[2023-06-27 09:21:33,150] [INFO] DFAST_QC pipeline started.
[2023-06-27 09:21:33,153] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 09:21:33,153] [INFO] DQC Reference Directory: /var/lib/cwl/stga740ce00-180c-4b18-9ff0-a50ebd6ad20a/dqc_reference
[2023-06-27 09:21:34,345] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 09:21:34,346] [INFO] Task started: Prodigal
[2023-06-27 09:21:34,346] [INFO] Running command: gunzip -c /var/lib/cwl/stg6970c943-51d1-444b-8e6f-8f0b043a834a/GCA_026647775.1_ASM2664777v1_genomic.fna.gz | prodigal -d GCA_026647775.1_ASM2664777v1_genomic.fna/cds.fna -a GCA_026647775.1_ASM2664777v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 09:21:53,060] [INFO] Task succeeded: Prodigal
[2023-06-27 09:21:53,061] [INFO] Task started: HMMsearch
[2023-06-27 09:21:53,061] [INFO] Running command: hmmsearch --tblout GCA_026647775.1_ASM2664777v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga740ce00-180c-4b18-9ff0-a50ebd6ad20a/dqc_reference/reference_markers.hmm GCA_026647775.1_ASM2664777v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 09:21:53,429] [INFO] Task succeeded: HMMsearch
[2023-06-27 09:21:53,431] [INFO] Found 6/6 markers.
[2023-06-27 09:21:53,515] [INFO] Query marker FASTA was written to GCA_026647775.1_ASM2664777v1_genomic.fna/markers.fasta
[2023-06-27 09:21:53,516] [INFO] Task started: Blastn
[2023-06-27 09:21:53,516] [INFO] Running command: blastn -query GCA_026647775.1_ASM2664777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga740ce00-180c-4b18-9ff0-a50ebd6ad20a/dqc_reference/reference_markers.fasta -out GCA_026647775.1_ASM2664777v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 09:21:54,317] [INFO] Task succeeded: Blastn
[2023-06-27 09:21:54,344] [INFO] Selected 27 target genomes.
[2023-06-27 09:21:54,344] [INFO] Target genome list was writen to GCA_026647775.1_ASM2664777v1_genomic.fna/target_genomes.txt
[2023-06-27 09:21:54,349] [INFO] Task started: fastANI
[2023-06-27 09:21:54,350] [INFO] Running command: fastANI --query /var/lib/cwl/stg6970c943-51d1-444b-8e6f-8f0b043a834a/GCA_026647775.1_ASM2664777v1_genomic.fna.gz --refList GCA_026647775.1_ASM2664777v1_genomic.fna/target_genomes.txt --output GCA_026647775.1_ASM2664777v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 09:22:26,415] [INFO] Task succeeded: fastANI
[2023-06-27 09:22:26,415] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga740ce00-180c-4b18-9ff0-a50ebd6ad20a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 09:22:26,416] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga740ce00-180c-4b18-9ff0-a50ebd6ad20a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 09:22:26,436] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 09:22:26,436] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 09:22:26,436] [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
Sandaracinus amylolyticus	strain=DSM 53668	GCA_000737325.2	927083	927083	type	True	76.7331	1269	2437	95	below_threshold
Polyangium spumosum	strain=DSM 14734	GCA_009649845.1	889282	889282	type	True	75.2883	830	2437	95	below_threshold
Labilithrix luteola	strain=DSM 27648	GCA_001263205.1	1391654	1391654	type	True	75.2251	505	2437	95	below_threshold
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	75.2213	863	2437	95	below_threshold
Polyangium fumosum	strain=DSM 14668	GCA_005144585.1	889272	889272	neotype	True	75.2004	825	2437	95	below_threshold
Geobacter pickeringii	strain=G13	GCA_000817955.1	345632	345632	type	True	75.1671	60	2437	95	below_threshold
Chondromyces crocatus	strain=Cm c5	GCA_001189295.1	52	52	type	True	75.0607	460	2437	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	75.0164	334	2437	95	below_threshold
Malikia granosa	strain=P1	GCA_002980595.1	263067	263067	type	True	74.9062	153	2437	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	74.9023	333	2437	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	74.8995	360	2437	95	below_threshold
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	74.8944	647	2437	95	below_threshold
Salinarimonas rosea	strain=DSM 21201	GCA_000429045.1	552063	552063	type	True	74.8839	533	2437	95	below_threshold
Rhizomicrobium electricum	strain=DSM 21034	GCA_011762045.1	480070	480070	type	True	74.8669	85	2437	95	below_threshold
Bauldia litoralis	strain=ATCC 35022	GCA_900104485.1	665467	665467	type	True	74.863	157	2437	95	below_threshold
Pseudomonas tohonis	strain=TUM18999	GCA_012767755.2	2725477	2725477	type	True	74.8598	164	2437	95	below_threshold
Aeromicrobium massiliense	strain=JC14	GCA_000312105.1	1464554	1464554	type	True	74.8396	292	2437	95	below_threshold
Pseudoxanthomonas sangjuensis	strain=DSM 28345	GCA_010211755.1	1503750	1503750	type	True	74.8329	197	2437	95	below_threshold
Pseudomonas carbonaria	strain=CIP 111764	GCA_904061905.1	2762745	2762745	type	True	74.8321	153	2437	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	74.781	295	2437	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	74.7516	402	2437	95	below_threshold
Oceanithermus profundus	strain=DSM 14977	GCA_000183745.1	187137	187137	type	True	74.7468	164	2437	95	below_threshold
Pimelobacter simplex	strain=ATCC 6946	GCA_900114845.1	2045	2045	type	True	74.7184	451	2437	95	below_threshold
Pimelobacter simplex	strain=NBRC 12069	GCA_006538965.1	2045	2045	type	True	74.7153	458	2437	95	below_threshold
Luteimonas abyssi	strain=XH031	GCA_001482195.1	1247514	1247514	type	True	74.707	187	2437	95	below_threshold
Saccharothrix saharensis	strain=DSM 45456	GCA_006716745.1	571190	571190	type	True	74.6833	396	2437	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 09:22:26,438] [INFO] DFAST Taxonomy check result was written to GCA_026647775.1_ASM2664777v1_genomic.fna/tc_result.tsv
[2023-06-27 09:22:26,439] [INFO] ===== Taxonomy check completed =====
[2023-06-27 09:22:26,439] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 09:22:26,439] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga740ce00-180c-4b18-9ff0-a50ebd6ad20a/dqc_reference/checkm_data
[2023-06-27 09:22:26,441] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 09:22:26,518] [INFO] Task started: CheckM
[2023-06-27 09:22:26,519] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026647775.1_ASM2664777v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026647775.1_ASM2664777v1_genomic.fna/checkm_input GCA_026647775.1_ASM2664777v1_genomic.fna/checkm_result
[2023-06-27 09:23:52,639] [INFO] Task succeeded: CheckM
[2023-06-27 09:23:52,640] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.71%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 09:23:52,667] [INFO] ===== Completeness check finished =====
[2023-06-27 09:23:52,667] [INFO] ===== Start GTDB Search =====
[2023-06-27 09:23:52,668] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026647775.1_ASM2664777v1_genomic.fna/markers.fasta)
[2023-06-27 09:23:52,668] [INFO] Task started: Blastn
[2023-06-27 09:23:52,668] [INFO] Running command: blastn -query GCA_026647775.1_ASM2664777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga740ce00-180c-4b18-9ff0-a50ebd6ad20a/dqc_reference/reference_markers_gtdb.fasta -out GCA_026647775.1_ASM2664777v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 09:23:53,945] [INFO] Task succeeded: Blastn
[2023-06-27 09:23:53,950] [INFO] Selected 19 target genomes.
[2023-06-27 09:23:53,950] [INFO] Target genome list was writen to GCA_026647775.1_ASM2664777v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 09:23:53,958] [INFO] Task started: fastANI
[2023-06-27 09:23:53,959] [INFO] Running command: fastANI --query /var/lib/cwl/stg6970c943-51d1-444b-8e6f-8f0b043a834a/GCA_026647775.1_ASM2664777v1_genomic.fna.gz --refList GCA_026647775.1_ASM2664777v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026647775.1_ASM2664777v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 09:24:24,339] [INFO] Task succeeded: fastANI
[2023-06-27 09:24:24,361] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 09:24:24,361] [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
GCA_004213565.1	s__MED-G138 sp004213565	77.945	1121	2437	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Sandaracinaceae;g__MED-G138	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737325.1	s__Sandaracinus amylolyticus	76.7685	1247	2437	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Sandaracinaceae;g__Sandaracinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699025.1	s__GCA-2699025 sp002699025	76.2257	1022	2437	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__GCA-2699025	95.0	99.90	99.85	0.97	0.97	3	-
GCA_017303575.1	s__JAFLCL01 sp017303575	76.197	904	2437	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Sandaracinaceae;g__JAFLCL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009992505.1	s__JAADHO01 sp009992505	76.1927	303	2437	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__JAADHO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903828805.1	s__Sandaracinus sp903828805	76.149	552	2437	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Sandaracinaceae;g__Sandaracinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017644045.1	s__UBA1660 sp017644045	76.0419	772	2437	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__UBA1660	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012744445.1	s__JAAYBZ01 sp012744445	75.9586	517	2437	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__JAAYBZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002320815.1	s__UBA1660 sp002320815	75.9023	673	2437	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__UBA1660	95.0	99.96	99.96	0.96	0.96	2	-
GCA_013151775.1	s__JAADHO01 sp013151775	75.8233	467	2437	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__JAADHO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016706685.1	s__JADJJE01 sp016706685	75.7731	557	2437	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__JADJJE01	95.0	99.15	99.06	0.93	0.90	7	-
GCA_003647065.1	s__B10-G4 sp003647065	75.7011	339	2437	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__B10-G4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016704445.1	s__SCUS01 sp016704445	75.3482	699	2437	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Ga0077539;g__SCUS01	95.0	98.47	98.28	0.90	0.89	4	-
GCA_016212965.1	s__JACRDA01 sp016212965	75.2947	912	2437	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JACRDA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144635.1	s__Polyangium sp005144635	75.2289	857	2437	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Polyangium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016190375.1	s__JACPQR01 sp016190375	75.0861	558	2437	d__Bacteria;p__Myxococcota;c__Polyangia;o__JACPQR01;f__JACPQR01;g__JACPQR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792845.1	s__JAEUKH01 sp016792845	75.0423	466	2437	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Ga0077539;g__JAEUKH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200545.1	s__DP-19 sp016200545	74.9063	349	2437	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UTPRO1;f__UTPRO1;g__DP-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007121785.1	s__SKTG01 sp007121785	74.6857	171	2437	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__SKTG01	95.0	99.65	99.65	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-06-27 09:24:24,368] [INFO] GTDB search result was written to GCA_026647775.1_ASM2664777v1_genomic.fna/result_gtdb.tsv
[2023-06-27 09:24:24,369] [INFO] ===== GTDB Search completed =====
[2023-06-27 09:24:24,376] [INFO] DFAST_QC result json was written to GCA_026647775.1_ASM2664777v1_genomic.fna/dqc_result.json
[2023-06-27 09:24:24,376] [INFO] DFAST_QC completed!
[2023-06-27 09:24:24,376] [INFO] Total running time: 0h2m51s