[2024-01-25 20:17:05,678] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:17:05,681] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:17:05,681] [INFO] DQC Reference Directory: /var/lib/cwl/stgea9e9863-c560-4333-905c-2da76ab57b1e/dqc_reference
[2024-01-25 20:17:06,853] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:17:06,854] [INFO] Task started: Prodigal
[2024-01-25 20:17:06,854] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ecdfa00-2559-43fb-bda6-857e75f09bb0/GCF_000147335.1_ASM14733v1_genomic.fna.gz | prodigal -d GCF_000147335.1_ASM14733v1_genomic.fna/cds.fna -a GCF_000147335.1_ASM14733v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:17:20,060] [INFO] Task succeeded: Prodigal
[2024-01-25 20:17:20,061] [INFO] Task started: HMMsearch
[2024-01-25 20:17:20,061] [INFO] Running command: hmmsearch --tblout GCF_000147335.1_ASM14733v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea9e9863-c560-4333-905c-2da76ab57b1e/dqc_reference/reference_markers.hmm GCF_000147335.1_ASM14733v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:17:20,474] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:17:20,475] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3ecdfa00-2559-43fb-bda6-857e75f09bb0/GCF_000147335.1_ASM14733v1_genomic.fna.gz]
[2024-01-25 20:17:20,540] [INFO] Query marker FASTA was written to GCF_000147335.1_ASM14733v1_genomic.fna/markers.fasta
[2024-01-25 20:17:20,541] [INFO] Task started: Blastn
[2024-01-25 20:17:20,543] [INFO] Running command: blastn -query GCF_000147335.1_ASM14733v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea9e9863-c560-4333-905c-2da76ab57b1e/dqc_reference/reference_markers.fasta -out GCF_000147335.1_ASM14733v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:17:21,099] [INFO] Task succeeded: Blastn
[2024-01-25 20:17:21,101] [INFO] Selected 15 target genomes.
[2024-01-25 20:17:21,102] [INFO] Target genome list was writen to GCF_000147335.1_ASM14733v1_genomic.fna/target_genomes.txt
[2024-01-25 20:17:21,116] [INFO] Task started: fastANI
[2024-01-25 20:17:21,116] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ecdfa00-2559-43fb-bda6-857e75f09bb0/GCF_000147335.1_ASM14733v1_genomic.fna.gz --refList GCF_000147335.1_ASM14733v1_genomic.fna/target_genomes.txt --output GCF_000147335.1_ASM14733v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:17:36,216] [INFO] Task succeeded: fastANI
[2024-01-25 20:17:36,216] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea9e9863-c560-4333-905c-2da76ab57b1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:17:36,216] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea9e9863-c560-4333-905c-2da76ab57b1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:17:36,223] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:17:36,224] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:17:36,224] [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
Gloeothece verrucosa	strain=PCC 7822	GCA_000147335.1	2546359	2546359	type	True	100.0	2606	2610	95	conclusive
Gloeothece citriformis	strain=PCC 7424	GCA_000021825.1	2546356	2546356	type	True	79.7625	1152	2610	95	below_threshold
Euhalothece natronophila	strain=Z-M001	GCA_007904085.1	577489	577489	type	True	76.563	59	2610	95	below_threshold
Crocosphaera subtropica	strain=ATCC 51142	GCA_000017845.1	2546360	2546360	type	True	76.492	175	2610	95	below_threshold
Rippkaea orientalis	strain=PCC 8801	GCA_000021805.1	2546366	2546366	type	True	76.3177	206	2610	95	below_threshold
Nostoc punctiforme	strain=ATCC 29133; PCC 73102	GCA_000020025.1	272131	272131	type	True	76.1684	82	2610	95	below_threshold
Microcystis aeruginosa	strain=NIES-843	GCA_000010625.1	1126	1126	suspected-type	True	76.1234	141	2610	95	below_threshold
Fischerella thermalis	strain=PCC 7521	GCA_000317225.1	372787	372787	type	True	75.7295	58	2610	95	below_threshold
Gloeocapsopsis crepidinum	strain=LEGE 06123	GCA_015207655.1	693223	693223	type	True	75.6012	57	2610	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:17:36,225] [INFO] DFAST Taxonomy check result was written to GCF_000147335.1_ASM14733v1_genomic.fna/tc_result.tsv
[2024-01-25 20:17:36,226] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:17:36,226] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:17:36,226] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea9e9863-c560-4333-905c-2da76ab57b1e/dqc_reference/checkm_data
[2024-01-25 20:17:36,227] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:17:36,300] [INFO] Task started: CheckM
[2024-01-25 20:17:36,300] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000147335.1_ASM14733v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000147335.1_ASM14733v1_genomic.fna/checkm_input GCF_000147335.1_ASM14733v1_genomic.fna/checkm_result
[2024-01-25 20:18:18,274] [INFO] Task succeeded: CheckM
[2024-01-25 20:18:18,275] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:18:18,299] [INFO] ===== Completeness check finished =====
[2024-01-25 20:18:18,299] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:18:18,301] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000147335.1_ASM14733v1_genomic.fna/markers.fasta)
[2024-01-25 20:18:18,301] [INFO] Task started: Blastn
[2024-01-25 20:18:18,301] [INFO] Running command: blastn -query GCF_000147335.1_ASM14733v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea9e9863-c560-4333-905c-2da76ab57b1e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000147335.1_ASM14733v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:19,117] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:19,120] [INFO] Selected 21 target genomes.
[2024-01-25 20:18:19,120] [INFO] Target genome list was writen to GCF_000147335.1_ASM14733v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:18:19,147] [INFO] Task started: fastANI
[2024-01-25 20:18:19,147] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ecdfa00-2559-43fb-bda6-857e75f09bb0/GCF_000147335.1_ASM14733v1_genomic.fna.gz --refList GCF_000147335.1_ASM14733v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000147335.1_ASM14733v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:18:42,551] [INFO] Task succeeded: fastANI
[2024-01-25 20:18:42,564] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:18:42,564] [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_000147335.1	s__Gloeothece verrucosa	100.0	2606	2610	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Gloeothece	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000021825.1	s__Gloeothece citriformis	79.749	1152	2610	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Gloeothece	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000297435.1	s__Microcystis sp000297435	76.416	115	2610	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	97.53	95.21	0.88	0.79	9	-
GCF_000017845.1	s__Crocosphaera subtropica	76.4074	176	2610	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Crocosphaera	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000021805.1	s__Rippkaea orientalis	76.3804	206	2610	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Rippkaea	95.0	98.84	98.84	0.95	0.95	2	-
GCA_007095785.1	s__Microcystis aeruginosa_E	76.3411	135	2610	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	95.56	95.56	0.81	0.81	2	-
GCF_014698335.1	s__Microcystis panniformis	76.2074	126	2610	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	96.86	95.11	0.85	0.80	40	-
GCF_000010625.1	s__Microcystis aeruginosa	76.1433	138	2610	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.1724	96.68	95.93	0.87	0.77	17	-
GCF_003013815.1	s__Crocosphaera sp003013815	76.1328	201	2610	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Crocosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013393905.1	s__Nostoc sp013393905	76.1008	95	2610	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002218085.1	s__Hassallia sp002218085	76.0146	87	2610	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Hassallia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012031035.1	s__Hydrococcus sp012031035	76.0025	145	2610	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Hydrococcus	95.0	99.84	99.83	0.93	0.93	3	-
GCF_017312365.1	s__Chroococcus sp017312365	75.9926	179	2610	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Chroococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001890975.1	s__Roseofilum reptotaenium_A	75.906	65	2610	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Desertifilaceae;g__Roseofilum	95.0	97.72	97.70	0.90	0.89	3	-
GCF_014697125.1	s__Trichormus minutissima	75.8977	81	2610	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Trichormus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002368315.1	s__Fischerella sp002368315	75.8652	96	2610	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Fischerella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001276715.1	s__Planktothricoides sp001276715	75.8593	93	2610	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Oscillatoriaceae;g__Planktothricoides	95.0	99.30	99.29	0.94	0.94	3	-
GCF_000314005.1	s__Spirulina_A subsalsa	75.7793	78	2610	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Spirulinaceae;g__Spirulina_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003007785.1	s__Chroococcus hegewaldii	75.7727	183	2610	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Chroococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001698425.1	s__Kamptonema sp001698425	75.7219	71	2610	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Kamptonema	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:18:42,565] [INFO] GTDB search result was written to GCF_000147335.1_ASM14733v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:18:42,566] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:18:42,569] [INFO] DFAST_QC result json was written to GCF_000147335.1_ASM14733v1_genomic.fna/dqc_result.json
[2024-01-25 20:18:42,569] [INFO] DFAST_QC completed!
[2024-01-25 20:18:42,570] [INFO] Total running time: 0h1m37s