[2024-01-24 13:41:41,299] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:41,301] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:41,301] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c0635f4-33c0-4027-a4cb-0ba946fd1268/dqc_reference
[2024-01-24 13:41:42,538] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:42,539] [INFO] Task started: Prodigal
[2024-01-24 13:41:42,539] [INFO] Running command: gunzip -c /var/lib/cwl/stg9f746716-ebf9-4df3-88eb-aad647948bb6/GCF_000169335.1_ASM16933v1_genomic.fna.gz | prodigal -d GCF_000169335.1_ASM16933v1_genomic.fna/cds.fna -a GCF_000169335.1_ASM16933v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:52,566] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:52,567] [INFO] Task started: HMMsearch
[2024-01-24 13:41:52,567] [INFO] Running command: hmmsearch --tblout GCF_000169335.1_ASM16933v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c0635f4-33c0-4027-a4cb-0ba946fd1268/dqc_reference/reference_markers.hmm GCF_000169335.1_ASM16933v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:52,953] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:52,955] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9f746716-ebf9-4df3-88eb-aad647948bb6/GCF_000169335.1_ASM16933v1_genomic.fna.gz]
[2024-01-24 13:41:53,010] [INFO] Query marker FASTA was written to GCF_000169335.1_ASM16933v1_genomic.fna/markers.fasta
[2024-01-24 13:41:53,010] [INFO] Task started: Blastn
[2024-01-24 13:41:53,010] [INFO] Running command: blastn -query GCF_000169335.1_ASM16933v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c0635f4-33c0-4027-a4cb-0ba946fd1268/dqc_reference/reference_markers.fasta -out GCF_000169335.1_ASM16933v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:53,588] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:53,592] [INFO] Selected 13 target genomes.
[2024-01-24 13:41:53,592] [INFO] Target genome list was writen to GCF_000169335.1_ASM16933v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:53,628] [INFO] Task started: fastANI
[2024-01-24 13:41:53,628] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f746716-ebf9-4df3-88eb-aad647948bb6/GCF_000169335.1_ASM16933v1_genomic.fna.gz --refList GCF_000169335.1_ASM16933v1_genomic.fna/target_genomes.txt --output GCF_000169335.1_ASM16933v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:42:06,754] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:06,754] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c0635f4-33c0-4027-a4cb-0ba946fd1268/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:42:06,755] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c0635f4-33c0-4027-a4cb-0ba946fd1268/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:42:06,772] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:42:06,772] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:42:06,773] [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 chwakensis	strain=CCY0110	GCA_000169335.1	2546361	2546361	type	True	100.0	1864	1875	95	conclusive
Crocosphaera subtropica	strain=ATCC 51142	GCA_000017845.1	2546360	2546360	type	True	86.6498	1309	1875	95	below_threshold
Crocosphaera watsonii	strain=WH 8501	GCA_000167195.1	263511	263511	suspected-type	True	81.1442	939	1875	95	below_threshold
Rippkaea orientalis	strain=PCC 8801	GCA_000021805.1	2546366	2546366	type	True	77.0127	341	1875	95	below_threshold
Dactylococcopsis salina	strain=PCC 8305	GCA_000317615.1	292566	292566	type	True	76.2463	65	1875	95	below_threshold
Cyanobacterium aponinum	strain=PCC 10605	GCA_000317675.1	379064	379064	type	True	76.0797	98	1875	95	below_threshold
Planktothrix tepida	strain=PCC9214	GCA_904830955.1	1678309	1678309	type	True	75.7451	123	1875	95	below_threshold
Iningainema tapete	strain=BLCC-T55	GCA_014698965.1	2806730	2806730	type	True	75.5962	60	1875	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:42:06,774] [INFO] DFAST Taxonomy check result was written to GCF_000169335.1_ASM16933v1_genomic.fna/tc_result.tsv
[2024-01-24 13:42:06,775] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:42:06,775] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:42:06,776] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c0635f4-33c0-4027-a4cb-0ba946fd1268/dqc_reference/checkm_data
[2024-01-24 13:42:06,777] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:42:06,839] [INFO] Task started: CheckM
[2024-01-24 13:42:06,839] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000169335.1_ASM16933v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000169335.1_ASM16933v1_genomic.fna/checkm_input GCF_000169335.1_ASM16933v1_genomic.fna/checkm_result
[2024-01-24 13:42:41,502] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:41,504] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:41,529] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:41,530] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:41,530] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000169335.1_ASM16933v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:41,531] [INFO] Task started: Blastn
[2024-01-24 13:42:41,531] [INFO] Running command: blastn -query GCF_000169335.1_ASM16933v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c0635f4-33c0-4027-a4cb-0ba946fd1268/dqc_reference/reference_markers_gtdb.fasta -out GCF_000169335.1_ASM16933v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:42,288] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:42,292] [INFO] Selected 6 target genomes.
[2024-01-24 13:42:42,293] [INFO] Target genome list was writen to GCF_000169335.1_ASM16933v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:42,299] [INFO] Task started: fastANI
[2024-01-24 13:42:42,299] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f746716-ebf9-4df3-88eb-aad647948bb6/GCF_000169335.1_ASM16933v1_genomic.fna.gz --refList GCF_000169335.1_ASM16933v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000169335.1_ASM16933v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:50,942] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:50,954] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:50,954] [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_000169335.1	s__Crocosphaera chwakensis	100.0	1865	1875	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Crocosphaera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002172675.1	s__Crocosphaera sp002172675	88.8828	1332	1875	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_003013815.1	s__Crocosphaera sp003013815	87.2355	1276	1875	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_000017845.1	s__Crocosphaera subtropica	86.6486	1308	1875	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_000167195.1	s__Crocosphaera watsonii	81.1502	938	1875	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	76.9177	78	1875	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 13:42:50,956] [INFO] GTDB search result was written to GCF_000169335.1_ASM16933v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:50,957] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:50,961] [INFO] DFAST_QC result json was written to GCF_000169335.1_ASM16933v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:50,961] [INFO] DFAST_QC completed!
[2024-01-24 13:42:50,961] [INFO] Total running time: 0h1m10s