[2024-01-25 20:18:05,542] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:18:05,544] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:18:05,545] [INFO] DQC Reference Directory: /var/lib/cwl/stg354c8070-2ee7-4311-a387-ec456940b5f5/dqc_reference
[2024-01-25 20:18:06,715] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:18:06,716] [INFO] Task started: Prodigal
[2024-01-25 20:18:06,716] [INFO] Running command: gunzip -c /var/lib/cwl/stg3dbb6e91-8fdc-475f-9ba2-c5cf5081fc40/GCF_902497555.1_ASM90249755v1_genomic.fna.gz | prodigal -d GCF_902497555.1_ASM90249755v1_genomic.fna/cds.fna -a GCF_902497555.1_ASM90249755v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:18:34,376] [INFO] Task succeeded: Prodigal
[2024-01-25 20:18:34,376] [INFO] Task started: HMMsearch
[2024-01-25 20:18:34,376] [INFO] Running command: hmmsearch --tblout GCF_902497555.1_ASM90249755v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg354c8070-2ee7-4311-a387-ec456940b5f5/dqc_reference/reference_markers.hmm GCF_902497555.1_ASM90249755v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:18:34,875] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:18:34,876] [INFO] Found 6/6 markers.
[2024-01-25 20:18:34,975] [INFO] Query marker FASTA was written to GCF_902497555.1_ASM90249755v1_genomic.fna/markers.fasta
[2024-01-25 20:18:34,976] [INFO] Task started: Blastn
[2024-01-25 20:18:34,976] [INFO] Running command: blastn -query GCF_902497555.1_ASM90249755v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg354c8070-2ee7-4311-a387-ec456940b5f5/dqc_reference/reference_markers.fasta -out GCF_902497555.1_ASM90249755v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:36,412] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:36,415] [INFO] Selected 17 target genomes.
[2024-01-25 20:18:36,416] [INFO] Target genome list was writen to GCF_902497555.1_ASM90249755v1_genomic.fna/target_genomes.txt
[2024-01-25 20:18:36,435] [INFO] Task started: fastANI
[2024-01-25 20:18:36,435] [INFO] Running command: fastANI --query /var/lib/cwl/stg3dbb6e91-8fdc-475f-9ba2-c5cf5081fc40/GCF_902497555.1_ASM90249755v1_genomic.fna.gz --refList GCF_902497555.1_ASM90249755v1_genomic.fna/target_genomes.txt --output GCF_902497555.1_ASM90249755v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:19:20,726] [INFO] Task succeeded: fastANI
[2024-01-25 20:19:20,727] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg354c8070-2ee7-4311-a387-ec456940b5f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:19:20,727] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg354c8070-2ee7-4311-a387-ec456940b5f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:19:20,738] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:19:20,738] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:19:20,738] [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 camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	100.0	3516	3517	95	conclusive
Amycolatopsis pretoriensis	strain=DSM 44654	GCA_900107925.1	218821	218821	type	True	91.0072	2732	3517	95	below_threshold
Amycolatopsis pretoriensis	strain=NRRL B-24133	GCA_002156025.1	218821	218821	type	True	90.9736	2453	3517	95	below_threshold
Amycolatopsis lexingtonensis	strain=NRRL B-24131	GCA_002156005.1	218822	218822	type	True	89.2968	2336	3517	95	below_threshold
Amycolatopsis lexingtonensis	strain=DSM 44653	GCA_014873755.1	218822	218822	type	True	89.2829	2676	3517	95	below_threshold
Amycolatopsis eburnea	strain=GLM-1	GCA_003937945.1	2267691	2267691	type	True	89.2683	2573	3517	95	below_threshold
Amycolatopsis australiensis	strain=DSM 44671	GCA_900119165.1	546364	546364	type	True	89.2671	2388	3517	95	below_threshold
Amycolatopsis mediterranei	strain=S699	GCA_000220945.1	33910	33910	type	True	88.7544	2443	3517	95	below_threshold
Amycolatopsis vastitatis	strain=H5	GCA_002234595.1	1905142	1905142	type	True	88.7374	2396	3517	95	below_threshold
Amycolatopsis vancoresmycina	strain=DSM 44592	GCA_000388135.1	208444	208444	type	True	88.6527	2108	3517	95	below_threshold
Amycolatopsis balhimycina	strain=DSM 44591	GCA_000384295.1	208443	208443	type	True	88.6098	2465	3517	95	below_threshold
Amycolatopsis kentuckyensis	strain=NRRL B-24129	GCA_002155975.1	218823	218823	type	True	88.6082	2160	3517	95	below_threshold
Amycolatopsis jejuensis	strain=NRRL B-24427	GCA_000717335.1	330084	330084	type	True	80.8622	1474	3517	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	80.0991	1302	3517	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	79.2083	1154	3517	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	78.7108	1086	3517	95	below_threshold
Prauserella isguenensis	strain=CECT 8577	GCA_014191605.1	1470180	1470180	type	True	78.6358	834	3517	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:19:20,740] [INFO] DFAST Taxonomy check result was written to GCF_902497555.1_ASM90249755v1_genomic.fna/tc_result.tsv
[2024-01-25 20:19:20,742] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:19:20,742] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:19:20,742] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg354c8070-2ee7-4311-a387-ec456940b5f5/dqc_reference/checkm_data
[2024-01-25 20:19:20,743] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:19:20,847] [INFO] Task started: CheckM
[2024-01-25 20:19:20,848] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902497555.1_ASM90249755v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902497555.1_ASM90249755v1_genomic.fna/checkm_input GCF_902497555.1_ASM90249755v1_genomic.fna/checkm_result
[2024-01-25 20:21:49,395] [INFO] Task succeeded: CheckM
[2024-01-25 20:21:49,396] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:21:49,434] [INFO] ===== Completeness check finished =====
[2024-01-25 20:21:49,434] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:21:49,435] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902497555.1_ASM90249755v1_genomic.fna/markers.fasta)
[2024-01-25 20:21:49,435] [INFO] Task started: Blastn
[2024-01-25 20:21:49,435] [INFO] Running command: blastn -query GCF_902497555.1_ASM90249755v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg354c8070-2ee7-4311-a387-ec456940b5f5/dqc_reference/reference_markers_gtdb.fasta -out GCF_902497555.1_ASM90249755v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:21:51,599] [INFO] Task succeeded: Blastn
[2024-01-25 20:21:51,602] [INFO] Selected 14 target genomes.
[2024-01-25 20:21:51,602] [INFO] Target genome list was writen to GCF_902497555.1_ASM90249755v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:21:51,612] [INFO] Task started: fastANI
[2024-01-25 20:21:51,612] [INFO] Running command: fastANI --query /var/lib/cwl/stg3dbb6e91-8fdc-475f-9ba2-c5cf5081fc40/GCF_902497555.1_ASM90249755v1_genomic.fna.gz --refList GCF_902497555.1_ASM90249755v1_genomic.fna/target_genomes_gtdb.txt --output GCF_902497555.1_ASM90249755v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:22:36,464] [INFO] Task succeeded: fastANI
[2024-01-25 20:22:36,474] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:22:36,474] [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_902497555.1	s__Amycolatopsis sp902497555	100.0	3516	3517	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_900107925.1	s__Amycolatopsis pretoriensis	91.028	2727	3517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014873755.1	s__Amycolatopsis lexingtonensis	89.2839	2676	3517	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	89.2531	2577	3517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119165.1	s__Amycolatopsis australiensis	89.2304	2393	3517	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	88.7501	2446	3517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	1.00	0.99	7	-
GCF_002234595.1	s__Amycolatopsis vastitatis	88.7182	2400	3517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002904335.1	s__Amycolatopsis sp002904335	88.6863	2489	3517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000384295.1	s__Amycolatopsis balhimycina	88.6291	2460	3517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000716785.1	s__Amycolatopsis vancoresmycina	88.624	2490	3517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.98	99.98	1.00	1.00	2	-
GCF_014654205.1	s__Amycolatopsis bullii	88.517	2365	3517	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	88.4518	2418	3517	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	88.4113	2481	3517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717335.1	s__Amycolatopsis jejuensis	80.8686	1472	3517	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:22:36,475] [INFO] GTDB search result was written to GCF_902497555.1_ASM90249755v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:22:36,476] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:22:36,480] [INFO] DFAST_QC result json was written to GCF_902497555.1_ASM90249755v1_genomic.fna/dqc_result.json
[2024-01-25 20:22:36,481] [INFO] DFAST_QC completed!
[2024-01-25 20:22:36,481] [INFO] Total running time: 0h4m31s