[2023-06-17 04:57:19,141] [INFO] DFAST_QC pipeline started.
[2023-06-17 04:57:19,146] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 04:57:19,146] [INFO] DQC Reference Directory: /var/lib/cwl/stg38c3c92f-69ea-44c1-b830-1ff903707fb7/dqc_reference
[2023-06-17 04:57:20,493] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 04:57:20,494] [INFO] Task started: Prodigal
[2023-06-17 04:57:20,494] [INFO] Running command: gunzip -c /var/lib/cwl/stg668e7490-e913-452f-aab2-55c1ee3eb649/GCA_009995685.1_ASM999568v1_genomic.fna.gz | prodigal -d GCA_009995685.1_ASM999568v1_genomic.fna/cds.fna -a GCA_009995685.1_ASM999568v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 04:57:28,535] [INFO] Task succeeded: Prodigal
[2023-06-17 04:57:28,536] [INFO] Task started: HMMsearch
[2023-06-17 04:57:28,536] [INFO] Running command: hmmsearch --tblout GCA_009995685.1_ASM999568v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg38c3c92f-69ea-44c1-b830-1ff903707fb7/dqc_reference/reference_markers.hmm GCA_009995685.1_ASM999568v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 04:57:28,875] [INFO] Task succeeded: HMMsearch
[2023-06-17 04:57:28,878] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg668e7490-e913-452f-aab2-55c1ee3eb649/GCA_009995685.1_ASM999568v1_genomic.fna.gz]
[2023-06-17 04:57:28,922] [INFO] Query marker FASTA was written to GCA_009995685.1_ASM999568v1_genomic.fna/markers.fasta
[2023-06-17 04:57:28,923] [INFO] Task started: Blastn
[2023-06-17 04:57:28,923] [INFO] Running command: blastn -query GCA_009995685.1_ASM999568v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38c3c92f-69ea-44c1-b830-1ff903707fb7/dqc_reference/reference_markers.fasta -out GCA_009995685.1_ASM999568v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 04:57:29,521] [INFO] Task succeeded: Blastn
[2023-06-17 04:57:29,526] [INFO] Selected 17 target genomes.
[2023-06-17 04:57:29,527] [INFO] Target genome list was writen to GCA_009995685.1_ASM999568v1_genomic.fna/target_genomes.txt
[2023-06-17 04:57:29,536] [INFO] Task started: fastANI
[2023-06-17 04:57:29,536] [INFO] Running command: fastANI --query /var/lib/cwl/stg668e7490-e913-452f-aab2-55c1ee3eb649/GCA_009995685.1_ASM999568v1_genomic.fna.gz --refList GCA_009995685.1_ASM999568v1_genomic.fna/target_genomes.txt --output GCA_009995685.1_ASM999568v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 04:57:48,754] [INFO] Task succeeded: fastANI
[2023-06-17 04:57:48,755] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg38c3c92f-69ea-44c1-b830-1ff903707fb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 04:57:48,755] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg38c3c92f-69ea-44c1-b830-1ff903707fb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 04:57:48,762] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 04:57:48,762] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 04:57:48,762] [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	94.8885	1181	1349	95	below_threshold
Anabaena cylindrica	strain=NIES-19	GCA_002367955.1	1165	1165	type	True	76.0648	62	1349	95	below_threshold
Gloeothece citriformis	strain=PCC 7424	GCA_000021825.1	2546356	2546356	type	True	75.7711	122	1349	95	below_threshold
Rippkaea orientalis	strain=PCC 8801	GCA_000021805.1	2546366	2546366	type	True	75.615	129	1349	95	below_threshold
Planktothrix tepida	strain=PCC9214	GCA_904830955.1	1678309	1678309	type	True	75.5956	81	1349	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 04:57:48,764] [INFO] DFAST Taxonomy check result was written to GCA_009995685.1_ASM999568v1_genomic.fna/tc_result.tsv
[2023-06-17 04:57:48,765] [INFO] ===== Taxonomy check completed =====
[2023-06-17 04:57:48,765] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 04:57:48,765] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg38c3c92f-69ea-44c1-b830-1ff903707fb7/dqc_reference/checkm_data
[2023-06-17 04:57:48,766] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 04:57:48,817] [INFO] Task started: CheckM
[2023-06-17 04:57:48,817] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009995685.1_ASM999568v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009995685.1_ASM999568v1_genomic.fna/checkm_input GCA_009995685.1_ASM999568v1_genomic.fna/checkm_result
[2023-06-17 04:58:18,494] [INFO] Task succeeded: CheckM
[2023-06-17 04:58:18,496] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 04:58:18,532] [INFO] ===== Completeness check finished =====
[2023-06-17 04:58:18,532] [INFO] ===== Start GTDB Search =====
[2023-06-17 04:58:18,533] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009995685.1_ASM999568v1_genomic.fna/markers.fasta)
[2023-06-17 04:58:18,533] [INFO] Task started: Blastn
[2023-06-17 04:58:18,533] [INFO] Running command: blastn -query GCA_009995685.1_ASM999568v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38c3c92f-69ea-44c1-b830-1ff903707fb7/dqc_reference/reference_markers_gtdb.fasta -out GCA_009995685.1_ASM999568v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 04:58:19,328] [INFO] Task succeeded: Blastn
[2023-06-17 04:58:19,333] [INFO] Selected 11 target genomes.
[2023-06-17 04:58:19,333] [INFO] Target genome list was writen to GCA_009995685.1_ASM999568v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 04:58:19,336] [INFO] Task started: fastANI
[2023-06-17 04:58:19,336] [INFO] Running command: fastANI --query /var/lib/cwl/stg668e7490-e913-452f-aab2-55c1ee3eb649/GCA_009995685.1_ASM999568v1_genomic.fna.gz --refList GCA_009995685.1_ASM999568v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009995685.1_ASM999568v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 04:58:59,994] [INFO] Task succeeded: fastANI
[2023-06-17 04:59:00,017] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 04:59:00,017] [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
GCA_002282935.1	s__Microcystis sp002282935	97.2005	995	1349	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	97.42	97.13	0.79	0.76	36	conclusive
GCF_000010625.1	s__Microcystis aeruginosa	94.8779	1182	1349	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.1724	96.68	95.93	0.87	0.77	17	-
GCA_007095785.1	s__Microcystis aeruginosa_E	94.68	1060	1349	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	95.56	95.56	0.81	0.81	2	-
GCF_009792235.1	s__Microcystis viridis	94.5069	1129	1349	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	98.29	98.28	0.94	0.93	6	-
GCA_001264245.1	s__Microcystis panniformis_A	94.3079	1174	1349	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.1724	97.17	95.58	0.90	0.80	10	-
GCF_014696875.1	s__Microcystis wesenbergii	94.044	1043	1349	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	95.96	95.05	0.84	0.80	19	-
GCF_000297435.1	s__Microcystis sp000297435	93.8475	1007	1349	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	97.53	95.21	0.88	0.79	9	-
GCF_014698335.1	s__Microcystis panniformis	93.7167	1045	1349	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	93.6649	1027	1349	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	96.68	95.42	0.84	0.80	15	-
GCF_015206885.1	s__Microcystis aeruginosa_H	93.4216	949	1349	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	96.01	95.58	0.82	0.79	5	-
GCA_007095845.1	s__Microcystis aeruginosa_D	93.1006	1013	1349	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	97.82	95.43	0.91	0.87	4	-
--------------------------------------------------------------------------------
[2023-06-17 04:59:00,019] [INFO] GTDB search result was written to GCA_009995685.1_ASM999568v1_genomic.fna/result_gtdb.tsv
[2023-06-17 04:59:00,020] [INFO] ===== GTDB Search completed =====
[2023-06-17 04:59:00,023] [INFO] DFAST_QC result json was written to GCA_009995685.1_ASM999568v1_genomic.fna/dqc_result.json
[2023-06-17 04:59:00,023] [INFO] DFAST_QC completed!
[2023-06-17 04:59:00,023] [INFO] Total running time: 0h1m41s