[2024-01-24 10:47:06,588] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,597] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,597] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb66a327-a614-4527-badb-b06ce8a93b1a/dqc_reference
[2024-01-24 10:47:12,685] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,815] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,819] [INFO] Running command: gunzip -c /var/lib/cwl/stg7584436a-d150-4704-8c41-e1bda15c76e8/GCF_002289455.1_ASM228945v1_genomic.fna.gz | prodigal -d GCF_002289455.1_ASM228945v1_genomic.fna/cds.fna -a GCF_002289455.1_ASM228945v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:25,081] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:25,082] [INFO] Task started: HMMsearch
[2024-01-24 10:47:25,082] [INFO] Running command: hmmsearch --tblout GCF_002289455.1_ASM228945v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb66a327-a614-4527-badb-b06ce8a93b1a/dqc_reference/reference_markers.hmm GCF_002289455.1_ASM228945v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:25,496] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:25,498] [INFO] Found 6/6 markers.
[2024-01-24 10:47:25,559] [INFO] Query marker FASTA was written to GCF_002289455.1_ASM228945v1_genomic.fna/markers.fasta
[2024-01-24 10:47:25,560] [INFO] Task started: Blastn
[2024-01-24 10:47:25,561] [INFO] Running command: blastn -query GCF_002289455.1_ASM228945v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb66a327-a614-4527-badb-b06ce8a93b1a/dqc_reference/reference_markers.fasta -out GCF_002289455.1_ASM228945v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:26,148] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:26,153] [INFO] Selected 24 target genomes.
[2024-01-24 10:47:26,154] [INFO] Target genome list was writen to GCF_002289455.1_ASM228945v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:27,150] [INFO] Task started: fastANI
[2024-01-24 10:47:27,151] [INFO] Running command: fastANI --query /var/lib/cwl/stg7584436a-d150-4704-8c41-e1bda15c76e8/GCF_002289455.1_ASM228945v1_genomic.fna.gz --refList GCF_002289455.1_ASM228945v1_genomic.fna/target_genomes.txt --output GCF_002289455.1_ASM228945v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:58,504] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:58,505] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb66a327-a614-4527-badb-b06ce8a93b1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:58,505] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb66a327-a614-4527-badb-b06ce8a93b1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:58,519] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:58,520] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:58,520] [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
Calothrix elsteri	strain=CCALA 953	GCA_002289455.1	1247191	1247191	type	True	100.0	1905	1925	95	conclusive
Dulcicalothrix desertica	strain=PCC 7102	GCA_003991905.1	32056	32056	type	True	77.3414	463	1925	95	below_threshold
Dulcicalothrix desertica	strain=PCC 7102	GCA_007830875.1	32056	32056	type	True	77.2695	475	1925	95	below_threshold
Brasilonema sennae	strain=CENA114	GCA_006968745.1	1397703	1397703	type	True	76.6186	196	1925	95	below_threshold
Iningainema tapete	strain=BLCC-T55	GCA_014698965.1	2806730	2806730	type	True	76.4871	218	1925	95	below_threshold
Anabaena cylindrica	strain=PCC 7122	GCA_000317695.1	1165	1165	type	True	76.443	251	1925	95	below_threshold
Anabaena cylindrica	strain=NIES-19	GCA_002367955.1	1165	1165	type	True	76.4301	253	1925	95	below_threshold
Fischerella thermalis	strain=PCC 7521	GCA_000317225.1	372787	372787	type	True	76.4176	228	1925	95	below_threshold
Fischerella muscicola	strain=PCC 7414	GCA_000317205.1	92938	92938	type	True	76.3313	251	1925	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_003990575.1	1124	1124	type	True	76.2857	206	1925	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_000317285.1	1124	1124	type	True	76.2221	205	1925	95	below_threshold
Mastigocoleus testarum	strain=BC008	GCA_001456025.1	996925	996925	type	True	76.1945	212	1925	95	below_threshold
Nostoc favosum	strain=CHAB 5714	GCA_020829495.1	2907819	2907819	type	True	76.1851	268	1925	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:58,521] [INFO] DFAST Taxonomy check result was written to GCF_002289455.1_ASM228945v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:58,522] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:58,522] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:58,522] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb66a327-a614-4527-badb-b06ce8a93b1a/dqc_reference/checkm_data
[2024-01-24 10:47:58,523] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:58,589] [INFO] Task started: CheckM
[2024-01-24 10:47:58,589] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002289455.1_ASM228945v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002289455.1_ASM228945v1_genomic.fna/checkm_input GCF_002289455.1_ASM228945v1_genomic.fna/checkm_result
[2024-01-24 10:48:39,075] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:39,076] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:39,097] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:39,098] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:39,098] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002289455.1_ASM228945v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:39,099] [INFO] Task started: Blastn
[2024-01-24 10:48:39,099] [INFO] Running command: blastn -query GCF_002289455.1_ASM228945v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb66a327-a614-4527-badb-b06ce8a93b1a/dqc_reference/reference_markers_gtdb.fasta -out GCF_002289455.1_ASM228945v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:39,922] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:39,928] [INFO] Selected 18 target genomes.
[2024-01-24 10:48:39,928] [INFO] Target genome list was writen to GCF_002289455.1_ASM228945v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:40,030] [INFO] Task started: fastANI
[2024-01-24 10:48:40,030] [INFO] Running command: fastANI --query /var/lib/cwl/stg7584436a-d150-4704-8c41-e1bda15c76e8/GCF_002289455.1_ASM228945v1_genomic.fna.gz --refList GCF_002289455.1_ASM228945v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002289455.1_ASM228945v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:09,988] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:10,006] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:10,007] [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_002289455.1	s__Calothrix elsteri	100.0	1905	1925	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Calothrix	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012034595.1	s__Calothrix sp012034595	88.0226	1418	1925	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Calothrix	95.0	99.62	99.62	0.93	0.93	2	-
GCA_004296455.1	s__Calothrix sp004296455	81.3444	1191	1925	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Calothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317435.1	s__Calothrix sp000317435	79.6334	528	1925	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Calothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015272395.1	s__Calothrix sp015272395	77.3899	432	1925	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Calothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000582685.1	s__Hassallia hofmanni	77.3401	392	1925	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Hassallia	95.0	99.97	99.97	1.00	1.00	2	-
GCF_003991905.1	s__Calothrix desertica	77.3137	467	1925	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Calothrix	95.0	99.95	99.95	0.98	0.98	2	-
GCF_001904745.1	s__Calothrix sp001904745	77.2829	454	1925	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Calothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331305.1	s__Calothrix sp000331305	77.1651	507	1925	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Calothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002368415.1	s__Calothrix sp002368415	76.9766	483	1925	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Calothrix	95.0	100.00	100.00	1.00	1.00	2	-
GCA_015206945.1	s__Nostoc sp015206945	76.6443	260	1925	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014023275.1	s__Nostoc edaphicum_A	76.4767	270	1925	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015272215.1	s__Rivularia sp015272215	76.4713	247	1925	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Rivularia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016056275.1	s__Dendronalium phyllosphericum	76.4119	243	1925	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dendronalium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004323185.1	s__Fischerella prolifica	76.3862	271	1925	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Fischerella	95.0	97.11	96.24	0.86	0.82	3	-
GCF_000332295.1	s__Fortiea contorta	76.3188	233	1925	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Fortiea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015206895.1	s__Nostoc sp015206895	76.2673	259	1925	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:10,009] [INFO] GTDB search result was written to GCF_002289455.1_ASM228945v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:10,010] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:10,017] [INFO] DFAST_QC result json was written to GCF_002289455.1_ASM228945v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:10,017] [INFO] DFAST_QC completed!
[2024-01-24 10:49:10,017] [INFO] Total running time: 0h2m3s