[2023-06-28 19:09:20,845] [INFO] DFAST_QC pipeline started.
[2023-06-28 19:09:20,848] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 19:09:20,848] [INFO] DQC Reference Directory: /var/lib/cwl/stg3252d809-8b6d-45ca-bc2d-03c6d1778b72/dqc_reference
[2023-06-28 19:09:22,074] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 19:09:22,075] [INFO] Task started: Prodigal
[2023-06-28 19:09:22,076] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8a26b72-81c7-4636-a95c-62cd3eef1960/GCA_020246205.1_ASM2024620v1_genomic.fna.gz | prodigal -d GCA_020246205.1_ASM2024620v1_genomic.fna/cds.fna -a GCA_020246205.1_ASM2024620v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 19:09:30,065] [INFO] Task succeeded: Prodigal
[2023-06-28 19:09:30,066] [INFO] Task started: HMMsearch
[2023-06-28 19:09:30,066] [INFO] Running command: hmmsearch --tblout GCA_020246205.1_ASM2024620v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3252d809-8b6d-45ca-bc2d-03c6d1778b72/dqc_reference/reference_markers.hmm GCA_020246205.1_ASM2024620v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 19:09:30,402] [INFO] Task succeeded: HMMsearch
[2023-06-28 19:09:30,404] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf8a26b72-81c7-4636-a95c-62cd3eef1960/GCA_020246205.1_ASM2024620v1_genomic.fna.gz]
[2023-06-28 19:09:30,443] [INFO] Query marker FASTA was written to GCA_020246205.1_ASM2024620v1_genomic.fna/markers.fasta
[2023-06-28 19:09:30,443] [INFO] Task started: Blastn
[2023-06-28 19:09:30,443] [INFO] Running command: blastn -query GCA_020246205.1_ASM2024620v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3252d809-8b6d-45ca-bc2d-03c6d1778b72/dqc_reference/reference_markers.fasta -out GCA_020246205.1_ASM2024620v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:09:31,015] [INFO] Task succeeded: Blastn
[2023-06-28 19:09:31,019] [INFO] Selected 18 target genomes.
[2023-06-28 19:09:31,020] [INFO] Target genome list was writen to GCA_020246205.1_ASM2024620v1_genomic.fna/target_genomes.txt
[2023-06-28 19:09:31,021] [INFO] Task started: fastANI
[2023-06-28 19:09:31,022] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8a26b72-81c7-4636-a95c-62cd3eef1960/GCA_020246205.1_ASM2024620v1_genomic.fna.gz --refList GCA_020246205.1_ASM2024620v1_genomic.fna/target_genomes.txt --output GCA_020246205.1_ASM2024620v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 19:09:53,909] [INFO] Task succeeded: fastANI
[2023-06-28 19:09:53,909] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3252d809-8b6d-45ca-bc2d-03c6d1778b72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 19:09:53,910] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3252d809-8b6d-45ca-bc2d-03c6d1778b72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 19:09:53,917] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 19:09:53,917] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 19:09:53,917] [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	94.8006	1220	1437	95	below_threshold
Cylindrospermopsis raciborskii	strain=Cr2010	GCA_003367075.2	77022	77022	reftype	True	76.7017	53	1437	95	below_threshold
Gloeothece verrucosa	strain=PCC 7822	GCA_000147335.1	2546359	2546359	type	True	76.3237	117	1437	95	below_threshold
Rippkaea orientalis	strain=PCC 8801	GCA_000021805.1	2546366	2546366	type	True	76.1404	154	1437	95	below_threshold
Gloeothece citriformis	strain=PCC 7424	GCA_000021825.1	2546356	2546356	type	True	75.9876	147	1437	95	below_threshold
Crocosphaera watsonii	strain=WH 8501	GCA_000167195.1	263511	263511	suspected-type	True	75.8969	77	1437	95	below_threshold
Planktothrix tepida	strain=PCC9214	GCA_904830955.1	1678309	1678309	type	True	75.7941	84	1437	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 19:09:53,919] [INFO] DFAST Taxonomy check result was written to GCA_020246205.1_ASM2024620v1_genomic.fna/tc_result.tsv
[2023-06-28 19:09:53,920] [INFO] ===== Taxonomy check completed =====
[2023-06-28 19:09:53,920] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 19:09:53,920] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3252d809-8b6d-45ca-bc2d-03c6d1778b72/dqc_reference/checkm_data
[2023-06-28 19:09:53,921] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 19:09:53,970] [INFO] Task started: CheckM
[2023-06-28 19:09:53,970] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020246205.1_ASM2024620v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020246205.1_ASM2024620v1_genomic.fna/checkm_input GCA_020246205.1_ASM2024620v1_genomic.fna/checkm_result
[2023-06-28 19:10:23,181] [INFO] Task succeeded: CheckM
[2023-06-28 19:10:23,182] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 19:10:23,207] [INFO] ===== Completeness check finished =====
[2023-06-28 19:10:23,207] [INFO] ===== Start GTDB Search =====
[2023-06-28 19:10:23,207] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020246205.1_ASM2024620v1_genomic.fna/markers.fasta)
[2023-06-28 19:10:23,208] [INFO] Task started: Blastn
[2023-06-28 19:10:23,208] [INFO] Running command: blastn -query GCA_020246205.1_ASM2024620v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3252d809-8b6d-45ca-bc2d-03c6d1778b72/dqc_reference/reference_markers_gtdb.fasta -out GCA_020246205.1_ASM2024620v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:10:23,915] [INFO] Task succeeded: Blastn
[2023-06-28 19:10:23,919] [INFO] Selected 11 target genomes.
[2023-06-28 19:10:23,919] [INFO] Target genome list was writen to GCA_020246205.1_ASM2024620v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 19:10:23,920] [INFO] Task started: fastANI
[2023-06-28 19:10:23,920] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8a26b72-81c7-4636-a95c-62cd3eef1960/GCA_020246205.1_ASM2024620v1_genomic.fna.gz --refList GCA_020246205.1_ASM2024620v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020246205.1_ASM2024620v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 19:11:08,644] [INFO] Task succeeded: fastANI
[2023-06-28 19:11:08,660] [INFO] Found 11 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-28 19:11:08,660] [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_000981785.2	s__Microcystis aeruginosa_C	95.7433	1155	1437	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	96.68	95.42	0.84	0.80	15	inconclusive
GCF_014698335.1	s__Microcystis panniformis	95.0494	1167	1437	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	96.86	95.11	0.85	0.80	40	inconclusive
GCF_000297435.1	s__Microcystis sp000297435	94.9788	1048	1437	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	97.53	95.21	0.88	0.79	9	-
GCF_000010625.1	s__Microcystis aeruginosa	94.8101	1219	1437	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.1724	96.68	95.93	0.87	0.77	17	-
GCF_014696875.1	s__Microcystis wesenbergii	94.5585	1107	1437	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	95.96	95.05	0.84	0.80	19	-
GCA_001264245.1	s__Microcystis panniformis_A	94.4207	1219	1437	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.1724	97.17	95.58	0.90	0.80	10	-
GCF_015206885.1	s__Microcystis aeruginosa_H	94.3767	1075	1437	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	96.01	95.58	0.82	0.79	5	-
GCA_007095785.1	s__Microcystis aeruginosa_E	94.16	1091	1437	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	95.56	95.56	0.81	0.81	2	-
GCA_002282935.1	s__Microcystis sp002282935	94.0886	978	1437	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	97.42	97.13	0.79	0.76	36	-
GCF_008974145.1	s__Microcystis aeruginosa_G	94.0667	1038	1437	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	93.5599	1180	1437	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	98.29	98.28	0.94	0.93	6	-
--------------------------------------------------------------------------------
[2023-06-28 19:11:08,663] [INFO] GTDB search result was written to GCA_020246205.1_ASM2024620v1_genomic.fna/result_gtdb.tsv
[2023-06-28 19:11:08,663] [INFO] ===== GTDB Search completed =====
[2023-06-28 19:11:08,667] [INFO] DFAST_QC result json was written to GCA_020246205.1_ASM2024620v1_genomic.fna/dqc_result.json
[2023-06-28 19:11:08,667] [INFO] DFAST_QC completed!
[2023-06-28 19:11:08,667] [INFO] Total running time: 0h1m48s