[2024-01-24 13:37:15,354] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:15,357] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:15,357] [INFO] DQC Reference Directory: /var/lib/cwl/stgadc56e00-15e0-4c5a-aacf-4af6b42822be/dqc_reference
[2024-01-24 13:37:18,465] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:18,466] [INFO] Task started: Prodigal
[2024-01-24 13:37:18,466] [INFO] Running command: gunzip -c /var/lib/cwl/stg3da0343f-6bac-476c-844c-46199a51f146/GCF_007860045.1_ASM786004v1_genomic.fna.gz | prodigal -d GCF_007860045.1_ASM786004v1_genomic.fna/cds.fna -a GCF_007860045.1_ASM786004v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:38:03,822] [INFO] Task succeeded: Prodigal
[2024-01-24 13:38:03,823] [INFO] Task started: HMMsearch
[2024-01-24 13:38:03,823] [INFO] Running command: hmmsearch --tblout GCF_007860045.1_ASM786004v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgadc56e00-15e0-4c5a-aacf-4af6b42822be/dqc_reference/reference_markers.hmm GCF_007860045.1_ASM786004v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:38:04,329] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:38:04,331] [INFO] Found 6/6 markers.
[2024-01-24 13:38:04,400] [INFO] Query marker FASTA was written to GCF_007860045.1_ASM786004v1_genomic.fna/markers.fasta
[2024-01-24 13:38:04,400] [INFO] Task started: Blastn
[2024-01-24 13:38:04,401] [INFO] Running command: blastn -query GCF_007860045.1_ASM786004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgadc56e00-15e0-4c5a-aacf-4af6b42822be/dqc_reference/reference_markers.fasta -out GCF_007860045.1_ASM786004v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:05,009] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:05,013] [INFO] Selected 20 target genomes.
[2024-01-24 13:38:05,013] [INFO] Target genome list was writen to GCF_007860045.1_ASM786004v1_genomic.fna/target_genomes.txt
[2024-01-24 13:38:05,023] [INFO] Task started: fastANI
[2024-01-24 13:38:05,023] [INFO] Running command: fastANI --query /var/lib/cwl/stg3da0343f-6bac-476c-844c-46199a51f146/GCF_007860045.1_ASM786004v1_genomic.fna.gz --refList GCF_007860045.1_ASM786004v1_genomic.fna/target_genomes.txt --output GCF_007860045.1_ASM786004v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:38:43,747] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:43,748] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgadc56e00-15e0-4c5a-aacf-4af6b42822be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:38:43,748] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgadc56e00-15e0-4c5a-aacf-4af6b42822be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:38:43,760] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:38:43,760] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:38:43,760] [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 varia	strain=Pla52n	GCA_007860045.1	2528005	2528005	type	True	100.0	3165	3168	95	conclusive
Rhodopirellula pilleata	strain=Pla100	GCA_007859915.1	2714738	2714738	type	True	77.4393	271	3168	95	below_threshold
Roseiconus lacunae	strain=JC635	GCA_008312935.1	2605694	2605694	type	True	76.9082	201	3168	95	below_threshold
Rhodopirellula europaea	strain=6C	GCA_000338295.1	1263866	1263866	type	True	76.8538	183	3168	95	below_threshold
Stieleria neptunia	strain=Enr13	GCA_007754155.1	2527979	2527979	type	True	76.8342	373	3168	95	below_threshold
Stieleria maiorica	strain=Mal15	GCA_008035925.1	2795974	2795974	type	True	76.7646	375	3168	95	below_threshold
Crateriforma spongiae	strain=JC647	GCA_012290005.1	2724528	2724528	type	True	76.73	216	3168	95	below_threshold
Roseiconus nitratireducens	strain=JC645	GCA_008629675.1	2605748	2605748	type	True	76.6986	288	3168	95	below_threshold
Rubripirellula obstinata	strain=LF1	GCA_008374075.1	406547	406547	type	True	76.4705	179	3168	95	below_threshold
Crateriforma conspicua	strain=Mal65	GCA_007752935.1	2527996	2527996	type	True	76.4444	239	3168	95	below_threshold
Rubripirellula obstinata	strain=CECT 8602	GCA_001642955.1	406547	406547	type	True	76.4113	171	3168	95	below_threshold
Rhodopirellula bahusiensis	strain=SWK21	GCA_002727185.1	2014065	2014065	type	True	76.3822	231	3168	95	below_threshold
Rhodopirellula maiorica	strain=SM1	GCA_000346295.1	1265734	1265734	type	True	76.3103	195	3168	95	below_threshold
Rhodopirellula solitaria	strain=CA85	GCA_007859855.1	2527987	2527987	type	True	76.2407	146	3168	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:38:43,762] [INFO] DFAST Taxonomy check result was written to GCF_007860045.1_ASM786004v1_genomic.fna/tc_result.tsv
[2024-01-24 13:38:43,762] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:38:43,763] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:38:43,763] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgadc56e00-15e0-4c5a-aacf-4af6b42822be/dqc_reference/checkm_data
[2024-01-24 13:38:43,764] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:38:43,861] [INFO] Task started: CheckM
[2024-01-24 13:38:43,861] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007860045.1_ASM786004v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007860045.1_ASM786004v1_genomic.fna/checkm_input GCF_007860045.1_ASM786004v1_genomic.fna/checkm_result
[2024-01-24 13:40:57,771] [INFO] Task succeeded: CheckM
[2024-01-24 13:40:57,776] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:40:57,810] [INFO] ===== Completeness check finished =====
[2024-01-24 13:40:57,812] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:40:57,812] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007860045.1_ASM786004v1_genomic.fna/markers.fasta)
[2024-01-24 13:40:57,813] [INFO] Task started: Blastn
[2024-01-24 13:40:57,813] [INFO] Running command: blastn -query GCF_007860045.1_ASM786004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgadc56e00-15e0-4c5a-aacf-4af6b42822be/dqc_reference/reference_markers_gtdb.fasta -out GCF_007860045.1_ASM786004v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:58,738] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:58,743] [INFO] Selected 11 target genomes.
[2024-01-24 13:40:58,744] [INFO] Target genome list was writen to GCF_007860045.1_ASM786004v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:40:58,758] [INFO] Task started: fastANI
[2024-01-24 13:40:58,759] [INFO] Running command: fastANI --query /var/lib/cwl/stg3da0343f-6bac-476c-844c-46199a51f146/GCF_007860045.1_ASM786004v1_genomic.fna.gz --refList GCF_007860045.1_ASM786004v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007860045.1_ASM786004v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:29,733] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:29,746] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:29,747] [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_007860045.1	s__Stieleria varia	100.0	3165	3168	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_002289565.1	s__Stieleria sp002289565	76.8556	341	3168	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000338295.1	s__Rhodopirellula europaea	76.8537	183	3168	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	96.18	96.16	0.87	0.86	3	-
GCF_007754155.1	s__Stieleria neptunia	76.8515	372	3168	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007745635.1	s__Stieleria sp002167455	76.8067	167	3168	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	98.72	98.72	0.91	0.91	2	-
GCF_008035925.1	s__Stieleria maiorica	76.7635	375	3168	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	76.7423	374	3168	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008629675.1	s__Stieleria nitratireducens	76.6892	289	3168	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	76.6428	208	3168	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__K23-9	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014154935.1	s__Stieleria sp014154935	76.5842	379	3168	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000346295.1	s__Novipirellula maiorica	76.3018	196	3168	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:29,749] [INFO] GTDB search result was written to GCF_007860045.1_ASM786004v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:29,749] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:29,755] [INFO] DFAST_QC result json was written to GCF_007860045.1_ASM786004v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:29,756] [INFO] DFAST_QC completed!
[2024-01-24 13:41:29,756] [INFO] Total running time: 0h4m14s