[2024-01-24 13:21:45,913] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:45,917] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:45,918] [INFO] DQC Reference Directory: /var/lib/cwl/stg91439827-8d9b-40b4-984f-cacbcd44e6cd/dqc_reference
[2024-01-24 13:21:47,265] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:47,266] [INFO] Task started: Prodigal
[2024-01-24 13:21:47,266] [INFO] Running command: gunzip -c /var/lib/cwl/stgea51e395-1730-4a52-98ba-ec5b41077bac/GCF_002156005.1_ASM215600v1_genomic.fna.gz | prodigal -d GCF_002156005.1_ASM215600v1_genomic.fna/cds.fna -a GCF_002156005.1_ASM215600v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:15,888] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:15,889] [INFO] Task started: HMMsearch
[2024-01-24 13:22:15,889] [INFO] Running command: hmmsearch --tblout GCF_002156005.1_ASM215600v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg91439827-8d9b-40b4-984f-cacbcd44e6cd/dqc_reference/reference_markers.hmm GCF_002156005.1_ASM215600v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:16,352] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:16,353] [INFO] Found 6/6 markers.
[2024-01-24 13:22:16,439] [INFO] Query marker FASTA was written to GCF_002156005.1_ASM215600v1_genomic.fna/markers.fasta
[2024-01-24 13:22:16,440] [INFO] Task started: Blastn
[2024-01-24 13:22:16,440] [INFO] Running command: blastn -query GCF_002156005.1_ASM215600v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg91439827-8d9b-40b4-984f-cacbcd44e6cd/dqc_reference/reference_markers.fasta -out GCF_002156005.1_ASM215600v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:17,836] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:17,839] [INFO] Selected 16 target genomes.
[2024-01-24 13:22:17,839] [INFO] Target genome list was writen to GCF_002156005.1_ASM215600v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:17,844] [INFO] Task started: fastANI
[2024-01-24 13:22:17,845] [INFO] Running command: fastANI --query /var/lib/cwl/stgea51e395-1730-4a52-98ba-ec5b41077bac/GCF_002156005.1_ASM215600v1_genomic.fna.gz --refList GCF_002156005.1_ASM215600v1_genomic.fna/target_genomes.txt --output GCF_002156005.1_ASM215600v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:59,806] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:59,807] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg91439827-8d9b-40b4-984f-cacbcd44e6cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:59,807] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg91439827-8d9b-40b4-984f-cacbcd44e6cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:59,819] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:22:59,819] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:59,820] [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 lexingtonensis	strain=NRRL B-24131	GCA_002156005.1	218822	218822	type	True	100.0	3044	3085	95	conclusive
Amycolatopsis lexingtonensis	strain=DSM 44653	GCA_014873755.1	218822	218822	type	True	99.991	3084	3085	95	conclusive
Amycolatopsis eburnea	strain=GLM-1	GCA_003937945.1	2267691	2267691	type	True	94.2903	2546	3085	95	below_threshold
Amycolatopsis pretoriensis	strain=DSM 44654	GCA_900107925.1	218821	218821	type	True	89.49	2298	3085	95	below_threshold
Amycolatopsis pretoriensis	strain=NRRL B-24133	GCA_002156025.1	218821	218821	type	True	89.2955	2122	3085	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	89.2755	2354	3085	95	below_threshold
Amycolatopsis vancoresmycina	strain=NRRL B-24208	GCA_000716785.1	208444	208444	type	True	89.1484	2272	3085	95	below_threshold
Amycolatopsis vancoresmycina	strain=DSM 44592	GCA_000388135.1	208444	208444	type	True	89.1354	1945	3085	95	below_threshold
Amycolatopsis kentuckyensis	strain=NRRL B-24129	GCA_002155975.1	218823	218823	type	True	88.8678	2037	3085	95	below_threshold
Amycolatopsis mediterranei	strain=S699	GCA_000220945.1	33910	33910	type	True	88.8321	2204	3085	95	below_threshold
Amycolatopsis tolypomycina	strain=DSM 44544	GCA_900105945.1	208445	208445	type	True	88.7196	2242	3085	95	below_threshold
Amycolatopsis jejuensis	strain=NRRL B-24427	GCA_000717335.1	330084	330084	type	True	80.8653	1393	3085	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	80.3612	1195	3085	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	79.2022	1058	3085	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	78.6224	1029	3085	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	78.1548	922	3085	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:59,821] [INFO] DFAST Taxonomy check result was written to GCF_002156005.1_ASM215600v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:59,822] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:59,822] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:59,823] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg91439827-8d9b-40b4-984f-cacbcd44e6cd/dqc_reference/checkm_data
[2024-01-24 13:22:59,825] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:59,924] [INFO] Task started: CheckM
[2024-01-24 13:22:59,924] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002156005.1_ASM215600v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002156005.1_ASM215600v1_genomic.fna/checkm_input GCF_002156005.1_ASM215600v1_genomic.fna/checkm_result
[2024-01-24 13:24:24,544] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:24,544] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.24%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2024-01-24 13:24:24,568] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:24,568] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:24,569] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002156005.1_ASM215600v1_genomic.fna/markers.fasta)
[2024-01-24 13:24:24,569] [INFO] Task started: Blastn
[2024-01-24 13:24:24,569] [INFO] Running command: blastn -query GCF_002156005.1_ASM215600v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg91439827-8d9b-40b4-984f-cacbcd44e6cd/dqc_reference/reference_markers_gtdb.fasta -out GCF_002156005.1_ASM215600v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:26,709] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:26,714] [INFO] Selected 13 target genomes.
[2024-01-24 13:24:26,714] [INFO] Target genome list was writen to GCF_002156005.1_ASM215600v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:26,780] [INFO] Task started: fastANI
[2024-01-24 13:24:26,781] [INFO] Running command: fastANI --query /var/lib/cwl/stgea51e395-1730-4a52-98ba-ec5b41077bac/GCF_002156005.1_ASM215600v1_genomic.fna.gz --refList GCF_002156005.1_ASM215600v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002156005.1_ASM215600v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:25:05,189] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:05,211] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:25:05,212] [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_014873755.1	s__Amycolatopsis lexingtonensis	99.991	3084	3085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_003937945.1	s__Amycolatopsis eburnea	94.2367	2553	3085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107925.1	s__Amycolatopsis pretoriensis	89.5499	2289	3085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	1.00	1.00	2	-
GCF_902497555.1	s__Amycolatopsis sp902497555	89.2742	2354	3085	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	89.1869	2265	3085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002904335.1	s__Amycolatopsis sp002904335	88.9013	2207	3085	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	88.8631	2038	3085	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	88.8193	2206	3085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	1.00	0.99	7	-
GCF_014654205.1	s__Amycolatopsis bullii	88.8066	2170	3085	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	88.6553	2253	3085	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	88.5803	2223	3085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383915.1	s__Amycolatopsis benzoatilytica	81.6255	1476	3085	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	80.8902	1388	3085	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 13:25:05,214] [INFO] GTDB search result was written to GCF_002156005.1_ASM215600v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:25:05,215] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:25:05,219] [INFO] DFAST_QC result json was written to GCF_002156005.1_ASM215600v1_genomic.fna/dqc_result.json
[2024-01-24 13:25:05,219] [INFO] DFAST_QC completed!
[2024-01-24 13:25:05,220] [INFO] Total running time: 0h3m19s