[2023-06-30 10:00:25,532] [INFO] DFAST_QC pipeline started.
[2023-06-30 10:00:25,534] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 10:00:25,535] [INFO] DQC Reference Directory: /var/lib/cwl/stge9d4177d-a4b0-448a-85bb-49fe69bce5d2/dqc_reference
[2023-06-30 10:00:27,843] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 10:00:27,844] [INFO] Task started: Prodigal
[2023-06-30 10:00:27,844] [INFO] Running command: gunzip -c /var/lib/cwl/stg91cf1ce1-ddd1-4aff-bd85-15746b82e7f3/GCA_007095795.1_ASM709579v1_genomic.fna.gz | prodigal -d GCA_007095795.1_ASM709579v1_genomic.fna/cds.fna -a GCA_007095795.1_ASM709579v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 10:00:35,832] [INFO] Task succeeded: Prodigal
[2023-06-30 10:00:35,833] [INFO] Task started: HMMsearch
[2023-06-30 10:00:35,834] [INFO] Running command: hmmsearch --tblout GCA_007095795.1_ASM709579v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9d4177d-a4b0-448a-85bb-49fe69bce5d2/dqc_reference/reference_markers.hmm GCA_007095795.1_ASM709579v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 10:00:36,142] [INFO] Task succeeded: HMMsearch
[2023-06-30 10:00:36,144] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg91cf1ce1-ddd1-4aff-bd85-15746b82e7f3/GCA_007095795.1_ASM709579v1_genomic.fna.gz]
[2023-06-30 10:00:36,184] [INFO] Query marker FASTA was written to GCA_007095795.1_ASM709579v1_genomic.fna/markers.fasta
[2023-06-30 10:00:36,184] [INFO] Task started: Blastn
[2023-06-30 10:00:36,185] [INFO] Running command: blastn -query GCA_007095795.1_ASM709579v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9d4177d-a4b0-448a-85bb-49fe69bce5d2/dqc_reference/reference_markers.fasta -out GCA_007095795.1_ASM709579v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:00:36,761] [INFO] Task succeeded: Blastn
[2023-06-30 10:00:36,766] [INFO] Selected 18 target genomes.
[2023-06-30 10:00:36,766] [INFO] Target genome list was writen to GCA_007095795.1_ASM709579v1_genomic.fna/target_genomes.txt
[2023-06-30 10:00:36,790] [INFO] Task started: fastANI
[2023-06-30 10:00:36,791] [INFO] Running command: fastANI --query /var/lib/cwl/stg91cf1ce1-ddd1-4aff-bd85-15746b82e7f3/GCA_007095795.1_ASM709579v1_genomic.fna.gz --refList GCA_007095795.1_ASM709579v1_genomic.fna/target_genomes.txt --output GCA_007095795.1_ASM709579v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 10:00:56,893] [INFO] Task succeeded: fastANI
[2023-06-30 10:00:56,893] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge9d4177d-a4b0-448a-85bb-49fe69bce5d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 10:00:56,894] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge9d4177d-a4b0-448a-85bb-49fe69bce5d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 10:00:56,906] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 10:00:56,906] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 10:00:56,906] [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	93.4211	1164	1421	95	below_threshold
Anabaena cylindrica	strain=PCC 7122	GCA_000317695.1	1165	1165	type	True	76.2775	59	1421	95	below_threshold
Anabaena cylindrica	strain=NIES-19	GCA_002367955.1	1165	1165	type	True	76.2323	60	1421	95	below_threshold
Crocosphaera watsonii	strain=WH 8501	GCA_000167195.1	263511	263511	suspected-type	True	76.0949	96	1421	95	below_threshold
Gloeothece citriformis	strain=PCC 7424	GCA_000021825.1	2546356	2546356	type	True	75.8987	150	1421	95	below_threshold
Crocosphaera chwakensis	strain=CCY0110	GCA_000169335.1	2546361	2546361	type	True	75.837	84	1421	95	below_threshold
Crocosphaera subtropica	strain=ATCC 51142	GCA_000017845.1	2546360	2546360	type	True	75.815	101	1421	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 10:00:56,908] [INFO] DFAST Taxonomy check result was written to GCA_007095795.1_ASM709579v1_genomic.fna/tc_result.tsv
[2023-06-30 10:00:56,909] [INFO] ===== Taxonomy check completed =====
[2023-06-30 10:00:56,909] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 10:00:56,910] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9d4177d-a4b0-448a-85bb-49fe69bce5d2/dqc_reference/checkm_data
[2023-06-30 10:00:56,912] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 10:00:57,037] [INFO] Task started: CheckM
[2023-06-30 10:00:57,037] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_007095795.1_ASM709579v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_007095795.1_ASM709579v1_genomic.fna/checkm_input GCA_007095795.1_ASM709579v1_genomic.fna/checkm_result
[2023-06-30 10:01:26,404] [INFO] Task succeeded: CheckM
[2023-06-30 10:01:26,406] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 10:01:26,430] [INFO] ===== Completeness check finished =====
[2023-06-30 10:01:26,431] [INFO] ===== Start GTDB Search =====
[2023-06-30 10:01:26,431] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_007095795.1_ASM709579v1_genomic.fna/markers.fasta)
[2023-06-30 10:01:26,432] [INFO] Task started: Blastn
[2023-06-30 10:01:26,432] [INFO] Running command: blastn -query GCA_007095795.1_ASM709579v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9d4177d-a4b0-448a-85bb-49fe69bce5d2/dqc_reference/reference_markers_gtdb.fasta -out GCA_007095795.1_ASM709579v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:01:27,198] [INFO] Task succeeded: Blastn
[2023-06-30 10:01:27,204] [INFO] Selected 11 target genomes.
[2023-06-30 10:01:27,204] [INFO] Target genome list was writen to GCA_007095795.1_ASM709579v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 10:01:27,245] [INFO] Task started: fastANI
[2023-06-30 10:01:27,246] [INFO] Running command: fastANI --query /var/lib/cwl/stg91cf1ce1-ddd1-4aff-bd85-15746b82e7f3/GCA_007095795.1_ASM709579v1_genomic.fna.gz --refList GCA_007095795.1_ASM709579v1_genomic.fna/target_genomes_gtdb.txt --output GCA_007095795.1_ASM709579v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 10:02:10,252] [INFO] Task succeeded: fastANI
[2023-06-30 10:02:10,271] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 10:02:10,272] [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_007095845.1	s__Microcystis aeruginosa_D	99.9743	1391	1421	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	97.82	95.43	0.91	0.87	4	conclusive
GCF_015206885.1	s__Microcystis aeruginosa_H	94.5758	1032	1421	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	96.01	95.58	0.82	0.79	5	-
GCA_001264245.1	s__Microcystis panniformis_A	94.1386	1185	1421	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.1724	97.17	95.58	0.90	0.80	10	-
GCF_014698335.1	s__Microcystis panniformis	94.09	1130	1421	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	96.86	95.11	0.85	0.80	40	-
GCF_014696875.1	s__Microcystis wesenbergii	93.8805	1109	1421	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	95.96	95.05	0.84	0.80	19	-
GCA_007095785.1	s__Microcystis aeruginosa_E	93.8802	1053	1421	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	95.56	95.56	0.81	0.81	2	-
GCA_009995705.1	s__Microcystis aeruginosa_F	93.7912	1099	1421	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000297435.1	s__Microcystis sp000297435	93.6575	1019	1421	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	97.53	95.21	0.88	0.79	9	-
GCF_008974145.1	s__Microcystis aeruginosa_G	93.6539	1014	1421	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000010625.1	s__Microcystis aeruginosa	93.4392	1162	1421	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.1724	96.68	95.93	0.87	0.77	17	-
GCF_009792235.1	s__Microcystis viridis	93.3567	1158	1421	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	98.29	98.28	0.94	0.93	6	-
--------------------------------------------------------------------------------
[2023-06-30 10:02:10,274] [INFO] GTDB search result was written to GCA_007095795.1_ASM709579v1_genomic.fna/result_gtdb.tsv
[2023-06-30 10:02:10,275] [INFO] ===== GTDB Search completed =====
[2023-06-30 10:02:10,279] [INFO] DFAST_QC result json was written to GCA_007095795.1_ASM709579v1_genomic.fna/dqc_result.json
[2023-06-30 10:02:10,280] [INFO] DFAST_QC completed!
[2023-06-30 10:02:10,280] [INFO] Total running time: 0h1m45s