[2024-01-24 12:37:24,029] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:24,031] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:24,031] [INFO] DQC Reference Directory: /var/lib/cwl/stgc5c4289a-7561-4c7c-aba8-eecb629fa461/dqc_reference
[2024-01-24 12:37:25,356] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:25,357] [INFO] Task started: Prodigal
[2024-01-24 12:37:25,357] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b35993a-88da-48ab-8a21-17208a4d95ce/GCF_000017845.1_ASM1784v1_genomic.fna.gz | prodigal -d GCF_000017845.1_ASM1784v1_genomic.fna/cds.fna -a GCF_000017845.1_ASM1784v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:35,312] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:35,313] [INFO] Task started: HMMsearch
[2024-01-24 12:37:35,313] [INFO] Running command: hmmsearch --tblout GCF_000017845.1_ASM1784v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc5c4289a-7561-4c7c-aba8-eecb629fa461/dqc_reference/reference_markers.hmm GCF_000017845.1_ASM1784v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:35,675] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:35,677] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8b35993a-88da-48ab-8a21-17208a4d95ce/GCF_000017845.1_ASM1784v1_genomic.fna.gz]
[2024-01-24 12:37:35,723] [INFO] Query marker FASTA was written to GCF_000017845.1_ASM1784v1_genomic.fna/markers.fasta
[2024-01-24 12:37:35,723] [INFO] Task started: Blastn
[2024-01-24 12:37:35,723] [INFO] Running command: blastn -query GCF_000017845.1_ASM1784v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5c4289a-7561-4c7c-aba8-eecb629fa461/dqc_reference/reference_markers.fasta -out GCF_000017845.1_ASM1784v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:36,276] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:36,281] [INFO] Selected 15 target genomes.
[2024-01-24 12:37:36,282] [INFO] Target genome list was writen to GCF_000017845.1_ASM1784v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:36,287] [INFO] Task started: fastANI
[2024-01-24 12:37:36,288] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b35993a-88da-48ab-8a21-17208a4d95ce/GCF_000017845.1_ASM1784v1_genomic.fna.gz --refList GCF_000017845.1_ASM1784v1_genomic.fna/target_genomes.txt --output GCF_000017845.1_ASM1784v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:51,866] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:51,867] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc5c4289a-7561-4c7c-aba8-eecb629fa461/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:51,867] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc5c4289a-7561-4c7c-aba8-eecb629fa461/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:51,876] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:51,876] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:51,876] [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
Crocosphaera subtropica	strain=ATCC 51142	GCA_000017845.1	2546360	2546360	type	True	100.0	1817	1817	95	conclusive
Crocosphaera chwakensis	strain=CCY0110	GCA_000169335.1	2546361	2546361	type	True	86.7635	1303	1817	95	below_threshold
Crocosphaera watsonii	strain=WH 8501	GCA_000167195.1	263511	263511	suspected-type	True	81.3155	990	1817	95	below_threshold
Rippkaea orientalis	strain=PCC 8801	GCA_000021805.1	2546366	2546366	type	True	77.2101	404	1817	95	below_threshold
Gloeothece verrucosa	strain=PCC 7822	GCA_000147335.1	2546359	2546359	type	True	76.3054	165	1817	95	below_threshold
Limnospira indica	strain=PCC 8005	GCA_000973065.1	147322	147322	type	True	76.1699	60	1817	95	below_threshold
Nostoc punctiforme	strain=ATCC 29133; PCC 73102	GCA_000020025.1	272131	272131	type	True	76.076	67	1817	95	below_threshold
Microcystis aeruginosa	strain=NIES-843	GCA_000010625.1	1126	1126	suspected-type	True	75.9701	108	1817	95	below_threshold
Limnospira indica	strain=PCC 8005	GCA_000176895.2	147322	147322	type	True	75.9407	55	1817	95	below_threshold
Nostoc favosum	strain=CHAB 5714	GCA_020829495.1	2907819	2907819	type	True	75.5895	50	1817	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:51,878] [INFO] DFAST Taxonomy check result was written to GCF_000017845.1_ASM1784v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:51,878] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:51,878] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:51,879] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc5c4289a-7561-4c7c-aba8-eecb629fa461/dqc_reference/checkm_data
[2024-01-24 12:37:51,880] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:51,934] [INFO] Task started: CheckM
[2024-01-24 12:37:51,935] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000017845.1_ASM1784v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000017845.1_ASM1784v1_genomic.fna/checkm_input GCF_000017845.1_ASM1784v1_genomic.fna/checkm_result
[2024-01-24 12:38:26,289] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:26,291] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:26,315] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:26,315] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:26,316] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000017845.1_ASM1784v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:26,316] [INFO] Task started: Blastn
[2024-01-24 12:38:26,316] [INFO] Running command: blastn -query GCF_000017845.1_ASM1784v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5c4289a-7561-4c7c-aba8-eecb629fa461/dqc_reference/reference_markers_gtdb.fasta -out GCF_000017845.1_ASM1784v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:27,056] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:27,060] [INFO] Selected 6 target genomes.
[2024-01-24 12:38:27,060] [INFO] Target genome list was writen to GCF_000017845.1_ASM1784v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:27,132] [INFO] Task started: fastANI
[2024-01-24 12:38:27,133] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b35993a-88da-48ab-8a21-17208a4d95ce/GCF_000017845.1_ASM1784v1_genomic.fna.gz --refList GCF_000017845.1_ASM1784v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000017845.1_ASM1784v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:35,395] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:35,407] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:35,407] [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_000017845.1	s__Crocosphaera subtropica	100.0	1816	1817	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Crocosphaera	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003013815.1	s__Crocosphaera sp003013815	87.4221	1276	1817	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_000169335.1	s__Crocosphaera chwakensis	86.7849	1303	1817	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Crocosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002172675.1	s__Crocosphaera sp002172675	86.7785	1289	1817	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_000167195.1	s__Crocosphaera watsonii	81.3224	989	1817	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Crocosphaera	95.0	99.01	98.50	0.92	0.88	4	-
GCF_000025125.1	s__Atelocyanobacterium thalassa	76.4657	69	1817	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Atelocyanobacterium	95.0	99.95	99.95	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:35,409] [INFO] GTDB search result was written to GCF_000017845.1_ASM1784v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:35,409] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:35,412] [INFO] DFAST_QC result json was written to GCF_000017845.1_ASM1784v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:35,412] [INFO] DFAST_QC completed!
[2024-01-24 12:38:35,412] [INFO] Total running time: 0h1m11s