[2024-01-24 15:02:19,010] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:19,012] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:19,013] [INFO] DQC Reference Directory: /var/lib/cwl/stg15588b05-f12e-4768-a7ca-0d9ce8f3f8e2/dqc_reference
[2024-01-24 15:02:20,832] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:20,833] [INFO] Task started: Prodigal
[2024-01-24 15:02:20,834] [INFO] Running command: gunzip -c /var/lib/cwl/stg9b5e3ec4-7f6b-4630-80b0-f405daa2d194/GCF_002234595.1_ASM223459v1_genomic.fna.gz | prodigal -d GCF_002234595.1_ASM223459v1_genomic.fna/cds.fna -a GCF_002234595.1_ASM223459v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:52,880] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:52,881] [INFO] Task started: HMMsearch
[2024-01-24 15:02:52,881] [INFO] Running command: hmmsearch --tblout GCF_002234595.1_ASM223459v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15588b05-f12e-4768-a7ca-0d9ce8f3f8e2/dqc_reference/reference_markers.hmm GCF_002234595.1_ASM223459v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:53,364] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:53,365] [INFO] Found 6/6 markers.
[2024-01-24 15:02:53,450] [INFO] Query marker FASTA was written to GCF_002234595.1_ASM223459v1_genomic.fna/markers.fasta
[2024-01-24 15:02:53,451] [INFO] Task started: Blastn
[2024-01-24 15:02:53,451] [INFO] Running command: blastn -query GCF_002234595.1_ASM223459v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15588b05-f12e-4768-a7ca-0d9ce8f3f8e2/dqc_reference/reference_markers.fasta -out GCF_002234595.1_ASM223459v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:54,837] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:54,841] [INFO] Selected 17 target genomes.
[2024-01-24 15:02:54,841] [INFO] Target genome list was writen to GCF_002234595.1_ASM223459v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:54,848] [INFO] Task started: fastANI
[2024-01-24 15:02:54,849] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b5e3ec4-7f6b-4630-80b0-f405daa2d194/GCF_002234595.1_ASM223459v1_genomic.fna.gz --refList GCF_002234595.1_ASM223459v1_genomic.fna/target_genomes.txt --output GCF_002234595.1_ASM223459v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:41,708] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:41,708] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15588b05-f12e-4768-a7ca-0d9ce8f3f8e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:41,709] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15588b05-f12e-4768-a7ca-0d9ce8f3f8e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:41,724] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:03:41,724] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:41,725] [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 vastitatis	strain=H5	GCA_002234595.1	1905142	1905142	type	True	100.0	3487	3494	95	conclusive
Amycolatopsis balhimycina	strain=DSM 44591	GCA_000384295.1	208443	208443	type	True	93.5045	2668	3494	95	below_threshold
Amycolatopsis mediterranei	strain=S699	GCA_000220945.1	33910	33910	type	True	90.4373	2532	3494	95	below_threshold
Amycolatopsis kentuckyensis	strain=NRRL B-24129	GCA_002155975.1	218823	218823	type	True	89.9984	2162	3494	95	below_threshold
Amycolatopsis vancoresmycina	strain=NRRL B-24208	GCA_000716785.1	208444	208444	type	True	89.9453	2387	3494	95	below_threshold
Amycolatopsis vancoresmycina	strain=DSM 44592	GCA_000388135.1	208444	208444	type	True	89.832	2006	3494	95	below_threshold
Amycolatopsis rifamycinica	strain=DSM 46095	GCA_000695625.1	287986	287986	type	True	89.8089	2290	3494	95	below_threshold
Amycolatopsis tolypomycina	strain=DSM 44544	GCA_900105945.1	208445	208445	type	True	89.6721	2467	3494	95	below_threshold
Amycolatopsis lexingtonensis	strain=DSM 44653	GCA_014873755.1	218822	218822	type	True	89.0846	2378	3494	95	below_threshold
Amycolatopsis lexingtonensis	strain=NRRL B-24131	GCA_002156005.1	218822	218822	type	True	88.9781	2116	3494	95	below_threshold
Amycolatopsis eburnea	strain=GLM-1	GCA_003937945.1	2267691	2267691	type	True	88.9096	2317	3494	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	88.7019	2386	3494	95	below_threshold
Amycolatopsis jejuensis	strain=NRRL B-24427	GCA_000717335.1	330084	330084	type	True	81.0207	1410	3494	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	80.1732	1279	3494	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	79.2394	1083	3494	95	below_threshold
Prauserella isguenensis	strain=CECT 8577	GCA_014191605.1	1470180	1470180	type	True	78.6787	818	3494	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	78.5496	1095	3494	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:41,727] [INFO] DFAST Taxonomy check result was written to GCF_002234595.1_ASM223459v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:41,727] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:41,727] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:41,728] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15588b05-f12e-4768-a7ca-0d9ce8f3f8e2/dqc_reference/checkm_data
[2024-01-24 15:03:41,729] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:41,834] [INFO] Task started: CheckM
[2024-01-24 15:03:41,835] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002234595.1_ASM223459v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002234595.1_ASM223459v1_genomic.fna/checkm_input GCF_002234595.1_ASM223459v1_genomic.fna/checkm_result
[2024-01-24 15:06:11,041] [INFO] Task succeeded: CheckM
[2024-01-24 15:06:11,043] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:06:11,072] [INFO] ===== Completeness check finished =====
[2024-01-24 15:06:11,072] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:06:11,073] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002234595.1_ASM223459v1_genomic.fna/markers.fasta)
[2024-01-24 15:06:11,073] [INFO] Task started: Blastn
[2024-01-24 15:06:11,073] [INFO] Running command: blastn -query GCF_002234595.1_ASM223459v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15588b05-f12e-4768-a7ca-0d9ce8f3f8e2/dqc_reference/reference_markers_gtdb.fasta -out GCF_002234595.1_ASM223459v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:06:13,255] [INFO] Task succeeded: Blastn
[2024-01-24 15:06:13,259] [INFO] Selected 12 target genomes.
[2024-01-24 15:06:13,259] [INFO] Target genome list was writen to GCF_002234595.1_ASM223459v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:06:13,268] [INFO] Task started: fastANI
[2024-01-24 15:06:13,268] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b5e3ec4-7f6b-4630-80b0-f405daa2d194/GCF_002234595.1_ASM223459v1_genomic.fna.gz --refList GCF_002234595.1_ASM223459v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002234595.1_ASM223459v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:06:50,161] [INFO] Task succeeded: fastANI
[2024-01-24 15:06:50,179] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:06:50,180] [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_002234595.1	s__Amycolatopsis vastitatis	100.0	3487	3494	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_000384295.1	s__Amycolatopsis balhimycina	93.5037	2668	3494	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000220945.1	s__Amycolatopsis mediterranei	90.4561	2529	3494	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	90.2044	2426	3494	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002155975.1	s__Amycolatopsis kentuckyensis	89.9786	2163	3494	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014654205.1	s__Amycolatopsis bullii	89.9424	2332	3494	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	89.8284	2286	3494	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	89.7249	2406	3494	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	89.6429	2470	3494	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002904295.1	s__Amycolatopsis sp002904295	89.505	2342	3494	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	89.0577	2382	3494	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003937945.1	s__Amycolatopsis eburnea	88.9353	2313	3494	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:06:50,183] [INFO] GTDB search result was written to GCF_002234595.1_ASM223459v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:06:50,184] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:06:50,190] [INFO] DFAST_QC result json was written to GCF_002234595.1_ASM223459v1_genomic.fna/dqc_result.json
[2024-01-24 15:06:50,191] [INFO] DFAST_QC completed!
[2024-01-24 15:06:50,191] [INFO] Total running time: 0h4m31s