[2024-01-24 13:27:57,942] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:57,944] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:57,944] [INFO] DQC Reference Directory: /var/lib/cwl/stg73818d03-7e6d-4228-a5e7-28cc64bf91f6/dqc_reference
[2024-01-24 13:27:59,189] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:59,190] [INFO] Task started: Prodigal
[2024-01-24 13:27:59,190] [INFO] Running command: gunzip -c /var/lib/cwl/stg53649a7f-a636-410a-9c80-947c8db51246/GCF_000317205.1_FisPCC7414_1.0_genomic.fna.gz | prodigal -d GCF_000317205.1_FisPCC7414_1.0_genomic.fna/cds.fna -a GCF_000317205.1_FisPCC7414_1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:12,862] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:12,862] [INFO] Task started: HMMsearch
[2024-01-24 13:28:12,863] [INFO] Running command: hmmsearch --tblout GCF_000317205.1_FisPCC7414_1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg73818d03-7e6d-4228-a5e7-28cc64bf91f6/dqc_reference/reference_markers.hmm GCF_000317205.1_FisPCC7414_1.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:13,221] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:13,222] [INFO] Found 6/6 markers.
[2024-01-24 13:28:13,278] [INFO] Query marker FASTA was written to GCF_000317205.1_FisPCC7414_1.0_genomic.fna/markers.fasta
[2024-01-24 13:28:13,279] [INFO] Task started: Blastn
[2024-01-24 13:28:13,279] [INFO] Running command: blastn -query GCF_000317205.1_FisPCC7414_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg73818d03-7e6d-4228-a5e7-28cc64bf91f6/dqc_reference/reference_markers.fasta -out GCF_000317205.1_FisPCC7414_1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:13,904] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:13,912] [INFO] Selected 14 target genomes.
[2024-01-24 13:28:13,913] [INFO] Target genome list was writen to GCF_000317205.1_FisPCC7414_1.0_genomic.fna/target_genomes.txt
[2024-01-24 13:28:13,927] [INFO] Task started: fastANI
[2024-01-24 13:28:13,927] [INFO] Running command: fastANI --query /var/lib/cwl/stg53649a7f-a636-410a-9c80-947c8db51246/GCF_000317205.1_FisPCC7414_1.0_genomic.fna.gz --refList GCF_000317205.1_FisPCC7414_1.0_genomic.fna/target_genomes.txt --output GCF_000317205.1_FisPCC7414_1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:39,102] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:39,103] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg73818d03-7e6d-4228-a5e7-28cc64bf91f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:39,103] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg73818d03-7e6d-4228-a5e7-28cc64bf91f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:39,115] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:39,115] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:39,115] [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
Fischerella muscicola	strain=PCC 7414	GCA_000317205.1	92938	92938	type	True	100.0	2179	2185	95	conclusive
Fischerella thermalis	strain=PCC 7521	GCA_000317225.1	372787	372787	type	True	93.1717	1559	2185	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_000317285.1	1124	1124	type	True	79.3742	1097	2185	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_003990575.1	1124	1124	type	True	79.3182	1109	2185	95	below_threshold
Nostoc favosum	strain=CHAB 5714	GCA_020829495.1	2907819	2907819	type	True	77.7364	648	2185	95	below_threshold
Brasilonema bromeliae	strain=SPC951	GCA_012912135.1	383615	383615	type	True	77.3734	513	2185	95	below_threshold
Nostoc punctiforme	strain=ATCC 29133; PCC 73102	GCA_000020025.1	272131	272131	type	True	77.3515	620	2185	95	below_threshold
Iningainema tapete	strain=BLCC-T55	GCA_014698965.1	2806730	2806730	type	True	77.1488	572	2185	95	below_threshold
Aetokthonos hydrillicola	strain=CCALA 1050	GCA_017591665.1	1550245	1550245	type	True	76.8302	426	2185	95	below_threshold
Anabaena cylindrica	strain=NIES-19	GCA_002367955.1	1165	1165	type	True	76.7944	439	2185	95	below_threshold
Mastigocoleus testarum	strain=BC008	GCA_001456025.1	996925	996925	type	True	76.1915	283	2185	95	below_threshold
Gloeothece citriformis	strain=PCC 7424	GCA_000021825.1	2546356	2546356	type	True	75.414	95	2185	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:39,117] [INFO] DFAST Taxonomy check result was written to GCF_000317205.1_FisPCC7414_1.0_genomic.fna/tc_result.tsv
[2024-01-24 13:28:39,118] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:39,118] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:39,118] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg73818d03-7e6d-4228-a5e7-28cc64bf91f6/dqc_reference/checkm_data
[2024-01-24 13:28:39,120] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:39,199] [INFO] Task started: CheckM
[2024-01-24 13:28:39,199] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000317205.1_FisPCC7414_1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000317205.1_FisPCC7414_1.0_genomic.fna/checkm_input GCF_000317205.1_FisPCC7414_1.0_genomic.fna/checkm_result
[2024-01-24 13:29:24,446] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:24,447] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:24,470] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:24,470] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:24,471] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000317205.1_FisPCC7414_1.0_genomic.fna/markers.fasta)
[2024-01-24 13:29:24,471] [INFO] Task started: Blastn
[2024-01-24 13:29:24,471] [INFO] Running command: blastn -query GCF_000317205.1_FisPCC7414_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg73818d03-7e6d-4228-a5e7-28cc64bf91f6/dqc_reference/reference_markers_gtdb.fasta -out GCF_000317205.1_FisPCC7414_1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:25,275] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:25,278] [INFO] Selected 7 target genomes.
[2024-01-24 13:29:25,278] [INFO] Target genome list was writen to GCF_000317205.1_FisPCC7414_1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:25,285] [INFO] Task started: fastANI
[2024-01-24 13:29:25,285] [INFO] Running command: fastANI --query /var/lib/cwl/stg53649a7f-a636-410a-9c80-947c8db51246/GCF_000317205.1_FisPCC7414_1.0_genomic.fna.gz --refList GCF_000317205.1_FisPCC7414_1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000317205.1_FisPCC7414_1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:43,994] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:44,001] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:44,001] [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_000317205.1	s__Fischerella muscicola	100.0	2179	2185	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Fischerella	95.0	99.84	99.68	0.97	0.95	3	conclusive
GCF_000317225.1	s__Fischerella thermalis	93.165	1561	2185	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Fischerella	95.0	98.97	96.56	0.93	0.78	35	-
GCF_000317245.1	s__Fischerella muscicola_A	86.3723	1541	2185	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Fischerella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002368315.1	s__Fischerella sp002368315	85.9614	1551	2185	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Fischerella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004323185.1	s__Fischerella prolifica	85.5752	1593	2185	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Fischerella	95.0	97.11	96.24	0.86	0.82	3	-
GCF_000447295.1	s__Fischerella sp000447295	85.3966	1554	2185	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Fischerella	95.0	97.38	97.38	0.86	0.86	2	-
GCF_000517105.1	s__Fischerella sp000517105	81.3427	1389	2185	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Fischerella	95.0	97.28	97.28	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:44,003] [INFO] GTDB search result was written to GCF_000317205.1_FisPCC7414_1.0_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:44,004] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:44,006] [INFO] DFAST_QC result json was written to GCF_000317205.1_FisPCC7414_1.0_genomic.fna/dqc_result.json
[2024-01-24 13:29:44,006] [INFO] DFAST_QC completed!
[2024-01-24 13:29:44,006] [INFO] Total running time: 0h1m46s