[2024-01-24 11:30:49,198] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:30:49,201] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:30:49,201] [INFO] DQC Reference Directory: /var/lib/cwl/stg8cbbcbf6-5683-4457-8a3f-5e4fd2980ccf/dqc_reference
[2024-01-24 11:30:50,416] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:30:50,417] [INFO] Task started: Prodigal
[2024-01-24 11:30:50,417] [INFO] Running command: gunzip -c /var/lib/cwl/stgd34c1355-45bc-4dbe-b81a-d4a102973121/GCF_015207655.1_ASM1520765v1_genomic.fna.gz | prodigal -d GCF_015207655.1_ASM1520765v1_genomic.fna/cds.fna -a GCF_015207655.1_ASM1520765v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:31:01,500] [INFO] Task succeeded: Prodigal
[2024-01-24 11:31:01,501] [INFO] Task started: HMMsearch
[2024-01-24 11:31:01,501] [INFO] Running command: hmmsearch --tblout GCF_015207655.1_ASM1520765v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8cbbcbf6-5683-4457-8a3f-5e4fd2980ccf/dqc_reference/reference_markers.hmm GCF_015207655.1_ASM1520765v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:31:01,842] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:31:01,844] [INFO] Found 6/6 markers.
[2024-01-24 11:31:01,892] [INFO] Query marker FASTA was written to GCF_015207655.1_ASM1520765v1_genomic.fna/markers.fasta
[2024-01-24 11:31:01,893] [INFO] Task started: Blastn
[2024-01-24 11:31:01,893] [INFO] Running command: blastn -query GCF_015207655.1_ASM1520765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8cbbcbf6-5683-4457-8a3f-5e4fd2980ccf/dqc_reference/reference_markers.fasta -out GCF_015207655.1_ASM1520765v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:31:02,474] [INFO] Task succeeded: Blastn
[2024-01-24 11:31:02,477] [INFO] Selected 21 target genomes.
[2024-01-24 11:31:02,478] [INFO] Target genome list was writen to GCF_015207655.1_ASM1520765v1_genomic.fna/target_genomes.txt
[2024-01-24 11:31:02,500] [INFO] Task started: fastANI
[2024-01-24 11:31:02,500] [INFO] Running command: fastANI --query /var/lib/cwl/stgd34c1355-45bc-4dbe-b81a-d4a102973121/GCF_015207655.1_ASM1520765v1_genomic.fna.gz --refList GCF_015207655.1_ASM1520765v1_genomic.fna/target_genomes.txt --output GCF_015207655.1_ASM1520765v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:31:22,378] [INFO] Task succeeded: fastANI
[2024-01-24 11:31:22,379] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8cbbcbf6-5683-4457-8a3f-5e4fd2980ccf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:31:22,380] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8cbbcbf6-5683-4457-8a3f-5e4fd2980ccf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:31:22,394] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:31:22,394] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:31:22,394] [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
Gloeocapsopsis crepidinum	strain=LEGE 06123	GCA_015207655.1	693223	693223	type	True	100.0	1809	1815	95	conclusive
Gloeocapsopsis dulcis	strain=AAB1	GCA_002964865.1	2859516	2859516	type	True	88.1446	1344	1815	95	below_threshold
Brasilonema sennae	strain=CENA114	GCA_006968745.1	1397703	1397703	type	True	76.1443	123	1815	95	below_threshold
Iningainema tapete	strain=BLCC-T55	GCA_014698965.1	2806730	2806730	type	True	76.105	152	1815	95	below_threshold
Brasilonema bromeliae	strain=SPC951	GCA_012912135.1	383615	383615	type	True	76.0212	112	1815	95	below_threshold
Scytonema hofmannii	strain=PCC 7110	GCA_000346485.2	34078	34078	type	True	75.9325	152	1815	95	below_threshold
Nostoc punctiforme	strain=ATCC 29133; PCC 73102	GCA_000020025.1	272131	272131	type	True	75.9168	145	1815	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_000317285.1	1124	1124	type	True	75.8739	178	1815	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_003990575.1	1124	1124	type	True	75.8598	180	1815	95	below_threshold
Nostoc favosum	strain=CHAB 5714	GCA_020829495.1	2907819	2907819	type	True	75.8548	152	1815	95	below_threshold
Anabaena cylindrica	strain=NIES-19	GCA_002367955.1	1165	1165	type	True	75.74	128	1815	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:31:22,396] [INFO] DFAST Taxonomy check result was written to GCF_015207655.1_ASM1520765v1_genomic.fna/tc_result.tsv
[2024-01-24 11:31:22,396] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:31:22,396] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:31:22,396] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8cbbcbf6-5683-4457-8a3f-5e4fd2980ccf/dqc_reference/checkm_data
[2024-01-24 11:31:22,397] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:31:22,450] [INFO] Task started: CheckM
[2024-01-24 11:31:22,451] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015207655.1_ASM1520765v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015207655.1_ASM1520765v1_genomic.fna/checkm_input GCF_015207655.1_ASM1520765v1_genomic.fna/checkm_result
[2024-01-24 11:31:59,901] [INFO] Task succeeded: CheckM
[2024-01-24 11:31:59,902] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:31:59,922] [INFO] ===== Completeness check finished =====
[2024-01-24 11:31:59,922] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:31:59,923] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015207655.1_ASM1520765v1_genomic.fna/markers.fasta)
[2024-01-24 11:31:59,923] [INFO] Task started: Blastn
[2024-01-24 11:31:59,923] [INFO] Running command: blastn -query GCF_015207655.1_ASM1520765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8cbbcbf6-5683-4457-8a3f-5e4fd2980ccf/dqc_reference/reference_markers_gtdb.fasta -out GCF_015207655.1_ASM1520765v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:32:00,637] [INFO] Task succeeded: Blastn
[2024-01-24 11:32:00,641] [INFO] Selected 6 target genomes.
[2024-01-24 11:32:00,642] [INFO] Target genome list was writen to GCF_015207655.1_ASM1520765v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:32:00,647] [INFO] Task started: fastANI
[2024-01-24 11:32:00,648] [INFO] Running command: fastANI --query /var/lib/cwl/stgd34c1355-45bc-4dbe-b81a-d4a102973121/GCF_015207655.1_ASM1520765v1_genomic.fna.gz --refList GCF_015207655.1_ASM1520765v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015207655.1_ASM1520765v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:32:09,312] [INFO] Task succeeded: fastANI
[2024-01-24 11:32:09,321] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:32:09,322] [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_015207655.1	s__Gloeocapsopsis crepidinum	100.0	1809	1815	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Chroococcidiopsidaceae;g__Gloeocapsopsis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002749975.1	s__Gloeocapsopsis sp002749975	94.3237	1597	1815	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Chroococcidiopsidaceae;g__Gloeocapsopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002964865.1	s__Gloeocapsopsis dulcis	88.1477	1344	1815	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Chroococcidiopsidaceae;g__Gloeocapsopsis	95.0	99.99	99.99	0.98	0.98	2	-
GCF_000317555.1	s__Chroogloeocystis sp000317555	84.2232	1389	1815	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Chroococcidiopsidaceae;g__Chroogloeocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001904655.1	s__Chroogloeocystis siderophila	83.7776	1262	1815	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Chroococcidiopsidaceae;g__Chroogloeocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002939305.1	s__Chroogloeocystis sp002939305	82.6136	1224	1815	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Chroococcidiopsidaceae;g__Chroogloeocystis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:32:09,323] [INFO] GTDB search result was written to GCF_015207655.1_ASM1520765v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:32:09,324] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:32:09,327] [INFO] DFAST_QC result json was written to GCF_015207655.1_ASM1520765v1_genomic.fna/dqc_result.json
[2024-01-24 11:32:09,327] [INFO] DFAST_QC completed!
[2024-01-24 11:32:09,327] [INFO] Total running time: 0h1m20s