[2024-01-25 17:51:35,510] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:51:35,512] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:51:35,512] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ceb58ca-3b45-47e1-9497-9df6eb0d828d/dqc_reference
[2024-01-25 17:51:36,746] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:51:36,747] [INFO] Task started: Prodigal
[2024-01-25 17:51:36,747] [INFO] Running command: gunzip -c /var/lib/cwl/stg0cfd8fd9-3b78-4d91-9568-4e4b82c98d17/GCF_000332235.1_ASM33223v1_genomic.fna.gz | prodigal -d GCF_000332235.1_ASM33223v1_genomic.fna/cds.fna -a GCF_000332235.1_ASM33223v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:51:47,268] [INFO] Task succeeded: Prodigal
[2024-01-25 17:51:47,269] [INFO] Task started: HMMsearch
[2024-01-25 17:51:47,269] [INFO] Running command: hmmsearch --tblout GCF_000332235.1_ASM33223v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ceb58ca-3b45-47e1-9497-9df6eb0d828d/dqc_reference/reference_markers.hmm GCF_000332235.1_ASM33223v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:51:47,508] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:51:47,509] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0cfd8fd9-3b78-4d91-9568-4e4b82c98d17/GCF_000332235.1_ASM33223v1_genomic.fna.gz]
[2024-01-25 17:51:47,544] [INFO] Query marker FASTA was written to GCF_000332235.1_ASM33223v1_genomic.fna/markers.fasta
[2024-01-25 17:51:47,544] [INFO] Task started: Blastn
[2024-01-25 17:51:47,544] [INFO] Running command: blastn -query GCF_000332235.1_ASM33223v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ceb58ca-3b45-47e1-9497-9df6eb0d828d/dqc_reference/reference_markers.fasta -out GCF_000332235.1_ASM33223v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:51:48,118] [INFO] Task succeeded: Blastn
[2024-01-25 17:51:48,121] [INFO] Selected 21 target genomes.
[2024-01-25 17:51:48,121] [INFO] Target genome list was writen to GCF_000332235.1_ASM33223v1_genomic.fna/target_genomes.txt
[2024-01-25 17:51:48,141] [INFO] Task started: fastANI
[2024-01-25 17:51:48,142] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cfd8fd9-3b78-4d91-9568-4e4b82c98d17/GCF_000332235.1_ASM33223v1_genomic.fna.gz --refList GCF_000332235.1_ASM33223v1_genomic.fna/target_genomes.txt --output GCF_000332235.1_ASM33223v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:52:04,889] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:04,889] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ceb58ca-3b45-47e1-9497-9df6eb0d828d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:52:04,890] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ceb58ca-3b45-47e1-9497-9df6eb0d828d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:52:04,895] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:52:04,895] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:52:04,895] [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
Cyanobacterium aponinum	strain=PCC 10605	GCA_000317675.1	379064	379064	type	True	78.2886	480	1421	95	below_threshold
Rippkaea orientalis	strain=PCC 8801	GCA_000021805.1	2546366	2546366	type	True	76.3885	70	1421	95	below_threshold
Gloeothece citriformis	strain=PCC 7424	GCA_000021825.1	2546356	2546356	type	True	75.9556	89	1421	95	below_threshold
Dactylococcopsis salina	strain=PCC 8305	GCA_000317615.1	292566	292566	type	True	75.9513	56	1421	95	below_threshold
Waterburya agarophytonicola	strain=KI4	GCA_020640915.1	2886916	2886916	type	True	75.3073	74	1421	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:52:04,896] [INFO] DFAST Taxonomy check result was written to GCF_000332235.1_ASM33223v1_genomic.fna/tc_result.tsv
[2024-01-25 17:52:04,897] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:52:04,897] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:52:04,897] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ceb58ca-3b45-47e1-9497-9df6eb0d828d/dqc_reference/checkm_data
[2024-01-25 17:52:04,898] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:52:04,942] [INFO] Task started: CheckM
[2024-01-25 17:52:04,942] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000332235.1_ASM33223v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000332235.1_ASM33223v1_genomic.fna/checkm_input GCF_000332235.1_ASM33223v1_genomic.fna/checkm_result
[2024-01-25 17:52:38,839] [INFO] Task succeeded: CheckM
[2024-01-25 17:52:38,840] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:52:38,856] [INFO] ===== Completeness check finished =====
[2024-01-25 17:52:38,857] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:52:38,857] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000332235.1_ASM33223v1_genomic.fna/markers.fasta)
[2024-01-25 17:52:38,857] [INFO] Task started: Blastn
[2024-01-25 17:52:38,857] [INFO] Running command: blastn -query GCF_000332235.1_ASM33223v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ceb58ca-3b45-47e1-9497-9df6eb0d828d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000332235.1_ASM33223v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:39,821] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:39,824] [INFO] Selected 12 target genomes.
[2024-01-25 17:52:39,824] [INFO] Target genome list was writen to GCF_000332235.1_ASM33223v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:52:39,837] [INFO] Task started: fastANI
[2024-01-25 17:52:39,837] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cfd8fd9-3b78-4d91-9568-4e4b82c98d17/GCF_000332235.1_ASM33223v1_genomic.fna.gz --refList GCF_000332235.1_ASM33223v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000332235.1_ASM33223v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:52:53,193] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:53,200] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:52:53,201] [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_000332235.1	s__Geminocystis herdmanii	100.0	1421	1421	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Cyanobacteriaceae;g__Geminocystis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001548115.1	s__Geminocystis sp001548115	81.4449	832	1421	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Cyanobacteriaceae;g__Geminocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009993045.1	s__Geminocystis sp009993045	80.1667	633	1421	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Cyanobacteriaceae;g__Geminocystis	95.0	99.95	99.93	0.95	0.94	5	-
GCA_016743215.1	s__Geminocystis sp016743215	79.9895	646	1421	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Cyanobacteriaceae;g__Geminocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001548095.1	s__Geminocystis sp001548095	79.9379	703	1421	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Cyanobacteriaceae;g__Geminocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317675.1	s__PCC-10605 sp000317675	78.2718	481	1421	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Cyanobacteriaceae;g__PCC-10605	95.0	98.28	97.96	0.91	0.90	4	-
GCA_003566215.1	s__Cyanobacterium sp003566215	76.7558	121	1421	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Cyanobacteriaceae;g__Cyanobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011088145.1	s__JAALKG01 sp011088145	76.6671	170	1421	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Cyanobacteriaceae;g__JAALKG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932785.1	s__Hyella disjuncta	75.7682	98	1421	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Hyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900659865.1	s__Hyella patelloides	75.398	89	1421	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Hyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:52:53,202] [INFO] GTDB search result was written to GCF_000332235.1_ASM33223v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:52:53,203] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:52:53,206] [INFO] DFAST_QC result json was written to GCF_000332235.1_ASM33223v1_genomic.fna/dqc_result.json
[2024-01-25 17:52:53,206] [INFO] DFAST_QC completed!
[2024-01-25 17:52:53,206] [INFO] Total running time: 0h1m18s