[2023-06-18 11:32:25,196] [INFO] DFAST_QC pipeline started.
[2023-06-18 11:32:25,199] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 11:32:25,200] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e0916fc-e5fe-403e-99ae-a8b6418e2c4b/dqc_reference
[2023-06-18 11:32:27,523] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 11:32:27,524] [INFO] Task started: Prodigal
[2023-06-18 11:32:27,524] [INFO] Running command: gunzip -c /var/lib/cwl/stg2dca4da1-5fe2-4670-a373-859e2250a03a/GCA_013696175.1_ASM1369617v1_genomic.fna.gz | prodigal -d GCA_013696175.1_ASM1369617v1_genomic.fna/cds.fna -a GCA_013696175.1_ASM1369617v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 11:32:36,503] [INFO] Task succeeded: Prodigal
[2023-06-18 11:32:36,504] [INFO] Task started: HMMsearch
[2023-06-18 11:32:36,504] [INFO] Running command: hmmsearch --tblout GCA_013696175.1_ASM1369617v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e0916fc-e5fe-403e-99ae-a8b6418e2c4b/dqc_reference/reference_markers.hmm GCA_013696175.1_ASM1369617v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 11:32:36,733] [INFO] Task succeeded: HMMsearch
[2023-06-18 11:32:36,735] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2dca4da1-5fe2-4670-a373-859e2250a03a/GCA_013696175.1_ASM1369617v1_genomic.fna.gz]
[2023-06-18 11:32:36,766] [INFO] Query marker FASTA was written to GCA_013696175.1_ASM1369617v1_genomic.fna/markers.fasta
[2023-06-18 11:32:36,766] [INFO] Task started: Blastn
[2023-06-18 11:32:36,766] [INFO] Running command: blastn -query GCA_013696175.1_ASM1369617v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e0916fc-e5fe-403e-99ae-a8b6418e2c4b/dqc_reference/reference_markers.fasta -out GCA_013696175.1_ASM1369617v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:32:37,729] [INFO] Task succeeded: Blastn
[2023-06-18 11:32:37,734] [INFO] Selected 22 target genomes.
[2023-06-18 11:32:37,734] [INFO] Target genome list was writen to GCA_013696175.1_ASM1369617v1_genomic.fna/target_genomes.txt
[2023-06-18 11:32:37,746] [INFO] Task started: fastANI
[2023-06-18 11:32:37,746] [INFO] Running command: fastANI --query /var/lib/cwl/stg2dca4da1-5fe2-4670-a373-859e2250a03a/GCA_013696175.1_ASM1369617v1_genomic.fna.gz --refList GCA_013696175.1_ASM1369617v1_genomic.fna/target_genomes.txt --output GCA_013696175.1_ASM1369617v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 11:33:02,659] [INFO] Task succeeded: fastANI
[2023-06-18 11:33:02,660] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e0916fc-e5fe-403e-99ae-a8b6418e2c4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 11:33:02,661] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e0916fc-e5fe-403e-99ae-a8b6418e2c4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 11:33:02,681] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 11:33:02,681] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 11:33:02,681] [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
Saccharopolyspora subtropica	strain=CGMCC 4.7206	GCA_014646075.1	1530170	1530170	type	True	77.6114	232	918	95	below_threshold
Saccharopolyspora rhizosphaerae	strain=H219	GCA_003931915.1	2492662	2492662	type	True	77.4579	202	918	95	below_threshold
Saccharopolyspora hirsuta	strain=VKM Ac-666	GCA_008630535.1	1837	1837	type	True	77.4495	257	918	95	below_threshold
Actinokineospora enzanensis	strain=DSM 44649	GCA_000374445.1	155975	155975	type	True	77.3926	223	918	95	below_threshold
Saccharopolyspora spinosa	strain=NRRL 18395	GCA_000194155.1	60894	60894	type	True	77.31	227	918	95	below_threshold
Streptoalloteichus hindustanus	strain=DSM 44523	GCA_900129375.1	2017	2017	type	True	77.3088	247	918	95	below_threshold
Pseudonocardia acaciae	strain=DSM 45401	GCA_000620785.1	551276	551276	type	True	77.2973	291	918	95	below_threshold
Saccharopolyspora elongata	strain=7K502	GCA_004348985.1	2530387	2530387	type	True	77.2613	258	918	95	below_threshold
Saccharopolyspora spinosa	strain=DSM 44228	GCA_002846475.1	60894	60894	type	True	77.2586	230	918	95	below_threshold
Allokutzneria albata	strain=DSM 44149	GCA_900103775.1	211114	211114	type	True	77.2535	248	918	95	below_threshold
Allokutzneria albata	strain=NRRL B-24461	GCA_000720955.1	211114	211114	type	True	77.2359	249	918	95	below_threshold
Amycolatopsis acididurans	strain=K13G38	GCA_012328925.1	2724524	2724524	type	True	77.2308	197	918	95	below_threshold
Kutzneria kofuensis	strain=DSM 43851	GCA_014203355.1	103725	103725	type	True	77.172	254	918	95	below_threshold
Actinokineospora spheciospongiae	strain=EG49	GCA_000564855.1	909613	909613	type	True	77.0997	256	918	95	below_threshold
Saccharopolyspora flava	strain=DSM 44771	GCA_900116135.1	95161	95161	type	True	77.0933	241	918	95	below_threshold
Crossiella cryophila	strain=DSM 44230	GCA_014204915.1	43355	43355	type	True	77.0835	273	918	95	below_threshold
Actinophytocola xanthii	strain=11-183	GCA_001921205.1	1912961	1912961	type	True	77.0511	239	918	95	below_threshold
Pseudonocardia antarctica	strain=DSM 44749	GCA_013408715.1	237656	237656	type	True	77.0317	233	918	95	below_threshold
Amycolatopsis albispora	strain=WP1	GCA_003312875.1	1804986	1804986	type	True	76.9718	263	918	95	below_threshold
Lentzea guizhouensis	strain=DHS C013	GCA_001701025.1	1586287	1586287	type	True	76.8311	202	918	95	below_threshold
Saccharothrix deserti	strain=BMP B8144	GCA_009769385.1	2593674	2593674	type	True	76.8066	245	918	95	below_threshold
Sciscionella marina	strain=DSM 45152	GCA_000379465.1	508770	508770	type	True	76.4718	187	918	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 11:33:02,684] [INFO] DFAST Taxonomy check result was written to GCA_013696175.1_ASM1369617v1_genomic.fna/tc_result.tsv
[2023-06-18 11:33:02,685] [INFO] ===== Taxonomy check completed =====
[2023-06-18 11:33:02,685] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 11:33:02,685] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e0916fc-e5fe-403e-99ae-a8b6418e2c4b/dqc_reference/checkm_data
[2023-06-18 11:33:02,686] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 11:33:02,727] [INFO] Task started: CheckM
[2023-06-18 11:33:02,727] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013696175.1_ASM1369617v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013696175.1_ASM1369617v1_genomic.fna/checkm_input GCA_013696175.1_ASM1369617v1_genomic.fna/checkm_result
[2023-06-18 11:33:33,507] [INFO] Task succeeded: CheckM
[2023-06-18 11:33:33,508] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.81%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 11:33:33,535] [INFO] ===== Completeness check finished =====
[2023-06-18 11:33:33,536] [INFO] ===== Start GTDB Search =====
[2023-06-18 11:33:33,536] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013696175.1_ASM1369617v1_genomic.fna/markers.fasta)
[2023-06-18 11:33:33,536] [INFO] Task started: Blastn
[2023-06-18 11:33:33,537] [INFO] Running command: blastn -query GCA_013696175.1_ASM1369617v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e0916fc-e5fe-403e-99ae-a8b6418e2c4b/dqc_reference/reference_markers_gtdb.fasta -out GCA_013696175.1_ASM1369617v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:33:34,934] [INFO] Task succeeded: Blastn
[2023-06-18 11:33:34,941] [INFO] Selected 10 target genomes.
[2023-06-18 11:33:34,941] [INFO] Target genome list was writen to GCA_013696175.1_ASM1369617v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 11:33:34,979] [INFO] Task started: fastANI
[2023-06-18 11:33:34,979] [INFO] Running command: fastANI --query /var/lib/cwl/stg2dca4da1-5fe2-4670-a373-859e2250a03a/GCA_013696175.1_ASM1369617v1_genomic.fna.gz --refList GCA_013696175.1_ASM1369617v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013696175.1_ASM1369617v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 11:33:43,950] [INFO] Task succeeded: fastANI
[2023-06-18 11:33:43,963] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 11:33:43,963] [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_003244245.1	s__GCA-003244245 sp003244245	99.0072	766	918	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__GCA-003244245	95.0	99.00	99.00	0.83	0.83	2	conclusive
GCA_003244055.1	s__GCA-003244245 sp003244055	87.2693	684	918	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__GCA-003244245	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019243635.1	s__GCA-003244245 sp019243635	83.5421	556	918	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__GCA-003244245	95.0	99.98	99.98	0.96	0.96	2	-
GCA_019240665.1	s__GCA-003244245 sp019240665	83.3251	442	918	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__GCA-003244245	95.0	99.34	99.34	0.87	0.87	2	-
GCA_019244165.1	s__GCA-003244245 sp019244165	81.9756	433	918	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__GCA-003244245	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019247305.1	s__GCA-003244245 sp019247305	81.7917	479	918	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__GCA-003244245	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009379815.1	s__WHSY01 sp009379815	78.3789	304	918	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__WHSY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377865.1	s__WHSY01 sp009377865	78.1121	299	918	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__WHSY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646075.1	s__Saccharopolyspora subtropica	77.6248	231	918	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620785.1	s__Pseudonocardia acaciae	77.2882	292	918	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 11:33:43,965] [INFO] GTDB search result was written to GCA_013696175.1_ASM1369617v1_genomic.fna/result_gtdb.tsv
[2023-06-18 11:33:43,966] [INFO] ===== GTDB Search completed =====
[2023-06-18 11:33:43,970] [INFO] DFAST_QC result json was written to GCA_013696175.1_ASM1369617v1_genomic.fna/dqc_result.json
[2023-06-18 11:33:43,970] [INFO] DFAST_QC completed!
[2023-06-18 11:33:43,970] [INFO] Total running time: 0h1m19s