[2024-01-24 11:26:07,450] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:07,455] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:07,455] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f449af3-9253-4e04-b103-f140c250dbef/dqc_reference
[2024-01-24 11:26:08,780] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:08,781] [INFO] Task started: Prodigal
[2024-01-24 11:26:08,781] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ca3a14e-f72a-4f14-a5ce-a39794c2b12a/GCF_022267515.1_ASM2226751v1_genomic.fna.gz | prodigal -d GCF_022267515.1_ASM2226751v1_genomic.fna/cds.fna -a GCF_022267515.1_ASM2226751v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:25,801] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:25,802] [INFO] Task started: HMMsearch
[2024-01-24 11:26:25,802] [INFO] Running command: hmmsearch --tblout GCF_022267515.1_ASM2226751v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f449af3-9253-4e04-b103-f140c250dbef/dqc_reference/reference_markers.hmm GCF_022267515.1_ASM2226751v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:26,246] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:26,248] [INFO] Found 6/6 markers.
[2024-01-24 11:26:26,299] [INFO] Query marker FASTA was written to GCF_022267515.1_ASM2226751v1_genomic.fna/markers.fasta
[2024-01-24 11:26:26,299] [INFO] Task started: Blastn
[2024-01-24 11:26:26,299] [INFO] Running command: blastn -query GCF_022267515.1_ASM2226751v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f449af3-9253-4e04-b103-f140c250dbef/dqc_reference/reference_markers.fasta -out GCF_022267515.1_ASM2226751v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:26,940] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:26,943] [INFO] Selected 21 target genomes.
[2024-01-24 11:26:26,943] [INFO] Target genome list was writen to GCF_022267515.1_ASM2226751v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:26,967] [INFO] Task started: fastANI
[2024-01-24 11:26:26,967] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ca3a14e-f72a-4f14-a5ce-a39794c2b12a/GCF_022267515.1_ASM2226751v1_genomic.fna.gz --refList GCF_022267515.1_ASM2226751v1_genomic.fna/target_genomes.txt --output GCF_022267515.1_ASM2226751v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:53,288] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:53,288] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f449af3-9253-4e04-b103-f140c250dbef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:53,288] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f449af3-9253-4e04-b103-f140c250dbef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:53,296] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:53,296] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:53,296] [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
Rubinisphaera margarita	strain=ICM_H10	GCA_022267515.1	2909586	2909586	type	True	100.0	1983	1983	95	conclusive
Rubinisphaera brasiliensis	strain=DSM 5305	GCA_000165715.3	119	119	type	True	77.3809	302	1983	95	below_threshold
Rubinisphaera italica	strain=Pan54	GCA_007859715.1	2527969	2527969	type	True	76.4016	265	1983	95	below_threshold
Maioricimonas rarisocia	strain=Mal4	GCA_007747795.1	2528026	2528026	type	True	76.2339	177	1983	95	below_threshold
Planctomicrobium piriforme	strain=DSM 26348	GCA_900113665.1	1576369	1576369	type	True	75.9913	117	1983	95	below_threshold
Polystyrenella longa	strain=Pla110	GCA_007750395.1	2528007	2528007	type	True	75.8973	55	1983	95	below_threshold
Stieleria varia	strain=Pla52n	GCA_007860045.1	2528005	2528005	type	True	75.4031	51	1983	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:53,299] [INFO] DFAST Taxonomy check result was written to GCF_022267515.1_ASM2226751v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:53,299] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:53,300] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:53,300] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f449af3-9253-4e04-b103-f140c250dbef/dqc_reference/checkm_data
[2024-01-24 11:26:53,305] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:53,371] [INFO] Task started: CheckM
[2024-01-24 11:26:53,371] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022267515.1_ASM2226751v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022267515.1_ASM2226751v1_genomic.fna/checkm_input GCF_022267515.1_ASM2226751v1_genomic.fna/checkm_result
[2024-01-24 11:27:43,602] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:43,604] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:43,627] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:43,627] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:43,628] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022267515.1_ASM2226751v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:43,628] [INFO] Task started: Blastn
[2024-01-24 11:27:43,628] [INFO] Running command: blastn -query GCF_022267515.1_ASM2226751v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f449af3-9253-4e04-b103-f140c250dbef/dqc_reference/reference_markers_gtdb.fasta -out GCF_022267515.1_ASM2226751v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:44,477] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:44,482] [INFO] Selected 21 target genomes.
[2024-01-24 11:27:44,482] [INFO] Target genome list was writen to GCF_022267515.1_ASM2226751v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:44,501] [INFO] Task started: fastANI
[2024-01-24 11:27:44,501] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ca3a14e-f72a-4f14-a5ce-a39794c2b12a/GCF_022267515.1_ASM2226751v1_genomic.fna.gz --refList GCF_022267515.1_ASM2226751v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022267515.1_ASM2226751v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:03,848] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:03,863] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:28:03,864] [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_017795105.1	s__Rubinisphaera sp017795105	85.0462	1530	1983	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Rubinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000165715.2	s__Rubinisphaera brasiliensis	77.3912	301	1983	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Rubinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002359185.1	s__Rubinisphaera sp002359185	76.547	265	1983	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Rubinisphaera	95.0	99.90	99.90	0.94	0.94	2	-
GCF_007859715.1	s__Rubinisphaera italica	76.404	265	1983	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Rubinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014584345.1	s__Rubinisphaera sp014584345	75.9513	160	1983	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Rubinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001610835.1	s__Planctomyces_A sp001610835	75.8441	111	1983	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Planctomyces_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003671275.1	s__TH-plancto1 sp003671275	75.7198	65	1983	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__TH-plancto1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005778225.1	s__SXPC01 sp005778225	75.6989	53	1983	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXPC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003669575.1	s__TH-plancto1 sp003669575	75.562	54	1983	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__TH-plancto1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706765.1	s__Gimesia sp002706765	75.4749	67	1983	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	99.96	99.96	0.97	0.97	2	-
GCA_003696385.1	s__J052 sp003696385	75.4624	50	1983	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__J052	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013813775.1	s__JACCRE01 sp013813775	75.4501	91	1983	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JACCRE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795125.1	s__JAEUIG01 sp016795125	75.3636	74	1983	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JAEUIG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009691905.1	s__SIAF01 sp009691905	74.9931	59	1983	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__UBA10511;g__SIAF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:03,865] [INFO] GTDB search result was written to GCF_022267515.1_ASM2226751v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:03,866] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:03,869] [INFO] DFAST_QC result json was written to GCF_022267515.1_ASM2226751v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:03,869] [INFO] DFAST_QC completed!
[2024-01-24 11:28:03,869] [INFO] Total running time: 0h1m56s