[2024-01-24 13:46:01,064] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:01,066] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:01,067] [INFO] DQC Reference Directory: /var/lib/cwl/stg71c1f7f8-871b-48b8-b821-e7a219aed095/dqc_reference
[2024-01-24 13:46:02,440] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:02,441] [INFO] Task started: Prodigal
[2024-01-24 13:46:02,441] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f443dda-4fce-420b-8ad6-f0c8a65cbaf9/GCF_013450155.1_ASM1345015v1_genomic.fna.gz | prodigal -d GCF_013450155.1_ASM1345015v1_genomic.fna/cds.fna -a GCF_013450155.1_ASM1345015v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:17,212] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:17,213] [INFO] Task started: HMMsearch
[2024-01-24 13:46:17,213] [INFO] Running command: hmmsearch --tblout GCF_013450155.1_ASM1345015v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg71c1f7f8-871b-48b8-b821-e7a219aed095/dqc_reference/reference_markers.hmm GCF_013450155.1_ASM1345015v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:17,488] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:17,490] [INFO] Found 6/6 markers.
[2024-01-24 13:46:17,538] [INFO] Query marker FASTA was written to GCF_013450155.1_ASM1345015v1_genomic.fna/markers.fasta
[2024-01-24 13:46:17,539] [INFO] Task started: Blastn
[2024-01-24 13:46:17,539] [INFO] Running command: blastn -query GCF_013450155.1_ASM1345015v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71c1f7f8-871b-48b8-b821-e7a219aed095/dqc_reference/reference_markers.fasta -out GCF_013450155.1_ASM1345015v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:18,616] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:18,620] [INFO] Selected 19 target genomes.
[2024-01-24 13:46:18,621] [INFO] Target genome list was writen to GCF_013450155.1_ASM1345015v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:18,643] [INFO] Task started: fastANI
[2024-01-24 13:46:18,644] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f443dda-4fce-420b-8ad6-f0c8a65cbaf9/GCF_013450155.1_ASM1345015v1_genomic.fna.gz --refList GCF_013450155.1_ASM1345015v1_genomic.fna/target_genomes.txt --output GCF_013450155.1_ASM1345015v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:41,331] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:41,332] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg71c1f7f8-871b-48b8-b821-e7a219aed095/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:41,332] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg71c1f7f8-871b-48b8-b821-e7a219aed095/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:41,347] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:41,347] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:41,347] [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
Haloechinothrix aidingensis	strain=YIM 98757	GCA_013450155.1	2752311	2752311	type	True	100.0	1607	1607	95	conclusive
Haloechinothrix alba	strain=DSM 45207	GCA_900188115.1	664784	664784	type	True	93.7858	1268	1607	95	below_threshold
Haloechinothrix halophila	strain=YIM 93223	GCA_000504245.1	1069073	1069073	type	True	78.6747	615	1607	95	below_threshold
Amycolatopsis arida	strain=DSM 45648	GCA_004365925.1	587909	587909	type	True	78.5245	607	1607	95	below_threshold
Amycolatopsis arida	strain=CGMCC 4.5579	GCA_900115565.1	587909	587909	type	True	78.5221	603	1607	95	below_threshold
Prauserella muralis	strain=DSM 45305	GCA_003202285.1	588067	588067	type	True	78.4446	620	1607	95	below_threshold
Saccharomonospora iraqiensis	strain=IQ-H1	GCA_000430445.1	52698	52698	type	True	78.4396	454	1607	95	below_threshold
Prauserella muralis	strain=DSM 45305	GCA_007993965.1	588067	588067	type	True	78.3911	637	1607	95	below_threshold
Saccharomonospora iraqiensis subsp. paurometabolica	strain=YIM 90007	GCA_000231035.3	208085	52698	type	True	78.2675	486	1607	95	below_threshold
Amycolatopsis albispora	strain=WP1	GCA_003312875.1	1804986	1804986	type	True	78.1653	601	1607	95	below_threshold
Saccharomonospora halophila	strain=8	GCA_000383775.1	129922	129922	type	True	78.143	423	1607	95	below_threshold
Amycolatopsis alkalitolerans	strain=SYSUP0005	GCA_006152065.1	2547244	2547244	type	True	78.0446	474	1607	95	below_threshold
Amycolatopsis bartoniae	strain=DSM 45807	GCA_014191255.1	941986	941986	type	True	78.0055	573	1607	95	below_threshold
Amycolatopsis bartoniae	strain=DSM 45807	GCA_007713755.1	941986	941986	type	True	77.9509	562	1607	95	below_threshold
Amycolatopsis thermoflava	strain=N1165	GCA_000473265.1	84480	84480	type	True	77.9263	602	1607	95	below_threshold
Amycolatopsis acidicola	strain=K81G1	GCA_007713735.2	2596893	2596893	type	True	77.7999	544	1607	95	below_threshold
Amycolatopsis australiensis	strain=DSM 44671	GCA_900119165.1	546364	546364	type	True	77.6535	591	1607	95	below_threshold
Amycolatopsis azurea	strain=DSM 43854	GCA_000340415.1	36819	36819	type	True	77.4565	505	1607	95	below_threshold
Amycolatopsis lexingtonensis	strain=NRRL B-24131	GCA_002156005.1	218822	218822	type	True	77.3972	574	1607	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:41,349] [INFO] DFAST Taxonomy check result was written to GCF_013450155.1_ASM1345015v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:41,350] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:41,350] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:41,351] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg71c1f7f8-871b-48b8-b821-e7a219aed095/dqc_reference/checkm_data
[2024-01-24 13:46:41,352] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:41,401] [INFO] Task started: CheckM
[2024-01-24 13:46:41,402] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013450155.1_ASM1345015v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013450155.1_ASM1345015v1_genomic.fna/checkm_input GCF_013450155.1_ASM1345015v1_genomic.fna/checkm_result
[2024-01-24 13:47:25,882] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:25,884] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:25,905] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:25,906] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:25,906] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013450155.1_ASM1345015v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:25,906] [INFO] Task started: Blastn
[2024-01-24 13:47:25,907] [INFO] Running command: blastn -query GCF_013450155.1_ASM1345015v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71c1f7f8-871b-48b8-b821-e7a219aed095/dqc_reference/reference_markers_gtdb.fasta -out GCF_013450155.1_ASM1345015v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:27,450] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:27,455] [INFO] Selected 17 target genomes.
[2024-01-24 13:47:27,455] [INFO] Target genome list was writen to GCF_013450155.1_ASM1345015v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:27,545] [INFO] Task started: fastANI
[2024-01-24 13:47:27,546] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f443dda-4fce-420b-8ad6-f0c8a65cbaf9/GCF_013450155.1_ASM1345015v1_genomic.fna.gz --refList GCF_013450155.1_ASM1345015v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013450155.1_ASM1345015v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:47,961] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:47,980] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:47,981] [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_013450155.1	s__Haloechinothrix aidingensis	100.0	1607	1607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Haloechinothrix	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900188115.1	s__Haloechinothrix alba	93.8141	1266	1607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Haloechinothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377395.1	s__Amycolatopsis_C sp009377395	79.0	578	1607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000504245.1	s__Amycolatopsis_C halophila	78.6679	616	1607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115565.1	s__Yuhushiella arida	78.5284	602	1607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Yuhushiella	95.0	100.00	100.00	0.99	0.99	2	-
GCA_009377475.1	s__Amycolatopsis_C sp009377475	78.4482	600	1607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009379975.1	s__Amycolatopsis_C sp009379975	78.3869	500	1607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003001955.1	s__Saccharomonospora shujinwangii	78.343	602	1607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000231035.2	s__Saccharomonospora paurometabolica	78.2842	483	1607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	96.0038	N/A	N/A	N/A	N/A	1	-
GCF_016464705.1	s__Saccharomonospora sp016464705	78.2771	593	1607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003312875.1	s__Amycolatopsis albispora	78.1662	601	1607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007713735.2	s__Amycolatopsis acidicola	77.7886	546	1607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000231075.2	s__Amycolatopsis sp000231075	77.7884	605	1607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.4849	N/A	N/A	N/A	N/A	1	-
GCA_009379845.1	s__Tamaricihabitans sp009379845	77.6147	398	1607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Tamaricihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003937945.1	s__Amycolatopsis eburnea	77.5502	614	1607	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	77.4747	613	1607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	1.00	1.00	2	-
GCF_008386585.1	s__AN110305 sp008386585	77.2285	502	1607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__AN110305	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:47,982] [INFO] GTDB search result was written to GCF_013450155.1_ASM1345015v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:47,983] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:47,988] [INFO] DFAST_QC result json was written to GCF_013450155.1_ASM1345015v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:47,988] [INFO] DFAST_QC completed!
[2024-01-24 13:47:47,989] [INFO] Total running time: 0h1m47s