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	96.73	95.05	0.82	0.76	3	-
GCF_000169335.1	s__Crocosphaera chwakensis	75.4236	66	1623	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Crocosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014696825.1	s__RDYJ01 sp014696825	75.4059	61	1623	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__RDYJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015207705.1	s__Anabaenopsis sp015207705	75.404	50	1623	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Anabaenopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003013815.1	s__Crocosphaera sp003013815	75.3567	56	1623	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Crocosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016056275.1	s__Dendronalium phyllosphericum	75.334	61	1623	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dendronalium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903848645.1	s__Dolichospermum sp903848645	75.3191	56	1623	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dolichospermum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012031965.1	s__Brasilonema sp012031965	75.3115	60	1623	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Brasilonema	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017114945.1	s__Nostoc sp017114945	75.2037	51	1623	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017114995.1	s__Nostoc sp017114995	75.1989	57	1623	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003326195.1	s__Nostoc punctiforme_A	75.0847	62	1623	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	97.25	97.17	0.91	0.90	3	-
--------------------------------------------------------------------------------
[2023-03-19 04:54:33,613] [INFO] GTDB search result was written to OceanDNA-b16118/result_gtdb.tsv
[2023-03-19 04:54:33,614] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:54:33,615] [INFO] DFAST_QC result json was written to OceanDNA-b16118/dqc_result.json
[2023-03-19 04:54:33,615] [INFO] DFAST_QC completed!
[2023-03-19 04:54:33,615] [INFO] Total running time: 0h2m15s