[2023-03-18 04:16:54,163] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:16:54,164] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:16:54,164] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a207627-469a-4575-834f-7df912e1c50a/dqc_reference
[2023-03-18 04:16:55,825] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:16:55,826] [INFO] Task started: Prodigal
[2023-03-18 04:16:55,826] [INFO] Running command: cat /var/lib/cwl/stge1f52fc5-913f-4259-add7-badc168e7fc3/OceanDNA-b16119.fa | prodigal -d OceanDNA-b16119/cds.fna -a OceanDNA-b16119/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:17:25,255] [INFO] Task succeeded: Prodigal
[2023-03-18 04:17:25,255] [INFO] Task started: HMMsearch
[2023-03-18 04:17:25,255] [INFO] Running command: hmmsearch --tblout OceanDNA-b16119/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a207627-469a-4575-834f-7df912e1c50a/dqc_reference/reference_markers.hmm OceanDNA-b16119/protein.faa > /dev/null
[2023-03-18 04:17:25,526] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:17:25,527] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge1f52fc5-913f-4259-add7-badc168e7fc3/OceanDNA-b16119.fa]
[2023-03-18 04:17:25,558] [INFO] Query marker FASTA was written to OceanDNA-b16119/markers.fasta
[2023-03-18 04:17:25,559] [INFO] Task started: Blastn
[2023-03-18 04:17:25,560] [INFO] Running command: blastn -query OceanDNA-b16119/markers.fasta -db /var/lib/cwl/stg3a207627-469a-4575-834f-7df912e1c50a/dqc_reference/reference_markers.fasta -out OceanDNA-b16119/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:17:26,071] [INFO] Task succeeded: Blastn
[2023-03-18 04:17:26,072] [INFO] Selected 16 target genomes.
[2023-03-18 04:17:26,072] [INFO] Target genome list was writen to OceanDNA-b16119/target_genomes.txt
[2023-03-18 04:17:26,105] [INFO] Task started: fastANI
[2023-03-18 04:17:26,105] [INFO] Running command: fastANI --query /var/lib/cwl/stge1f52fc5-913f-4259-add7-badc168e7fc3/OceanDNA-b16119.fa --refList OceanDNA-b16119/target_genomes.txt --output OceanDNA-b16119/fastani_result.tsv --threads 1
[2023-03-18 04:17:39,516] [INFO] Task succeeded: fastANI
[2023-03-18 04:17:39,517] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a207627-469a-4575-834f-7df912e1c50a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:17:39,517] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a207627-469a-4575-834f-7df912e1c50a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:17:39,525] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:17:39,525] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 04:17:39,525] [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	75.8072	132	1895	95	below_threshold
Anabaena cylindrica	strain=NIES-19	GCA_002367955.1	1165	1165	type	True	75.3755	81	1895	95	below_threshold
Crocosphaera subtropica	strain=ATCC 51142	GCA_000017845.1	2546360	2546360	type	True	75.3708	64	1895	95	below_threshold
Anabaena cylindrica	strain=PCC 7122	GCA_000317695.1	1165	1165	type	True	75.3445	81	1895	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_003990575.1	1124	1124	type	True	75.2887	77	1895	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_000317285.1	1124	1124	type	True	75.2767	75	1895	95	below_threshold
Fischerella thermalis	strain=PCC 7521	GCA_000317225.1	372787	372787	type	True	75.2723	62	1895	95	below_threshold
Rippkaea orientalis	strain=PCC 8801	GCA_000021805.1	2546366	2546366	type	True	75.2306	80	1895	95	below_threshold
Fischerella muscicola	strain=PCC 7414	GCA_000317205.1	92938	92938	type	True	75.1109	79	1895	95	below_threshold
Argonema galeatum	strain=A003/A1	GCA_023333595.1	2942762	2942762	type	True	75.0221	54	1895	95	below_threshold
Argonema antarcticum	strain=A004/B2	GCA_023333585.1	2942763	2942763	type	True	74.9269	54	1895	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 04:17:39,526] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16119/tc_result.tsv
[2023-03-18 04:17:39,526] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:17:39,526] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:17:39,526] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a207627-469a-4575-834f-7df912e1c50a/dqc_reference/checkm_data
[2023-03-18 04:17:39,527] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:17:39,551] [INFO] Task started: CheckM
[2023-03-18 04:17:39,552] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16119/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16119/checkm_input OceanDNA-b16119/checkm_result
[2023-03-18 04:18:50,337] [INFO] Task succeeded: CheckM
[2023-03-18 04:18:50,338] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:18:50,374] [INFO] ===== Completeness check finished =====
[2023-03-18 04:18:50,374] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:18:50,374] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16119/markers.fasta)
[2023-03-18 04:18:50,375] [INFO] Task started: Blastn
[2023-03-18 04:18:50,375] [INFO] Running command: blastn -query OceanDNA-b16119/markers.fasta -db /var/lib/cwl/stg3a207627-469a-4575-834f-7df912e1c50a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16119/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:18:51,059] [INFO] Task succeeded: Blastn
[2023-03-18 04:18:51,060] [INFO] Selected 27 target genomes.
[2023-03-18 04:18:51,060] [INFO] Target genome list was writen to OceanDNA-b16119/target_genomes_gtdb.txt
[2023-03-18 04:18:51,340] [INFO] Task started: fastANI
[2023-03-18 04:18:51,340] [INFO] Running command: fastANI --query /var/lib/cwl/stge1f52fc5-913f-4259-add7-badc168e7fc3/OceanDNA-b16119.fa --refList OceanDNA-b16119/target_genomes_gtdb.txt --output OceanDNA-b16119/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:19:16,270] [INFO] Task succeeded: fastANI
[2023-03-18 04:19:16,284] [INFO] Found 26 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 04:19:16,285] [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_002355455.1	s__Stanieria sp002355455	76.0263	102	1895	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Stanieria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317575.1	s__Stanieria cyanosphaera	75.8071	132	1895	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Stanieria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010692635.1	s__SIO2C1 sp010692635	75.8062	102	1895	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Coleofasciculaceae;g__SIO2C1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934005.1	s__Cuspidothrix issatschenkoi	75.5065	69	1895	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Cuspidothrix	95.0	95.84	95.84	0.79	0.79	2	-
GCF_015207875.1	s__Dolichospermum sp015207875	75.4746	66	1895	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dolichospermum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000734895.2	s__Calothrix sp000734895	75.4568	80	1895	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Calothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001548115.1	s__Geminocystis sp001548115	75.4558	61	1895	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Cyanobacteriaceae;g__Geminocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010672865.1	s__SIO1D9 sp010672865	75.4322	114	1895	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__SIO1D9;g__SIO1D9	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015207825.1	s__Cyanobacterium stanieri_B	75.3928	59	1895	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Cyanobacteriaceae;g__Cyanobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903848645.1	s__Dolichospermum sp903848645	75.388	76	1895	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dolichospermum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000972705.2	s__Lyngbya robusta	75.3723	58	1895	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Lyngbya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017845.1	s__Crocosphaera subtropica	75.3708	64	1895	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_000169335.1	s__Crocosphaera chwakensis	75.3267	64	1895	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_900659865.1	s__Hyella patelloides	75.3262	113	1895	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Hyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016888125.1	s__CCY15215 sp016888125	75.317	52	1895	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Spirulinaceae;g__CCY15215	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014698735.1	s__Anabaena variabilis_A	75.3037	78	1895	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Anabaena	95.0	95.36	95.36	0.83	0.82	3	-
GCF_000317285.1	s__Chlorogloeopsis fritschii	75.2767	75	1895	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Chlorogloeopsis	95.0	99.29	97.93	0.97	0.93	4	-
GCF_000317225.1	s__Fischerella thermalis	75.2723	62	1895	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Fischerella	95.0	98.97	96.56	0.93	0.78	35	-
GCF_009711975.1	s__Dolichospermum sp009711975	75.2615	83	1895	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dolichospermum	95.0	98.17	98.17	0.93	0.93	2	-
GCF_002368115.1	s__Dolichospermum compactum	75.259	68	1895	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dolichospermum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000314005.1	s__Spirulina_A subsalsa	75.245	67	1895	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Spirulinaceae;g__Spirulina_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012034765.1	s__Pleurocapsa sp012034765	75.179	69	1895	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	99.36	99.13	0.90	0.87	3	-
GCF_014698045.1	s__Nostoc_B sp014698045	75.1303	74	1895	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc_B	95.0	98.36	98.34	0.86	0.85	4	-
GCF_000317205.1	s__Fischerella muscicola	75.1109	79	1895	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Fischerella	95.0	99.84	99.68	0.97	0.95	3	-
GCF_000297435.1	s__Microcystis sp000297435	75.0501	53	1895	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	97.53	95.21	0.88	0.79	9	-
GCA_002172675.1	s__Crocosphaera sp002172675	74.9864	74	1895	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Crocosphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 04:19:16,285] [INFO] GTDB search result was written to OceanDNA-b16119/result_gtdb.tsv
[2023-03-18 04:19:16,285] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:19:16,287] [INFO] DFAST_QC result json was written to OceanDNA-b16119/dqc_result.json
[2023-03-18 04:19:16,287] [INFO] DFAST_QC completed!
[2023-03-18 04:19:16,287] [INFO] Total running time: 0h2m22s