[2023-06-17 04:33:34,172] [INFO] DFAST_QC pipeline started.
[2023-06-17 04:33:34,174] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 04:33:34,174] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d140af0-c42b-4c8a-a040-e53cb11c30fc/dqc_reference
[2023-06-17 04:33:37,143] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 04:33:37,144] [INFO] Task started: Prodigal
[2023-06-17 04:33:37,144] [INFO] Running command: gunzip -c /var/lib/cwl/stg6cfc84ae-ddb4-401d-8edf-5289a97e4605/GCA_003389435.1_ASM338943v1_genomic.fna.gz | prodigal -d GCA_003389435.1_ASM338943v1_genomic.fna/cds.fna -a GCA_003389435.1_ASM338943v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 04:33:46,594] [INFO] Task succeeded: Prodigal
[2023-06-17 04:33:46,595] [INFO] Task started: HMMsearch
[2023-06-17 04:33:46,595] [INFO] Running command: hmmsearch --tblout GCA_003389435.1_ASM338943v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d140af0-c42b-4c8a-a040-e53cb11c30fc/dqc_reference/reference_markers.hmm GCA_003389435.1_ASM338943v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 04:33:46,987] [INFO] Task succeeded: HMMsearch
[2023-06-17 04:33:46,989] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6cfc84ae-ddb4-401d-8edf-5289a97e4605/GCA_003389435.1_ASM338943v1_genomic.fna.gz]
[2023-06-17 04:33:47,038] [INFO] Query marker FASTA was written to GCA_003389435.1_ASM338943v1_genomic.fna/markers.fasta
[2023-06-17 04:33:47,038] [INFO] Task started: Blastn
[2023-06-17 04:33:47,038] [INFO] Running command: blastn -query GCA_003389435.1_ASM338943v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d140af0-c42b-4c8a-a040-e53cb11c30fc/dqc_reference/reference_markers.fasta -out GCA_003389435.1_ASM338943v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 04:33:47,632] [INFO] Task succeeded: Blastn
[2023-06-17 04:33:47,636] [INFO] Selected 17 target genomes.
[2023-06-17 04:33:47,637] [INFO] Target genome list was writen to GCA_003389435.1_ASM338943v1_genomic.fna/target_genomes.txt
[2023-06-17 04:33:47,679] [INFO] Task started: fastANI
[2023-06-17 04:33:47,679] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cfc84ae-ddb4-401d-8edf-5289a97e4605/GCA_003389435.1_ASM338943v1_genomic.fna.gz --refList GCA_003389435.1_ASM338943v1_genomic.fna/target_genomes.txt --output GCA_003389435.1_ASM338943v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 04:34:13,908] [INFO] Task succeeded: fastANI
[2023-06-17 04:34:13,909] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d140af0-c42b-4c8a-a040-e53cb11c30fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 04:34:13,909] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d140af0-c42b-4c8a-a040-e53cb11c30fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 04:34:13,918] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2023-06-17 04:34:13,918] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-17 04:34:13,918] [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
Microcystis aeruginosa	strain=NIES-843	GCA_000010625.1	1126	1126	suspected-type	True	97.551	1374	1598	95	conclusive
Gloeothece verrucosa	strain=PCC 7822	GCA_000147335.1	2546359	2546359	type	True	76.6146	127	1598	95	below_threshold
Rippkaea orientalis	strain=PCC 8801	GCA_000021805.1	2546366	2546366	type	True	76.2507	140	1598	95	below_threshold
Crocosphaera watsonii	strain=WH 8501	GCA_000167195.1	263511	263511	suspected-type	True	76.1174	88	1598	95	below_threshold
Crocosphaera subtropica	strain=ATCC 51142	GCA_000017845.1	2546360	2546360	type	True	76.095	88	1598	95	below_threshold
Gloeothece citriformis	strain=PCC 7424	GCA_000021825.1	2546356	2546356	type	True	75.9896	141	1598	95	below_threshold
Planktothrix tepida	strain=PCC9214	GCA_904830955.1	1678309	1678309	type	True	75.9391	98	1598	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 04:34:13,920] [INFO] DFAST Taxonomy check result was written to GCA_003389435.1_ASM338943v1_genomic.fna/tc_result.tsv
[2023-06-17 04:34:13,921] [INFO] ===== Taxonomy check completed =====
[2023-06-17 04:34:13,921] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 04:34:13,921] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d140af0-c42b-4c8a-a040-e53cb11c30fc/dqc_reference/checkm_data
[2023-06-17 04:34:13,923] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 04:34:13,977] [INFO] Task started: CheckM
[2023-06-17 04:34:13,978] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003389435.1_ASM338943v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003389435.1_ASM338943v1_genomic.fna/checkm_input GCA_003389435.1_ASM338943v1_genomic.fna/checkm_result
[2023-06-17 04:34:46,497] [INFO] Task succeeded: CheckM
[2023-06-17 04:34:46,499] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 04:34:46,548] [INFO] ===== Completeness check finished =====
[2023-06-17 04:34:46,548] [INFO] ===== Start GTDB Search =====
[2023-06-17 04:34:46,549] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003389435.1_ASM338943v1_genomic.fna/markers.fasta)
[2023-06-17 04:34:46,549] [INFO] Task started: Blastn
[2023-06-17 04:34:46,549] [INFO] Running command: blastn -query GCA_003389435.1_ASM338943v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d140af0-c42b-4c8a-a040-e53cb11c30fc/dqc_reference/reference_markers_gtdb.fasta -out GCA_003389435.1_ASM338943v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 04:34:47,335] [INFO] Task succeeded: Blastn
[2023-06-17 04:34:47,340] [INFO] Selected 12 target genomes.
[2023-06-17 04:34:47,340] [INFO] Target genome list was writen to GCA_003389435.1_ASM338943v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 04:34:47,342] [INFO] Task started: fastANI
[2023-06-17 04:34:47,342] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cfc84ae-ddb4-401d-8edf-5289a97e4605/GCA_003389435.1_ASM338943v1_genomic.fna.gz --refList GCA_003389435.1_ASM338943v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003389435.1_ASM338943v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 04:35:43,484] [INFO] Task succeeded: fastANI
[2023-06-17 04:35:43,505] [INFO] Found 12 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-17 04:35:43,506] [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_000010625.1	s__Microcystis aeruginosa	97.5745	1370	1598	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.1724	96.68	95.93	0.87	0.77	17	inconclusive
GCA_001264245.1	s__Microcystis panniformis_A	95.3964	1335	1598	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.1724	97.17	95.58	0.90	0.80	10	inconclusive
GCF_014696875.1	s__Microcystis wesenbergii	94.8129	1159	1598	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	95.96	95.05	0.84	0.80	19	-
GCA_002282935.1	s__Microcystis sp002282935	94.7592	1009	1598	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	97.42	97.13	0.79	0.76	36	-
GCF_014698335.1	s__Microcystis panniformis	94.6826	1151	1598	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	96.86	95.11	0.85	0.80	40	-
GCF_000981785.2	s__Microcystis aeruginosa_C	94.6481	1135	1598	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	96.68	95.42	0.84	0.80	15	-
GCF_000297435.1	s__Microcystis sp000297435	94.6072	1065	1598	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	97.53	95.21	0.88	0.79	9	-
GCA_007095785.1	s__Microcystis aeruginosa_E	94.4207	1103	1598	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	95.56	95.56	0.81	0.81	2	-
GCF_008974145.1	s__Microcystis aeruginosa_G	94.0438	1027	1598	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009792235.1	s__Microcystis viridis	93.856	1226	1598	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	98.29	98.28	0.94	0.93	6	-
GCA_007095845.1	s__Microcystis aeruginosa_D	93.6101	1100	1598	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	97.82	95.43	0.91	0.87	4	-
GCA_009995705.1	s__Microcystis aeruginosa_F	93.3577	1109	1598	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 04:35:43,508] [INFO] GTDB search result was written to GCA_003389435.1_ASM338943v1_genomic.fna/result_gtdb.tsv
[2023-06-17 04:35:43,509] [INFO] ===== GTDB Search completed =====
[2023-06-17 04:35:43,514] [INFO] DFAST_QC result json was written to GCA_003389435.1_ASM338943v1_genomic.fna/dqc_result.json
[2023-06-17 04:35:43,515] [INFO] DFAST_QC completed!
[2023-06-17 04:35:43,515] [INFO] Total running time: 0h2m9s