[2024-01-24 12:36:57,926] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:57,928] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:57,928] [INFO] DQC Reference Directory: /var/lib/cwl/stg7816bfb2-ee1c-4f14-ac4e-8c6fa702cf11/dqc_reference
[2024-01-24 12:36:59,297] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:59,298] [INFO] Task started: Prodigal
[2024-01-24 12:36:59,298] [INFO] Running command: gunzip -c /var/lib/cwl/stg86d3fa2b-b87d-4b51-8911-610d44176c23/GCF_000973065.1_ASM97306v1_genomic.fna.gz | prodigal -d GCF_000973065.1_ASM97306v1_genomic.fna/cds.fna -a GCF_000973065.1_ASM97306v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:12,972] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:12,972] [INFO] Task started: HMMsearch
[2024-01-24 12:37:12,972] [INFO] Running command: hmmsearch --tblout GCF_000973065.1_ASM97306v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7816bfb2-ee1c-4f14-ac4e-8c6fa702cf11/dqc_reference/reference_markers.hmm GCF_000973065.1_ASM97306v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:13,400] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:13,402] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg86d3fa2b-b87d-4b51-8911-610d44176c23/GCF_000973065.1_ASM97306v1_genomic.fna.gz]
[2024-01-24 12:37:13,481] [INFO] Query marker FASTA was written to GCF_000973065.1_ASM97306v1_genomic.fna/markers.fasta
[2024-01-24 12:37:13,481] [INFO] Task started: Blastn
[2024-01-24 12:37:13,481] [INFO] Running command: blastn -query GCF_000973065.1_ASM97306v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7816bfb2-ee1c-4f14-ac4e-8c6fa702cf11/dqc_reference/reference_markers.fasta -out GCF_000973065.1_ASM97306v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:14,041] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:14,045] [INFO] Selected 17 target genomes.
[2024-01-24 12:37:14,045] [INFO] Target genome list was writen to GCF_000973065.1_ASM97306v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:14,075] [INFO] Task started: fastANI
[2024-01-24 12:37:14,076] [INFO] Running command: fastANI --query /var/lib/cwl/stg86d3fa2b-b87d-4b51-8911-610d44176c23/GCF_000973065.1_ASM97306v1_genomic.fna.gz --refList GCF_000973065.1_ASM97306v1_genomic.fna/target_genomes.txt --output GCF_000973065.1_ASM97306v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:46,260] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:46,261] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7816bfb2-ee1c-4f14-ac4e-8c6fa702cf11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:46,261] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7816bfb2-ee1c-4f14-ac4e-8c6fa702cf11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:46,269] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:37:46,269] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:46,270] [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
Limnospira indica	strain=PCC 8005	GCA_000973065.1	147322	147322	type	True	100.0	2075	2076	95	conclusive
Limnospira indica	strain=PCC 8005	GCA_000176895.2	147322	147322	type	True	99.8813	1740	2076	95	conclusive
Planktothrix tepida	strain=PCC9214	GCA_904830955.1	1678309	1678309	type	True	76.3084	195	2076	95	below_threshold
Crocosphaera subtropica	strain=ATCC 51142	GCA_000017845.1	2546360	2546360	type	True	76.1921	63	2076	95	below_threshold
Iningainema tapete	strain=BLCC-T55	GCA_014698965.1	2806730	2806730	type	True	76.1305	63	2076	95	below_threshold
Anabaena cylindrica	strain=NIES-19	GCA_002367955.1	1165	1165	type	True	76.0299	76	2076	95	below_threshold
Okeania hirsuta	strain=PAB10Feb10-1	GCA_003838195.1	1458930	1458930	type	True	75.4495	96	2076	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:46,271] [INFO] DFAST Taxonomy check result was written to GCF_000973065.1_ASM97306v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:46,272] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:46,272] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:46,272] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7816bfb2-ee1c-4f14-ac4e-8c6fa702cf11/dqc_reference/checkm_data
[2024-01-24 12:37:46,274] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:46,336] [INFO] Task started: CheckM
[2024-01-24 12:37:46,337] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000973065.1_ASM97306v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000973065.1_ASM97306v1_genomic.fna/checkm_input GCF_000973065.1_ASM97306v1_genomic.fna/checkm_result
[2024-01-24 12:38:29,308] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:29,310] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:29,333] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:29,334] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:29,334] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000973065.1_ASM97306v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:29,335] [INFO] Task started: Blastn
[2024-01-24 12:38:29,335] [INFO] Running command: blastn -query GCF_000973065.1_ASM97306v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7816bfb2-ee1c-4f14-ac4e-8c6fa702cf11/dqc_reference/reference_markers_gtdb.fasta -out GCF_000973065.1_ASM97306v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:30,056] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:30,060] [INFO] Selected 16 target genomes.
[2024-01-24 12:38:30,060] [INFO] Target genome list was writen to GCF_000973065.1_ASM97306v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:30,101] [INFO] Task started: fastANI
[2024-01-24 12:38:30,101] [INFO] Running command: fastANI --query /var/lib/cwl/stg86d3fa2b-b87d-4b51-8911-610d44176c23/GCF_000973065.1_ASM97306v1_genomic.fna.gz --refList GCF_000973065.1_ASM97306v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000973065.1_ASM97306v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:39:07,313] [INFO] Task succeeded: fastANI
[2024-01-24 12:39:07,327] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:39:07,327] [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_012516315.1	s__Limnospira fusiformis	99.1325	1922	2076	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Limnospira	95.0	99.21	98.53	0.94	0.92	10	conclusive
GCF_016745315.1	s__Limnospira platensis	94.0797	1717	2076	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Limnospira	95.0	99.12	96.40	0.97	0.93	10	-
GCA_011390955.1	s__Planktothricoides sp011390955	78.6932	175	2076	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Oscillatoriaceae;g__Planktothricoides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001276715.1	s__Planktothricoides sp001276715	78.2561	160	2076	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Oscillatoriaceae;g__Planktothricoides	95.0	99.30	99.29	0.94	0.94	3	-
GCF_012295525.1	s__Oxynema aestuarii	77.3767	94	2076	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Oscillatoriaceae;g__Oxynema	95.0	97.71	95.88	0.95	0.91	3	-
GCF_002368275.1	s__Aulosira diplosiphon	76.098	87	2076	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Aulosira	95.0	99.95	99.93	0.99	0.99	3	-
GCF_000169095.1	s__Lyngbya sp000169095	76.0931	188	2076	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Lyngbya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000297435.1	s__Microcystis sp000297435	75.9982	66	2076	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	97.53	95.21	0.88	0.79	9	-
GCF_000478195.2	s__Lyngbya aestuarii	75.8867	174	2076	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Lyngbya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014698835.1	s__Nostoc paludosum	75.8044	81	2076	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	100.00	100.00	0.99	0.99	2	-
GCA_004293145.1	s__RDYJ01 sp004293145	75.4417	54	2076	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__RDYJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900659865.1	s__Hyella patelloides	75.4276	59	2076	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Hyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002289455.1	s__Calothrix elsteri	75.3719	54	2076	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Calothrix	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:39:07,329] [INFO] GTDB search result was written to GCF_000973065.1_ASM97306v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:39:07,330] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:39:07,333] [INFO] DFAST_QC result json was written to GCF_000973065.1_ASM97306v1_genomic.fna/dqc_result.json
[2024-01-24 12:39:07,333] [INFO] DFAST_QC completed!
[2024-01-24 12:39:07,333] [INFO] Total running time: 0h2m9s