[2024-01-24 12:44:11,026] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:11,028] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:11,029] [INFO] DQC Reference Directory: /var/lib/cwl/stgd39ac701-f7f0-42e8-b726-bf29ff0012cc/dqc_reference
[2024-01-24 12:44:12,535] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:12,536] [INFO] Task started: Prodigal
[2024-01-24 12:44:12,537] [INFO] Running command: gunzip -c /var/lib/cwl/stgbb0ac0fe-7393-4398-842d-2cca695ea024/GCF_024171865.1_ASM2417186v1_genomic.fna.gz | prodigal -d GCF_024171865.1_ASM2417186v1_genomic.fna/cds.fna -a GCF_024171865.1_ASM2417186v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:30,377] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:30,378] [INFO] Task started: HMMsearch
[2024-01-24 12:44:30,378] [INFO] Running command: hmmsearch --tblout GCF_024171865.1_ASM2417186v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd39ac701-f7f0-42e8-b726-bf29ff0012cc/dqc_reference/reference_markers.hmm GCF_024171865.1_ASM2417186v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:30,763] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:30,765] [INFO] Found 6/6 markers.
[2024-01-24 12:44:30,816] [INFO] Query marker FASTA was written to GCF_024171865.1_ASM2417186v1_genomic.fna/markers.fasta
[2024-01-24 12:44:30,817] [INFO] Task started: Blastn
[2024-01-24 12:44:30,817] [INFO] Running command: blastn -query GCF_024171865.1_ASM2417186v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd39ac701-f7f0-42e8-b726-bf29ff0012cc/dqc_reference/reference_markers.fasta -out GCF_024171865.1_ASM2417186v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:32,414] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:32,418] [INFO] Selected 13 target genomes.
[2024-01-24 12:44:32,418] [INFO] Target genome list was writen to GCF_024171865.1_ASM2417186v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:32,427] [INFO] Task started: fastANI
[2024-01-24 12:44:32,428] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb0ac0fe-7393-4398-842d-2cca695ea024/GCF_024171865.1_ASM2417186v1_genomic.fna.gz --refList GCF_024171865.1_ASM2417186v1_genomic.fna/target_genomes.txt --output GCF_024171865.1_ASM2417186v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:52,132] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:52,132] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd39ac701-f7f0-42e8-b726-bf29ff0012cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:52,133] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd39ac701-f7f0-42e8-b726-bf29ff0012cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:52,148] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:44:52,148] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:52,148] [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
Prauserella aidingensis	strain=DSM 45266	GCA_024171865.1	387890	387890	type	True	100.0	1831	1844	95	conclusive
Prauserella isguenensis	strain=CECT 8577	GCA_014191605.1	1470180	1470180	type	True	92.9161	1438	1844	95	below_threshold
Prauserella rugosa	strain=NRRL B-2295	GCA_000719975.1	43354	43354	type	True	84.3333	1276	1844	95	below_threshold
Prauserella rugosa	strain=DSM 43194	GCA_007829565.1	43354	43354	type	True	84.3165	1288	1844	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	80.3773	983	1844	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	79.4987	827	1844	95	below_threshold
Amycolatopsis thermoflava	strain=N1165	GCA_000473265.1	84480	84480	type	True	79.4463	882	1844	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	79.2127	802	1844	95	below_threshold
Saccharomonospora viridis	strain=DSM 43017	GCA_000023865.1	1852	1852	type	True	78.7353	584	1844	95	below_threshold
Amycolatopsis saalfeldensis	strain=DSM 44993	GCA_900110575.1	394193	394193	type	True	78.6159	852	1844	95	below_threshold
Amycolatopsis azurea	strain=DSM 43854	GCA_001995215.1	36819	36819	type	True	78.5797	784	1844	95	below_threshold
Amycolatopsis azurea	strain=DSM 43854	GCA_000340415.1	36819	36819	type	True	78.5474	775	1844	95	below_threshold
Lentzea californiensis	strain=DSM 43393	GCA_024648825.1	438851	438851	type	True	77.5934	593	1844	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:52,150] [INFO] DFAST Taxonomy check result was written to GCF_024171865.1_ASM2417186v1_genomic.fna/tc_result.tsv
[2024-01-24 12:44:52,150] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:52,151] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:52,151] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd39ac701-f7f0-42e8-b726-bf29ff0012cc/dqc_reference/checkm_data
[2024-01-24 12:44:52,152] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:52,212] [INFO] Task started: CheckM
[2024-01-24 12:44:52,212] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024171865.1_ASM2417186v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024171865.1_ASM2417186v1_genomic.fna/checkm_input GCF_024171865.1_ASM2417186v1_genomic.fna/checkm_result
[2024-01-24 12:45:55,281] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:55,283] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:55,309] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:55,310] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:55,310] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024171865.1_ASM2417186v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:55,311] [INFO] Task started: Blastn
[2024-01-24 12:45:55,311] [INFO] Running command: blastn -query GCF_024171865.1_ASM2417186v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd39ac701-f7f0-42e8-b726-bf29ff0012cc/dqc_reference/reference_markers_gtdb.fasta -out GCF_024171865.1_ASM2417186v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:57,593] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:57,598] [INFO] Selected 15 target genomes.
[2024-01-24 12:45:57,598] [INFO] Target genome list was writen to GCF_024171865.1_ASM2417186v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:57,615] [INFO] Task started: fastANI
[2024-01-24 12:45:57,615] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb0ac0fe-7393-4398-842d-2cca695ea024/GCF_024171865.1_ASM2417186v1_genomic.fna.gz --refList GCF_024171865.1_ASM2417186v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024171865.1_ASM2417186v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:19,002] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:19,019] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:46:19,019] [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_014191605.1	s__Saccharomonospora isguenensis	92.9161	1438	1844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014195435.1	s__Saccharomonospora sediminis	88.5221	1401	1844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719975.1	s__Saccharomonospora rugosa	84.3299	1277	1844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	99.54	99.08	0.98	0.95	3	-
GCF_001942305.1	s__Saccharomonospora sp001942305	83.7898	1165	1844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202235.1	s__Saccharomonospora sp003202235	80.5348	1022	1844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202285.1	s__Saccharomonospora muralis	80.4804	960	1844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016595675.1	s__Saccharomonospora sp016595675	80.346	989	1844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005146945.1	s__Saccharomonospora endophytica	80.3052	980	1844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	99.14	99.02	0.90	0.90	3	-
GCF_900115565.1	s__Yuhushiella arida	79.28	797	1844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Yuhushiella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900114035.1	s__Amycolatopsis sacchari	79.2287	807	1844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000504245.1	s__Amycolatopsis_C halophila	78.8849	548	1844	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_900119165.1	s__Amycolatopsis australiensis	78.8511	871	1844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002796545.1	s__Amycolatopsis sp002796545	78.6089	776	1844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.98	99.98	1.00	1.00	2	-
GCF_001995215.1	s__Amycolatopsis azurea	78.589	782	1844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014654365.1	s__Amycolatopsis oliviviridis	78.5872	779	1844	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 12:46:19,021] [INFO] GTDB search result was written to GCF_024171865.1_ASM2417186v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:19,021] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:19,025] [INFO] DFAST_QC result json was written to GCF_024171865.1_ASM2417186v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:19,025] [INFO] DFAST_QC completed!
[2024-01-24 12:46:19,025] [INFO] Total running time: 0h2m8s