[2024-01-24 12:13:38,727] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:38,728] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:38,729] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e4b74fc-70ba-4af0-a49d-3c9f1d508fa1/dqc_reference
[2024-01-24 12:13:39,952] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:39,953] [INFO] Task started: Prodigal
[2024-01-24 12:13:39,953] [INFO] Running command: gunzip -c /var/lib/cwl/stg57e8d7c4-e3d5-4f9a-ab1a-1bca4f483285/GCF_008035925.1_ASM803592v1_genomic.fna.gz | prodigal -d GCF_008035925.1_ASM803592v1_genomic.fna/cds.fna -a GCF_008035925.1_ASM803592v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:41,806] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:41,806] [INFO] Task started: HMMsearch
[2024-01-24 12:14:41,807] [INFO] Running command: hmmsearch --tblout GCF_008035925.1_ASM803592v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e4b74fc-70ba-4af0-a49d-3c9f1d508fa1/dqc_reference/reference_markers.hmm GCF_008035925.1_ASM803592v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:42,224] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:42,225] [INFO] Found 6/6 markers.
[2024-01-24 12:14:42,295] [INFO] Query marker FASTA was written to GCF_008035925.1_ASM803592v1_genomic.fna/markers.fasta
[2024-01-24 12:14:42,296] [INFO] Task started: Blastn
[2024-01-24 12:14:42,296] [INFO] Running command: blastn -query GCF_008035925.1_ASM803592v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e4b74fc-70ba-4af0-a49d-3c9f1d508fa1/dqc_reference/reference_markers.fasta -out GCF_008035925.1_ASM803592v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:42,986] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:42,991] [INFO] Selected 13 target genomes.
[2024-01-24 12:14:42,992] [INFO] Target genome list was writen to GCF_008035925.1_ASM803592v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:43,001] [INFO] Task started: fastANI
[2024-01-24 12:14:43,002] [INFO] Running command: fastANI --query /var/lib/cwl/stg57e8d7c4-e3d5-4f9a-ab1a-1bca4f483285/GCF_008035925.1_ASM803592v1_genomic.fna.gz --refList GCF_008035925.1_ASM803592v1_genomic.fna/target_genomes.txt --output GCF_008035925.1_ASM803592v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:05,080] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:05,081] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e4b74fc-70ba-4af0-a49d-3c9f1d508fa1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:05,081] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e4b74fc-70ba-4af0-a49d-3c9f1d508fa1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:05,091] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:05,091] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:05,091] [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
Stieleria maiorica	strain=Mal15	GCA_008035925.1	2795974	2795974	type	True	100.0	3298	3298	95	conclusive
Stieleria neptunia	strain=Enr13	GCA_007754155.1	2527979	2527979	type	True	81.3923	1945	3298	95	below_threshold
Roseiconus lacunae	strain=JC635	GCA_008312935.1	2605694	2605694	type	True	77.555	424	3298	95	below_threshold
Roseiconus nitratireducens	strain=JC645	GCA_008629675.1	2605748	2605748	type	True	77.392	615	3298	95	below_threshold
Crateriforma spongiae	strain=JC647	GCA_012290005.1	2724528	2724528	type	True	77.0393	315	3298	95	below_threshold
Stieleria varia	strain=Pla52n	GCA_007860045.1	2528005	2528005	type	True	76.9316	356	3298	95	below_threshold
Rhodopirellula aestuarii	strain=ICT_H3.1	GCA_023701485.1	2950107	2950107	type	True	76.5222	244	3298	95	below_threshold
Roseimaritima sediminicola	strain=JC651	GCA_009618275.1	2662066	2662066	type	True	76.4755	290	3298	95	below_threshold
Rubripirellula reticaptiva	strain=Poly59	GCA_007860175.1	2528013	2528013	type	True	76.1223	248	3298	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:05,093] [INFO] DFAST Taxonomy check result was written to GCF_008035925.1_ASM803592v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:05,094] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:05,094] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:05,094] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e4b74fc-70ba-4af0-a49d-3c9f1d508fa1/dqc_reference/checkm_data
[2024-01-24 12:15:05,095] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:05,190] [INFO] Task started: CheckM
[2024-01-24 12:15:05,190] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008035925.1_ASM803592v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008035925.1_ASM803592v1_genomic.fna/checkm_input GCF_008035925.1_ASM803592v1_genomic.fna/checkm_result
[2024-01-24 12:17:53,534] [INFO] Task succeeded: CheckM
[2024-01-24 12:17:53,535] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:17:53,564] [INFO] ===== Completeness check finished =====
[2024-01-24 12:17:53,565] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:17:53,565] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008035925.1_ASM803592v1_genomic.fna/markers.fasta)
[2024-01-24 12:17:53,565] [INFO] Task started: Blastn
[2024-01-24 12:17:53,566] [INFO] Running command: blastn -query GCF_008035925.1_ASM803592v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e4b74fc-70ba-4af0-a49d-3c9f1d508fa1/dqc_reference/reference_markers_gtdb.fasta -out GCF_008035925.1_ASM803592v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:17:54,455] [INFO] Task succeeded: Blastn
[2024-01-24 12:17:54,460] [INFO] Selected 7 target genomes.
[2024-01-24 12:17:54,460] [INFO] Target genome list was writen to GCF_008035925.1_ASM803592v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:17:54,466] [INFO] Task started: fastANI
[2024-01-24 12:17:54,466] [INFO] Running command: fastANI --query /var/lib/cwl/stg57e8d7c4-e3d5-4f9a-ab1a-1bca4f483285/GCF_008035925.1_ASM803592v1_genomic.fna.gz --refList GCF_008035925.1_ASM803592v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008035925.1_ASM803592v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:18:16,600] [INFO] Task succeeded: fastANI
[2024-01-24 12:18:16,612] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:18:16,613] [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_008035925.1	s__Stieleria maiorica	100.0	3298	3298	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014154935.1	s__Stieleria sp014154935	89.4056	2500	3298	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007754155.1	s__Stieleria neptunia	81.3875	1946	3298	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007753675.1	s__Stieleria sp007753675	81.3325	1926	3298	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002289565.1	s__Stieleria sp002289565	81.1209	1853	3298	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007860045.1	s__Stieleria varia	76.9391	355	3298	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007741555.1	s__K23-9 sp007741555	76.1804	250	3298	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__K23-9	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:18:16,614] [INFO] GTDB search result was written to GCF_008035925.1_ASM803592v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:18:16,615] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:18:16,618] [INFO] DFAST_QC result json was written to GCF_008035925.1_ASM803592v1_genomic.fna/dqc_result.json
[2024-01-24 12:18:16,618] [INFO] DFAST_QC completed!
[2024-01-24 12:18:16,618] [INFO] Total running time: 0h4m38s