[2024-01-24 12:30:52,582] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:52,584] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:52,584] [INFO] DQC Reference Directory: /var/lib/cwl/stgded1ac63-59bc-4fc1-9b19-92581d04bf7b/dqc_reference
[2024-01-24 12:30:53,935] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:53,936] [INFO] Task started: Prodigal
[2024-01-24 12:30:53,936] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c0590a1-ac14-48de-8c5b-022fb515d135/GCF_003385185.1_ASM338518v1_genomic.fna.gz | prodigal -d GCF_003385185.1_ASM338518v1_genomic.fna/cds.fna -a GCF_003385185.1_ASM338518v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:14,560] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:14,561] [INFO] Task started: HMMsearch
[2024-01-24 12:31:14,561] [INFO] Running command: hmmsearch --tblout GCF_003385185.1_ASM338518v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgded1ac63-59bc-4fc1-9b19-92581d04bf7b/dqc_reference/reference_markers.hmm GCF_003385185.1_ASM338518v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:14,893] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:14,894] [INFO] Found 6/6 markers.
[2024-01-24 12:31:14,955] [INFO] Query marker FASTA was written to GCF_003385185.1_ASM338518v1_genomic.fna/markers.fasta
[2024-01-24 12:31:14,955] [INFO] Task started: Blastn
[2024-01-24 12:31:14,955] [INFO] Running command: blastn -query GCF_003385185.1_ASM338518v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgded1ac63-59bc-4fc1-9b19-92581d04bf7b/dqc_reference/reference_markers.fasta -out GCF_003385185.1_ASM338518v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:16,192] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:16,199] [INFO] Selected 20 target genomes.
[2024-01-24 12:31:16,200] [INFO] Target genome list was writen to GCF_003385185.1_ASM338518v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:16,208] [INFO] Task started: fastANI
[2024-01-24 12:31:16,209] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c0590a1-ac14-48de-8c5b-022fb515d135/GCF_003385185.1_ASM338518v1_genomic.fna.gz --refList GCF_003385185.1_ASM338518v1_genomic.fna/target_genomes.txt --output GCF_003385185.1_ASM338518v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:47,111] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:47,112] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgded1ac63-59bc-4fc1-9b19-92581d04bf7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:47,112] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgded1ac63-59bc-4fc1-9b19-92581d04bf7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:47,130] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:47,131] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:47,131] [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 palatopharyngis	strain=DSM 44832	GCA_003385185.1	187982	187982	type	True	100.0	2255	2277	95	conclusive
Amycolatopsis marina	strain=CGMCC 4.3568	GCA_900111885.1	490629	490629	type	True	87.8207	1634	2277	95	below_threshold
Prauserella muralis	strain=DSM 45305	GCA_003202285.1	588067	588067	type	True	80.715	1015	2277	95	below_threshold
Prauserella muralis	strain=DSM 45305	GCA_007993965.1	588067	588067	type	True	80.7143	1012	2277	95	below_threshold
Amycolatopsis arida	strain=DSM 45648	GCA_004365925.1	587909	587909	type	True	80.3746	1011	2277	95	below_threshold
Amycolatopsis arida	strain=CGMCC 4.5579	GCA_900115565.1	587909	587909	type	True	80.3697	1011	2277	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	80.2747	1021	2277	95	below_threshold
Amycolatopsis cihanbeyliensis	strain=DSM 45679	GCA_006715045.1	1128664	1128664	type	True	80.1426	991	2277	95	below_threshold
Amycolatopsis nigrescens	strain=CSC17Ta-90	GCA_000384315.1	381445	381445	type	True	79.9385	1004	2277	95	below_threshold
Amycolatopsis anabasis	strain=EGI 650086	GCA_009765355.1	1840409	1840409	type	True	79.7588	981	2277	95	below_threshold
Amycolatopsis magusensis	strain=DSM 45510	GCA_017875555.1	882444	882444	type	True	79.6822	958	2277	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	79.5013	853	2277	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	79.4164	877	2277	95	below_threshold
Amycolatopsis saalfeldensis	strain=DSM 44993	GCA_900110575.1	394193	394193	type	True	79.3098	871	2277	95	below_threshold
Amycolatopsis sacchari	strain=DSM 44468	GCA_900114035.1	115433	115433	type	True	79.2723	809	2277	95	below_threshold
Amycolatopsis tolypomycina	strain=DSM 44544	GCA_900105945.1	208445	208445	type	True	79.1536	903	2277	95	below_threshold
Saccharomonospora amisosensis	strain=DSM 45685	GCA_011761185.1	1128677	1128677	type	True	79.0668	696	2277	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	78.9463	940	2277	95	below_threshold
Amycolatopsis pretoriensis	strain=DSM 44654	GCA_900107925.1	218821	218821	type	True	78.8696	911	2277	95	below_threshold
Lentzea aerocolonigenes	strain=DSM 40034	GCA_024171805.1	68170	68170	type	True	77.5231	604	2277	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:47,132] [INFO] DFAST Taxonomy check result was written to GCF_003385185.1_ASM338518v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:47,132] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:47,133] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:47,133] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgded1ac63-59bc-4fc1-9b19-92581d04bf7b/dqc_reference/checkm_data
[2024-01-24 12:31:47,134] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:47,195] [INFO] Task started: CheckM
[2024-01-24 12:31:47,195] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003385185.1_ASM338518v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003385185.1_ASM338518v1_genomic.fna/checkm_input GCF_003385185.1_ASM338518v1_genomic.fna/checkm_result
[2024-01-24 12:32:48,062] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:48,063] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:48,091] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:48,091] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:48,091] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003385185.1_ASM338518v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:48,092] [INFO] Task started: Blastn
[2024-01-24 12:32:48,092] [INFO] Running command: blastn -query GCF_003385185.1_ASM338518v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgded1ac63-59bc-4fc1-9b19-92581d04bf7b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003385185.1_ASM338518v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:49,825] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:49,829] [INFO] Selected 17 target genomes.
[2024-01-24 12:32:49,829] [INFO] Target genome list was writen to GCF_003385185.1_ASM338518v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:49,847] [INFO] Task started: fastANI
[2024-01-24 12:32:49,848] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c0590a1-ac14-48de-8c5b-022fb515d135/GCF_003385185.1_ASM338518v1_genomic.fna.gz --refList GCF_003385185.1_ASM338518v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003385185.1_ASM338518v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:14,847] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:14,865] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:14,865] [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_003385185.1	s__Amycolatopsis_D palatopharyngis	100.0	2245	2277	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis_D	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900111885.1	s__Amycolatopsis_D marina	87.8253	1633	2277	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202285.1	s__Saccharomonospora muralis	80.7452	1009	2277	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900115565.1	s__Yuhushiella arida	80.3583	1013	2277	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Yuhushiella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_016464705.1	s__Saccharomonospora sp016464705	80.1942	966	2277	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	80.1692	1006	2277	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715045.1	s__Amycolatopsis_D cihanbeyliensis	80.1473	990	2277	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003001955.1	s__Saccharomonospora shujinwangii	79.9791	951	2277	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000384315.1	s__Amycolatopsis nigrescens	79.93	1006	2277	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765355.1	s__Amycolatopsis anabasis	79.7639	980	2277	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002262875.1	s__Amycolatopsis antarctica	79.7156	860	2277	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004214935.1	s__Amycolatopsis suaedae	79.6436	936	2277	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001942305.1	s__Saccharomonospora sp001942305	79.4551	715	2277	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110575.1	s__Amycolatopsis saalfeldensis	79.3203	869	2277	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114035.1	s__Amycolatopsis sacchari	79.2632	811	2277	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018736145.1	s__Amycolatopsis sp018736145	79.2268	936	2277	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011761185.1	s__Saccharomonospora amisosensis	79.0737	695	2277	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:14,867] [INFO] GTDB search result was written to GCF_003385185.1_ASM338518v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:14,867] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:14,872] [INFO] DFAST_QC result json was written to GCF_003385185.1_ASM338518v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:14,872] [INFO] DFAST_QC completed!
[2024-01-24 12:33:14,872] [INFO] Total running time: 0h2m22s