[2024-01-24 15:18:50,579] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:50,581] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:50,581] [INFO] DQC Reference Directory: /var/lib/cwl/stg5af98ecd-b329-457d-bc55-5781bbeca661/dqc_reference
[2024-01-24 15:18:51,943] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:51,944] [INFO] Task started: Prodigal
[2024-01-24 15:18:51,944] [INFO] Running command: gunzip -c /var/lib/cwl/stgb6d30eee-c925-4b27-8d0d-9f059c9f3f40/GCF_012290005.1_ASM1229000v1_genomic.fna.gz | prodigal -d GCF_012290005.1_ASM1229000v1_genomic.fna/cds.fna -a GCF_012290005.1_ASM1229000v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:24,880] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:24,880] [INFO] Task started: HMMsearch
[2024-01-24 15:19:24,881] [INFO] Running command: hmmsearch --tblout GCF_012290005.1_ASM1229000v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5af98ecd-b329-457d-bc55-5781bbeca661/dqc_reference/reference_markers.hmm GCF_012290005.1_ASM1229000v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:25,264] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:25,266] [INFO] Found 6/6 markers.
[2024-01-24 15:19:25,326] [INFO] Query marker FASTA was written to GCF_012290005.1_ASM1229000v1_genomic.fna/markers.fasta
[2024-01-24 15:19:25,326] [INFO] Task started: Blastn
[2024-01-24 15:19:25,326] [INFO] Running command: blastn -query GCF_012290005.1_ASM1229000v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5af98ecd-b329-457d-bc55-5781bbeca661/dqc_reference/reference_markers.fasta -out GCF_012290005.1_ASM1229000v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:25,959] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:25,963] [INFO] Selected 25 target genomes.
[2024-01-24 15:19:25,963] [INFO] Target genome list was writen to GCF_012290005.1_ASM1229000v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:25,976] [INFO] Task started: fastANI
[2024-01-24 15:19:25,976] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6d30eee-c925-4b27-8d0d-9f059c9f3f40/GCF_012290005.1_ASM1229000v1_genomic.fna.gz --refList GCF_012290005.1_ASM1229000v1_genomic.fna/target_genomes.txt --output GCF_012290005.1_ASM1229000v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:53,541] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:53,541] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5af98ecd-b329-457d-bc55-5781bbeca661/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:53,542] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5af98ecd-b329-457d-bc55-5781bbeca661/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:53,556] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:53,556] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:53,556] [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
Crateriforma spongiae	strain=JC647	GCA_012290005.1	2724528	2724528	type	True	100.0	2272	2272	95	conclusive
Crateriforma conspicua	strain=Mal65	GCA_007752935.1	2527996	2527996	type	True	93.5323	2082	2272	95	below_threshold
Rhodopirellula bahusiensis	strain=SWK21	GCA_002727185.1	2014065	2014065	type	True	77.9468	237	2272	95	below_threshold
Rubripirellula lacrimiformis	strain=K22.7	GCA_007741535.1	1930273	1930273	type	True	77.7285	275	2272	95	below_threshold
Novipirellula aureliae	strain=Q31b	GCA_007860185.1	2527966	2527966	type	True	77.3871	117	2272	95	below_threshold
Rubripirellula tenax	strain=Poly51	GCA_007860125.1	2528015	2528015	type	True	77.0211	244	2272	95	below_threshold
Stieleria maiorica	strain=Mal15	GCA_008035925.1	2795974	2795974	type	True	77.002	307	2272	95	below_threshold
Rhodopirellula sallentina	strain=SM41	GCA_000346505.1	1263869	1263869	type	True	76.9885	195	2272	95	below_threshold
Rhodopirellula europaea	strain=6C	GCA_000338295.1	1263866	1263866	type	True	76.9435	217	2272	95	below_threshold
Rhodopirellula baltica	strain=1	GCA_000196115.1	265606	265606	type	True	76.941	194	2272	95	below_threshold
Stieleria neptunia	strain=Enr13	GCA_007754155.1	2527979	2527979	type	True	76.8096	307	2272	95	below_threshold
Rhodopirellula islandica	strain=K833	GCA_001027925.1	595434	595434	type	True	76.6805	220	2272	95	below_threshold
Roseiconus nitratireducens	strain=JC645	GCA_008629675.1	2605748	2605748	type	True	76.6087	251	2272	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:53,558] [INFO] DFAST Taxonomy check result was written to GCF_012290005.1_ASM1229000v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:53,559] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:53,559] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:53,560] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5af98ecd-b329-457d-bc55-5781bbeca661/dqc_reference/checkm_data
[2024-01-24 15:19:53,561] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:53,629] [INFO] Task started: CheckM
[2024-01-24 15:19:53,629] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012290005.1_ASM1229000v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012290005.1_ASM1229000v1_genomic.fna/checkm_input GCF_012290005.1_ASM1229000v1_genomic.fna/checkm_result
[2024-01-24 15:21:33,017] [INFO] Task succeeded: CheckM
[2024-01-24 15:21:33,018] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:21:33,039] [INFO] ===== Completeness check finished =====
[2024-01-24 15:21:33,039] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:21:33,039] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012290005.1_ASM1229000v1_genomic.fna/markers.fasta)
[2024-01-24 15:21:33,040] [INFO] Task started: Blastn
[2024-01-24 15:21:33,040] [INFO] Running command: blastn -query GCF_012290005.1_ASM1229000v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5af98ecd-b329-457d-bc55-5781bbeca661/dqc_reference/reference_markers_gtdb.fasta -out GCF_012290005.1_ASM1229000v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:21:33,845] [INFO] Task succeeded: Blastn
[2024-01-24 15:21:33,849] [INFO] Selected 19 target genomes.
[2024-01-24 15:21:33,849] [INFO] Target genome list was writen to GCF_012290005.1_ASM1229000v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:21:33,925] [INFO] Task started: fastANI
[2024-01-24 15:21:33,925] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6d30eee-c925-4b27-8d0d-9f059c9f3f40/GCF_012290005.1_ASM1229000v1_genomic.fna.gz --refList GCF_012290005.1_ASM1229000v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012290005.1_ASM1229000v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:22:00,982] [INFO] Task succeeded: fastANI
[2024-01-24 15:22:00,998] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:22:00,998] [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_012290005.1	s__Crateriforma spongiae	100.0	2272	2272	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Crateriforma	95.0	98.43	98.43	0.93	0.93	2	conclusive
GCF_007752935.1	s__Crateriforma conspicua	93.5193	2084	2272	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Crateriforma	95.0	98.96	98.96	0.93	0.93	2	-
GCF_002727185.1	s__Rhodopirellula bahusiensis	77.9612	236	2272	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014154935.1	s__Stieleria sp014154935	77.8732	323	2272	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007741535.1	s__Rubripirellula sp007741535	77.7187	273	2272	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007860185.1	s__Novipirellula aureliae	77.3871	117	2272	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007860175.1	s__Rubripirellula reticaptiva	77.2162	221	2272	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859865.1	s__Rubripirellula amarantea	77.1845	154	2272	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007753675.1	s__Stieleria sp007753675	77.1083	314	2272	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007860125.1	s__Rubripirellula tenax	77.0215	243	2272	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008035925.1	s__Stieleria maiorica	77.0005	307	2272	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000346505.1	s__Rhodopirellula sallentina	76.9885	195	2272	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000338295.1	s__Rhodopirellula europaea	76.9438	217	2272	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	96.18	96.16	0.87	0.86	3	-
GCF_000196115.1	s__Rhodopirellula baltica	76.9405	194	2272	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	97.96	97.13	0.94	0.89	5	-
GCF_007754155.1	s__Stieleria neptunia	76.8096	307	2272	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	76.7606	264	2272	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	76.6176	250	2272	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007127095.1	s__UBA6163 sp007127095	75.8466	116	2272	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA6163	95.0	99.08	99.08	0.89	0.86	3	-
GCA_002422955.1	s__UBA6163 sp002422955	75.6235	105	2272	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 15:22:01,000] [INFO] GTDB search result was written to GCF_012290005.1_ASM1229000v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:22:01,001] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:22:01,005] [INFO] DFAST_QC result json was written to GCF_012290005.1_ASM1229000v1_genomic.fna/dqc_result.json
[2024-01-24 15:22:01,005] [INFO] DFAST_QC completed!
[2024-01-24 15:22:01,005] [INFO] Total running time: 0h3m10s