[2024-01-24 13:46:55,889] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:55,891] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:55,891] [INFO] DQC Reference Directory: /var/lib/cwl/stga8fb627b-d259-4f6e-8455-0f945adaabb0/dqc_reference
[2024-01-24 13:46:57,251] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:57,252] [INFO] Task started: Prodigal
[2024-01-24 13:46:57,252] [INFO] Running command: gunzip -c /var/lib/cwl/stg87cfae21-f3b2-40f9-9e97-7cd96c257e88/GCF_008629675.1_ASM862967v1_genomic.fna.gz | prodigal -d GCF_008629675.1_ASM862967v1_genomic.fna/cds.fna -a GCF_008629675.1_ASM862967v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:47:36,400] [INFO] Task succeeded: Prodigal
[2024-01-24 13:47:36,401] [INFO] Task started: HMMsearch
[2024-01-24 13:47:36,401] [INFO] Running command: hmmsearch --tblout GCF_008629675.1_ASM862967v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8fb627b-d259-4f6e-8455-0f945adaabb0/dqc_reference/reference_markers.hmm GCF_008629675.1_ASM862967v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:47:36,769] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:47:36,771] [INFO] Found 6/6 markers.
[2024-01-24 13:47:36,842] [INFO] Query marker FASTA was written to GCF_008629675.1_ASM862967v1_genomic.fna/markers.fasta
[2024-01-24 13:47:36,842] [INFO] Task started: Blastn
[2024-01-24 13:47:36,842] [INFO] Running command: blastn -query GCF_008629675.1_ASM862967v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8fb627b-d259-4f6e-8455-0f945adaabb0/dqc_reference/reference_markers.fasta -out GCF_008629675.1_ASM862967v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:37,450] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:37,454] [INFO] Selected 16 target genomes.
[2024-01-24 13:47:37,455] [INFO] Target genome list was writen to GCF_008629675.1_ASM862967v1_genomic.fna/target_genomes.txt
[2024-01-24 13:47:37,474] [INFO] Task started: fastANI
[2024-01-24 13:47:37,475] [INFO] Running command: fastANI --query /var/lib/cwl/stg87cfae21-f3b2-40f9-9e97-7cd96c257e88/GCF_008629675.1_ASM862967v1_genomic.fna.gz --refList GCF_008629675.1_ASM862967v1_genomic.fna/target_genomes.txt --output GCF_008629675.1_ASM862967v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:56,214] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:56,215] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8fb627b-d259-4f6e-8455-0f945adaabb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:56,215] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8fb627b-d259-4f6e-8455-0f945adaabb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:56,223] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:56,223] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:56,224] [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
Roseiconus nitratireducens	strain=JC645	GCA_008629675.1	2605748	2605748	type	True	100.0	2691	2692	95	conclusive
Stieleria maiorica	strain=Mal15	GCA_008035925.1	2795974	2795974	type	True	77.5232	583	2692	95	below_threshold
Stieleria neptunia	strain=Enr13	GCA_007754155.1	2527979	2527979	type	True	77.4101	563	2692	95	below_threshold
Roseiconus lacunae	strain=JC635	GCA_008312935.1	2605694	2605694	type	True	76.9796	287	2692	95	below_threshold
Stieleria varia	strain=Pla52n	GCA_007860045.1	2528005	2528005	type	True	76.6773	286	2692	95	below_threshold
Crateriforma conspicua	strain=Mal65	GCA_007752935.1	2527996	2527996	type	True	76.5837	266	2692	95	below_threshold
Roseimaritima sediminicola	strain=JC651	GCA_009618275.1	2662066	2662066	type	True	76.5022	218	2692	95	below_threshold
Crateriforma spongiae	strain=JC647	GCA_012290005.1	2724528	2724528	type	True	76.4872	258	2692	95	below_threshold
Rhodopirellula rubra	strain=CECT 8075	GCA_014192335.1	980271	980271	type	True	76.4366	170	2692	95	below_threshold
Actinoallomurus spadix	strain=KCTC 9252	GCA_024055725.1	79912	79912	type	True	74.5452	51	2692	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:56,225] [INFO] DFAST Taxonomy check result was written to GCF_008629675.1_ASM862967v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:56,226] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:56,226] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:56,226] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8fb627b-d259-4f6e-8455-0f945adaabb0/dqc_reference/checkm_data
[2024-01-24 13:47:56,227] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:56,300] [INFO] Task started: CheckM
[2024-01-24 13:47:56,300] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008629675.1_ASM862967v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008629675.1_ASM862967v1_genomic.fna/checkm_input GCF_008629675.1_ASM862967v1_genomic.fna/checkm_result
[2024-01-24 13:49:45,996] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:45,997] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:46,033] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:46,034] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:46,034] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008629675.1_ASM862967v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:46,034] [INFO] Task started: Blastn
[2024-01-24 13:49:46,034] [INFO] Running command: blastn -query GCF_008629675.1_ASM862967v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8fb627b-d259-4f6e-8455-0f945adaabb0/dqc_reference/reference_markers_gtdb.fasta -out GCF_008629675.1_ASM862967v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:46,944] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:46,948] [INFO] Selected 12 target genomes.
[2024-01-24 13:49:46,948] [INFO] Target genome list was writen to GCF_008629675.1_ASM862967v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:46,956] [INFO] Task started: fastANI
[2024-01-24 13:49:46,957] [INFO] Running command: fastANI --query /var/lib/cwl/stg87cfae21-f3b2-40f9-9e97-7cd96c257e88/GCF_008629675.1_ASM862967v1_genomic.fna.gz --refList GCF_008629675.1_ASM862967v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008629675.1_ASM862967v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:08,039] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:08,049] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:08,049] [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_008629675.1	s__Stieleria nitratireducens	100.0	2691	2692	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	77.5366	576	2692	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008035925.1	s__Stieleria maiorica	77.526	582	2692	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	77.4392	563	2692	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	77.4054	559	2692	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	77.234	530	2692	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008312935.1	s__Stieleria lacunae	76.9907	286	2692	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002901265.1	s__Stieleria baltica_A	76.9346	265	2692	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	99.97	99.97	0.98	0.98	2	-
GCF_007752935.1	s__Crateriforma conspicua	76.5526	270	2692	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Crateriforma	95.0	98.96	98.96	0.93	0.93	2	-
GCF_014192335.1	s__Rhodopirellula rubra	76.4366	170	2692	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	95.37	95.37	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:08,113] [INFO] GTDB search result was written to GCF_008629675.1_ASM862967v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:08,114] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:08,121] [INFO] DFAST_QC result json was written to GCF_008629675.1_ASM862967v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:08,122] [INFO] DFAST_QC completed!
[2024-01-24 13:50:08,122] [INFO] Total running time: 0h3m12s