[2024-01-24 13:46:43,283] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:43,285] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:43,285] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a5466d4-0598-4a26-8f2c-1d8194191ed1/dqc_reference
[2024-01-24 13:46:44,659] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:44,660] [INFO] Task started: Prodigal
[2024-01-24 13:46:44,660] [INFO] Running command: gunzip -c /var/lib/cwl/stgb386895a-942e-4272-9ba7-3127763ffe06/GCF_007860135.1_ASM786013v1_genomic.fna.gz | prodigal -d GCF_007860135.1_ASM786013v1_genomic.fna/cds.fna -a GCF_007860135.1_ASM786013v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:47:25,196] [INFO] Task succeeded: Prodigal
[2024-01-24 13:47:25,196] [INFO] Task started: HMMsearch
[2024-01-24 13:47:25,197] [INFO] Running command: hmmsearch --tblout GCF_007860135.1_ASM786013v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a5466d4-0598-4a26-8f2c-1d8194191ed1/dqc_reference/reference_markers.hmm GCF_007860135.1_ASM786013v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:47:25,607] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:47:25,608] [INFO] Found 6/6 markers.
[2024-01-24 13:47:25,686] [INFO] Query marker FASTA was written to GCF_007860135.1_ASM786013v1_genomic.fna/markers.fasta
[2024-01-24 13:47:25,687] [INFO] Task started: Blastn
[2024-01-24 13:47:25,687] [INFO] Running command: blastn -query GCF_007860135.1_ASM786013v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a5466d4-0598-4a26-8f2c-1d8194191ed1/dqc_reference/reference_markers.fasta -out GCF_007860135.1_ASM786013v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:26,290] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:26,293] [INFO] Selected 20 target genomes.
[2024-01-24 13:47:26,294] [INFO] Target genome list was writen to GCF_007860135.1_ASM786013v1_genomic.fna/target_genomes.txt
[2024-01-24 13:47:26,315] [INFO] Task started: fastANI
[2024-01-24 13:47:26,316] [INFO] Running command: fastANI --query /var/lib/cwl/stgb386895a-942e-4272-9ba7-3127763ffe06/GCF_007860135.1_ASM786013v1_genomic.fna.gz --refList GCF_007860135.1_ASM786013v1_genomic.fna/target_genomes.txt --output GCF_007860135.1_ASM786013v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:53,407] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:53,407] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a5466d4-0598-4a26-8f2c-1d8194191ed1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:53,408] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a5466d4-0598-4a26-8f2c-1d8194191ed1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:53,418] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:53,419] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:53,419] [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
Novipirellula artificiosorum	strain=Poly41	GCA_007860135.1	2528016	2528016	type	True	100.0	3028	3031	95	conclusive
Novipirellula aureliae	strain=Q31b	GCA_007860185.1	2527966	2527966	type	True	78.1051	326	3031	95	below_threshold
Rhodopirellula pilleata	strain=Pla100	GCA_007859915.1	2714738	2714738	type	True	77.3136	174	3031	95	below_threshold
Rubripirellula obstinata	strain=CECT 8602	GCA_001642955.1	406547	406547	type	True	77.0399	147	3031	95	below_threshold
Rubripirellula obstinata	strain=LF1	GCA_008374075.1	406547	406547	type	True	76.9443	155	3031	95	below_threshold
Rhodopirellula maiorica	strain=SM1	GCA_000346295.1	1265734	1265734	type	True	76.814	265	3031	95	below_threshold
Rhodopirellula bahusiensis	strain=SWK21	GCA_002727185.1	2014065	2014065	type	True	76.735	154	3031	95	below_threshold
Novipirellula galeiformis	strain=Pla52o	GCA_007860095.1	2528004	2528004	type	True	76.6502	261	3031	95	below_threshold
Crateriforma conspicua	strain=Mal65	GCA_007752935.1	2527996	2527996	type	True	76.6327	158	3031	95	below_threshold
Stieleria neptunia	strain=Enr13	GCA_007754155.1	2527979	2527979	type	True	76.6002	206	3031	95	below_threshold
Rhodopirellula europaea	strain=6C	GCA_000338295.1	1263866	1263866	type	True	76.5418	152	3031	95	below_threshold
Rubripirellula lacrimiformis	strain=K22.7	GCA_007741535.1	1930273	1930273	type	True	76.4528	188	3031	95	below_threshold
Roseiconus nitratireducens	strain=JC645	GCA_008629675.1	2605748	2605748	type	True	76.0812	144	3031	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:53,421] [INFO] DFAST Taxonomy check result was written to GCF_007860135.1_ASM786013v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:53,421] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:53,421] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:53,422] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a5466d4-0598-4a26-8f2c-1d8194191ed1/dqc_reference/checkm_data
[2024-01-24 13:47:53,423] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:53,508] [INFO] Task started: CheckM
[2024-01-24 13:47:53,508] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007860135.1_ASM786013v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007860135.1_ASM786013v1_genomic.fna/checkm_input GCF_007860135.1_ASM786013v1_genomic.fna/checkm_result
[2024-01-24 13:49:43,597] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:43,598] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:43,624] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:43,624] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:43,625] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007860135.1_ASM786013v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:43,625] [INFO] Task started: Blastn
[2024-01-24 13:49:43,625] [INFO] Running command: blastn -query GCF_007860135.1_ASM786013v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a5466d4-0598-4a26-8f2c-1d8194191ed1/dqc_reference/reference_markers_gtdb.fasta -out GCF_007860135.1_ASM786013v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:44,392] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:44,396] [INFO] Selected 19 target genomes.
[2024-01-24 13:49:44,397] [INFO] Target genome list was writen to GCF_007860135.1_ASM786013v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:44,430] [INFO] Task started: fastANI
[2024-01-24 13:49:44,431] [INFO] Running command: fastANI --query /var/lib/cwl/stgb386895a-942e-4272-9ba7-3127763ffe06/GCF_007860135.1_ASM786013v1_genomic.fna.gz --refList GCF_007860135.1_ASM786013v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007860135.1_ASM786013v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:14,309] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:14,326] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:14,326] [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_007860135.1	s__Novipirellula artificiosorum	100.0	3028	3031	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007860185.1	s__Novipirellula aureliae	78.0867	327	3031	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007859835.1	s__Novipirellula sp007859835	77.9513	465	3031	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001642955.1	s__Rubripirellula obstinata	77.0057	149	3031	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	99.93	99.93	1.00	1.00	2	-
GCA_007741555.1	s__K23-9 sp007741555	76.9899	168	3031	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_001027925.1	s__Rhodopirellula islandica	76.9118	151	3031	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000346295.1	s__Novipirellula maiorica	76.8138	265	3031	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002727185.1	s__Rhodopirellula bahusiensis	76.7401	154	3031	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007860095.1	s__Novipirellula galeiformis	76.6482	261	3031	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007754155.1	s__Stieleria neptunia	76.6209	205	3031	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	76.5826	149	3031	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	96.18	96.16	0.87	0.86	3	-
GCA_007741535.1	s__Rubripirellula sp007741535	76.471	185	3031	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689655.1	s__Rubripirellula sp002689655	76.3481	64	3031	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	100.00	100.00	0.98	0.98	2	-
GCF_008629675.1	s__Stieleria nitratireducens	76.1207	142	3031	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007694185.1	s__UBA6163 sp007694185	76.0317	84	3031	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA6163	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:14,328] [INFO] GTDB search result was written to GCF_007860135.1_ASM786013v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:14,328] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:14,332] [INFO] DFAST_QC result json was written to GCF_007860135.1_ASM786013v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:14,332] [INFO] DFAST_QC completed!
[2024-01-24 13:50:14,332] [INFO] Total running time: 0h3m31s