[2023-03-19 00:04:59,421] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:04:59,421] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:04:59,421] [INFO] DQC Reference Directory: /var/lib/cwl/stg857537d1-1998-4a39-adea-3d8cbbd5f6e9/dqc_reference
[2023-03-19 00:05:00,572] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:05:00,572] [INFO] Task started: Prodigal
[2023-03-19 00:05:00,572] [INFO] Running command: cat /var/lib/cwl/stgcdc0ce40-5bda-42e7-8d57-0e550212494f/OceanDNA-b16111.fa | prodigal -d OceanDNA-b16111/cds.fna -a OceanDNA-b16111/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:05:29,620] [INFO] Task succeeded: Prodigal
[2023-03-19 00:05:29,620] [INFO] Task started: HMMsearch
[2023-03-19 00:05:29,620] [INFO] Running command: hmmsearch --tblout OceanDNA-b16111/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg857537d1-1998-4a39-adea-3d8cbbd5f6e9/dqc_reference/reference_markers.hmm OceanDNA-b16111/protein.faa > /dev/null
[2023-03-19 00:05:29,904] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:05:29,905] [INFO] Found 6/6 markers.
[2023-03-19 00:05:29,939] [INFO] Query marker FASTA was written to OceanDNA-b16111/markers.fasta
[2023-03-19 00:05:29,940] [INFO] Task started: Blastn
[2023-03-19 00:05:29,940] [INFO] Running command: blastn -query OceanDNA-b16111/markers.fasta -db /var/lib/cwl/stg857537d1-1998-4a39-adea-3d8cbbd5f6e9/dqc_reference/reference_markers.fasta -out OceanDNA-b16111/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:05:30,442] [INFO] Task succeeded: Blastn
[2023-03-19 00:05:30,443] [INFO] Selected 29 target genomes.
[2023-03-19 00:05:30,443] [INFO] Target genome list was writen to OceanDNA-b16111/target_genomes.txt
[2023-03-19 00:05:30,459] [INFO] Task started: fastANI
[2023-03-19 00:05:30,459] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdc0ce40-5bda-42e7-8d57-0e550212494f/OceanDNA-b16111.fa --refList OceanDNA-b16111/target_genomes.txt --output OceanDNA-b16111/fastani_result.tsv --threads 1
[2023-03-19 00:05:56,647] [INFO] Task succeeded: fastANI
[2023-03-19 00:05:56,647] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg857537d1-1998-4a39-adea-3d8cbbd5f6e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:05:56,648] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg857537d1-1998-4a39-adea-3d8cbbd5f6e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:05:56,657] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:05:56,657] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:05:56,657] [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
Moorena producens	strain=3L	GCA_000211815.1	1155739	1155739	type	True	76.6202	75	1869	95	below_threshold
Moorena producens	strain=3L	GCA_001942475.1	1155739	1155739	type	True	76.5478	78	1869	95	below_threshold
Planktothrix tepida	strain=PCC9214	GCA_904830955.1	1678309	1678309	type	True	76.085	220	1869	95	below_threshold
Planktothrix agardhii	strain=NIES-204	GCA_003609755.1	1160	1160	type	True	76.0565	165	1869	95	below_threshold
Limnospira indica	strain=PCC 8005	GCA_000973065.1	147322	147322	type	True	75.86	121	1869	95	below_threshold
Okeania hirsuta	strain=PAB10Feb10-1	GCA_003838195.1	1458930	1458930	type	True	75.7755	111	1869	95	below_threshold
Limnospira indica	strain=PCC 8005	GCA_000176895.2	147322	147322	type	True	75.7749	116	1869	95	below_threshold
Fischerella muscicola	strain=PCC 7414	GCA_000317205.1	92938	92938	type	True	75.5515	54	1869	95	below_threshold
Gloeothece verrucosa	strain=PCC 7822	GCA_000147335.1	2546359	2546359	type	True	75.4019	88	1869	95	below_threshold
Scytonema hofmannii	strain=PCC 7110	GCA_000346485.2	34078	34078	type	True	75.3503	58	1869	95	below_threshold
Crocosphaera chwakensis	strain=CCY0110	GCA_000169335.1	2546361	2546361	type	True	75.349	80	1869	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_000317285.1	1124	1124	type	True	75.305	52	1869	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_003990575.1	1124	1124	type	True	75.2901	53	1869	95	below_threshold
Gloeocapsopsis crepidinum	strain=LEGE 06123	GCA_015207655.1	693223	693223	type	True	75.1952	50	1869	95	below_threshold
Anabaena cylindrica	strain=PCC 7122	GCA_000317695.1	1165	1165	type	True	75.1288	77	1869	95	below_threshold
Anabaena cylindrica	strain=NIES-19	GCA_002367955.1	1165	1165	type	True	75.1196	78	1869	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:05:56,658] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16111/tc_result.tsv
[2023-03-19 00:05:56,658] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:05:56,658] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:05:56,658] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg857537d1-1998-4a39-adea-3d8cbbd5f6e9/dqc_reference/checkm_data
[2023-03-19 00:05:56,659] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:05:56,666] [INFO] Task started: CheckM
[2023-03-19 00:05:56,666] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16111/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16111/checkm_input OceanDNA-b16111/checkm_result
[2023-03-19 00:07:07,452] [INFO] Task succeeded: CheckM
[2023-03-19 00:07:07,453] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:07:07,456] [INFO] ===== Completeness check finished =====
[2023-03-19 00:07:07,456] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:07:07,456] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16111/markers.fasta)
[2023-03-19 00:07:07,458] [INFO] Task started: Blastn
[2023-03-19 00:07:07,458] [INFO] Running command: blastn -query OceanDNA-b16111/markers.fasta -db /var/lib/cwl/stg857537d1-1998-4a39-adea-3d8cbbd5f6e9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16111/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:07:08,174] [INFO] Task succeeded: Blastn
[2023-03-19 00:07:08,175] [INFO] Selected 37 target genomes.
[2023-03-19 00:07:08,175] [INFO] Target genome list was writen to OceanDNA-b16111/target_genomes_gtdb.txt
[2023-03-19 00:07:08,249] [INFO] Task started: fastANI
[2023-03-19 00:07:08,249] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdc0ce40-5bda-42e7-8d57-0e550212494f/OceanDNA-b16111.fa --refList OceanDNA-b16111/target_genomes_gtdb.txt --output OceanDNA-b16111/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:07:41,801] [INFO] Task succeeded: fastANI
[2023-03-19 00:07:41,817] [INFO] Found 29 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 00:07:41,818] [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_000211815.1	s__Moorea producens	76.6479	74	1869	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Coleofasciculaceae;g__Moorea	95.0	98.41	95.37	0.92	0.86	6	-
GCA_010671925.1	s__Moorea sp010671925	76.6332	107	1869	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Coleofasciculaceae;g__Moorea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000972705.2	s__Lyngbya robusta	76.5184	256	1869	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Lyngbya	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010692325.1	s__Moorea sp010692325	76.5088	73	1869	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Coleofasciculaceae;g__Moorea	95.0	97.88	97.68	0.88	0.86	3	-
GCF_000478195.2	s__Lyngbya aestuarii	76.4715	260	1869	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Lyngbya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000169095.1	s__Lyngbya sp000169095	76.4279	280	1869	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Lyngbya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900009145.1	s__Planktothrix tepida	76.085	212	1869	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Planktothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003609755.1	s__Planktothrix agardhii	76.0565	165	1869	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Planktothrix	96.6657	99.00	98.84	0.93	0.89	4	-
GCF_900010725.2	s__Planktothrix serta	76.0244	208	1869	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Planktothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014697575.1	s__Planktothrix sp014697575	75.9993	235	1869	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Planktothrix	95.0	95.88	95.88	0.86	0.86	2	-
GCF_900009135.1	s__Planktothrix sp900009135	75.982	215	1869	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Planktothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903893625.1	s__Planktothrix sp903893625	75.8762	211	1869	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Planktothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900009275.2	s__Planktothrix rubescens	75.8065	187	1869	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Planktothrix	96.6657	98.32	97.64	0.92	0.88	11	-
GCF_000009705.1	s__Trichormus sp000009705	75.5856	50	1869	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Trichormus	95.0	99.98	99.93	1.00	0.98	9	-
GCF_014695895.1	s__PCC7113 sp014695895	75.4304	63	1869	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Coleofasciculaceae;g__PCC7113	95.0	98.22	98.22	0.91	0.91	2	-
GCF_009856605.1	s__Trichormus variabilis	75.4119	55	1869	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Trichormus	95.0	99.97	99.87	1.00	0.98	9	-
GCF_002934005.1	s__Cuspidothrix issatschenkoi	75.3641	54	1869	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Cuspidothrix	95.0	95.84	95.84	0.79	0.79	2	-
GCF_000167195.1	s__Crocosphaera watsonii	75.3233	64	1869	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Crocosphaera	95.0	99.01	98.50	0.92	0.88	4	-
GCA_002749975.1	s__Gloeocapsopsis sp002749975	75.2991	52	1869	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Chroococcidiopsidaceae;g__Gloeocapsopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001890975.1	s__Roseofilum reptotaenium_A	75.2827	77	1869	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Desertifilaceae;g__Roseofilum	95.0	97.72	97.70	0.90	0.89	3	-
GCF_002412335.2	s__Microcoleus bourrellyi	75.2427	61	1869	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002340255.1	s__Roseofilum sp002340255	75.2122	60	1869	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Desertifilaceae;g__Roseofilum	95.0	99.04	97.93	0.93	0.88	11	-
GCA_012031035.1	s__Hydrococcus sp012031035	75.1845	52	1869	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Hydrococcus	95.0	99.84	99.83	0.93	0.93	3	-
GCF_015207505.1	s__Microcoleus sp015207505	75.1674	50	1869	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	96.23	96.23	0.84	0.84	3	-
GCF_000317695.1	s__Anabaena cylindrica	75.1288	77	1869	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Anabaena	95.0	99.99	99.98	0.99	0.99	3	-
GCA_004292745.1	s__Microcoleus sp004292745	75.0999	59	1869	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	99.54	99.38	0.91	0.88	6	-
GCF_009711935.1	s__Dolichospermum sp009711935	75.0792	66	1869	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dolichospermum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900185595.1	s__Calothrix_A rhizosoleniae	75.0307	56	1869	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Calothrix_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000332155.1	s__Kamptonema formosum	74.9283	73	1869	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Kamptonema	95.0	99.87	99.87	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-19 00:07:41,818] [INFO] GTDB search result was written to OceanDNA-b16111/result_gtdb.tsv
[2023-03-19 00:07:41,818] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:07:41,820] [INFO] DFAST_QC result json was written to OceanDNA-b16111/dqc_result.json
[2023-03-19 00:07:41,821] [INFO] DFAST_QC completed!
[2023-03-19 00:07:41,821] [INFO] Total running time: 0h2m42s