[2024-01-24 11:05:27,391] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:27,395] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:27,396] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1dc2ea3-ba5d-4549-884d-c17bb0b69f0f/dqc_reference
[2024-01-24 11:05:28,923] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:28,924] [INFO] Task started: Prodigal
[2024-01-24 11:05:28,924] [INFO] Running command: gunzip -c /var/lib/cwl/stgecb1e671-8475-45d2-892c-7560fdccb3f0/GCF_002155975.1_ASM215597v1_genomic.fna.gz | prodigal -d GCF_002155975.1_ASM215597v1_genomic.fna/cds.fna -a GCF_002155975.1_ASM215597v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:56,589] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:56,589] [INFO] Task started: HMMsearch
[2024-01-24 11:05:56,589] [INFO] Running command: hmmsearch --tblout GCF_002155975.1_ASM215597v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1dc2ea3-ba5d-4549-884d-c17bb0b69f0f/dqc_reference/reference_markers.hmm GCF_002155975.1_ASM215597v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:57,124] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:57,125] [INFO] Found 6/6 markers.
[2024-01-24 11:05:57,224] [INFO] Query marker FASTA was written to GCF_002155975.1_ASM215597v1_genomic.fna/markers.fasta
[2024-01-24 11:05:57,225] [INFO] Task started: Blastn
[2024-01-24 11:05:57,225] [INFO] Running command: blastn -query GCF_002155975.1_ASM215597v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1dc2ea3-ba5d-4549-884d-c17bb0b69f0f/dqc_reference/reference_markers.fasta -out GCF_002155975.1_ASM215597v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:58,646] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:58,654] [INFO] Selected 17 target genomes.
[2024-01-24 11:05:58,654] [INFO] Target genome list was writen to GCF_002155975.1_ASM215597v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:58,661] [INFO] Task started: fastANI
[2024-01-24 11:05:58,662] [INFO] Running command: fastANI --query /var/lib/cwl/stgecb1e671-8475-45d2-892c-7560fdccb3f0/GCF_002155975.1_ASM215597v1_genomic.fna.gz --refList GCF_002155975.1_ASM215597v1_genomic.fna/target_genomes.txt --output GCF_002155975.1_ASM215597v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:42,167] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:42,167] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1dc2ea3-ba5d-4549-884d-c17bb0b69f0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:42,168] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1dc2ea3-ba5d-4549-884d-c17bb0b69f0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:42,182] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:06:42,182] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:42,182] [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
Amycolatopsis kentuckyensis	strain=NRRL B-24129	GCA_002155975.1	218823	218823	type	True	100.0	2898	2941	95	conclusive
Amycolatopsis mediterranei	strain=S699	GCA_000220945.1	33910	33910	type	True	92.1316	2325	2941	95	below_threshold
Amycolatopsis rifamycinica	strain=DSM 46095	GCA_000695625.1	287986	287986	type	True	91.9135	2250	2941	95	below_threshold
Amycolatopsis tolypomycina	strain=DSM 44544	GCA_900105945.1	208445	208445	type	True	91.8516	2364	2941	95	below_threshold
Amycolatopsis vancoresmycina	strain=DSM 44592	GCA_000388135.1	208444	208444	type	True	90.8289	1939	2941	95	below_threshold
Amycolatopsis vancoresmycina	strain=NRRL B-24208	GCA_000716785.1	208444	208444	type	True	90.822	2285	2941	95	below_threshold
Amycolatopsis vastitatis	strain=H5	GCA_002234595.1	1905142	1905142	type	True	89.9861	2160	2941	95	below_threshold
Amycolatopsis balhimycina	strain=DSM 44591	GCA_000384295.1	208443	208443	type	True	89.529	2195	2941	95	below_threshold
Amycolatopsis lexingtonensis	strain=DSM 44653	GCA_014873755.1	218822	218822	type	True	88.9507	2265	2941	95	below_threshold
Amycolatopsis lexingtonensis	strain=NRRL B-24131	GCA_002156005.1	218822	218822	type	True	88.9117	2018	2941	95	below_threshold
Amycolatopsis pretoriensis	strain=DSM 44654	GCA_900107925.1	218821	218821	type	True	88.5982	2135	2941	95	below_threshold
Amycolatopsis pretoriensis	strain=NRRL B-24133	GCA_002156025.1	218821	218821	type	True	88.4956	1974	2941	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	88.4299	2227	2941	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	80.1514	1145	2941	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	78.9495	1013	2941	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	78.6394	993	2941	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	78.0157	875	2941	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:42,184] [INFO] DFAST Taxonomy check result was written to GCF_002155975.1_ASM215597v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:42,185] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:42,185] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:42,185] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1dc2ea3-ba5d-4549-884d-c17bb0b69f0f/dqc_reference/checkm_data
[2024-01-24 11:06:42,187] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:42,282] [INFO] Task started: CheckM
[2024-01-24 11:06:42,282] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002155975.1_ASM215597v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002155975.1_ASM215597v1_genomic.fna/checkm_input GCF_002155975.1_ASM215597v1_genomic.fna/checkm_result
[2024-01-24 11:08:13,073] [INFO] Task succeeded: CheckM
[2024-01-24 11:08:13,074] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:08:13,102] [INFO] ===== Completeness check finished =====
[2024-01-24 11:08:13,102] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:08:13,103] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002155975.1_ASM215597v1_genomic.fna/markers.fasta)
[2024-01-24 11:08:13,103] [INFO] Task started: Blastn
[2024-01-24 11:08:13,104] [INFO] Running command: blastn -query GCF_002155975.1_ASM215597v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1dc2ea3-ba5d-4549-884d-c17bb0b69f0f/dqc_reference/reference_markers_gtdb.fasta -out GCF_002155975.1_ASM215597v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:08:15,094] [INFO] Task succeeded: Blastn
[2024-01-24 11:08:15,099] [INFO] Selected 12 target genomes.
[2024-01-24 11:08:15,099] [INFO] Target genome list was writen to GCF_002155975.1_ASM215597v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:08:15,122] [INFO] Task started: fastANI
[2024-01-24 11:08:15,122] [INFO] Running command: fastANI --query /var/lib/cwl/stgecb1e671-8475-45d2-892c-7560fdccb3f0/GCF_002155975.1_ASM215597v1_genomic.fna.gz --refList GCF_002155975.1_ASM215597v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002155975.1_ASM215597v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:08:49,850] [INFO] Task succeeded: fastANI
[2024-01-24 11:08:49,863] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:08:49,863] [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_002155975.1	s__Amycolatopsis kentuckyensis	100.0	2898	2941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014654205.1	s__Amycolatopsis bullii	92.1748	2242	2941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000220945.1	s__Amycolatopsis mediterranei	92.1501	2323	2941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	1.00	0.99	7	-
GCF_002904335.1	s__Amycolatopsis sp002904335	92.1341	2276	2941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000695625.1	s__Amycolatopsis rifamycinica	91.903	2251	2941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105945.1	s__Amycolatopsis tolypomycina	91.8284	2366	2941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017308975.1	s__Amycolatopsis sp017308975	91.6984	2349	2941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013364075.1	s__Amycolatopsis sp013364075	91.6856	2392	2941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716785.1	s__Amycolatopsis vancoresmycina	90.8293	2283	2941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002904295.1	s__Amycolatopsis sp002904295	90.5464	2236	2941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002234595.1	s__Amycolatopsis vastitatis	89.9892	2159	2941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873755.1	s__Amycolatopsis lexingtonensis	88.9254	2270	2941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:08:49,865] [INFO] GTDB search result was written to GCF_002155975.1_ASM215597v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:08:49,865] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:08:49,871] [INFO] DFAST_QC result json was written to GCF_002155975.1_ASM215597v1_genomic.fna/dqc_result.json
[2024-01-24 11:08:49,872] [INFO] DFAST_QC completed!
[2024-01-24 11:08:49,872] [INFO] Total running time: 0h3m22s