[2024-01-24 14:22:58,544] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:58,545] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:58,546] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f9ad02f-ac84-4562-aa9e-d37d1f2a57f8/dqc_reference
[2024-01-24 14:23:01,561] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:23:01,562] [INFO] Task started: Prodigal
[2024-01-24 14:23:01,563] [INFO] Running command: gunzip -c /var/lib/cwl/stg41662865-ae60-4f29-b1be-9e85542420b4/GCF_014653695.1_ASM1465369v1_genomic.fna.gz | prodigal -d GCF_014653695.1_ASM1465369v1_genomic.fna/cds.fna -a GCF_014653695.1_ASM1465369v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:35,206] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:35,207] [INFO] Task started: HMMsearch
[2024-01-24 14:23:35,207] [INFO] Running command: hmmsearch --tblout GCF_014653695.1_ASM1465369v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f9ad02f-ac84-4562-aa9e-d37d1f2a57f8/dqc_reference/reference_markers.hmm GCF_014653695.1_ASM1465369v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:35,985] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:35,991] [INFO] Found 6/6 markers.
[2024-01-24 14:23:36,078] [INFO] Query marker FASTA was written to GCF_014653695.1_ASM1465369v1_genomic.fna/markers.fasta
[2024-01-24 14:23:36,079] [INFO] Task started: Blastn
[2024-01-24 14:23:36,079] [INFO] Running command: blastn -query GCF_014653695.1_ASM1465369v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f9ad02f-ac84-4562-aa9e-d37d1f2a57f8/dqc_reference/reference_markers.fasta -out GCF_014653695.1_ASM1465369v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:44,116] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:44,121] [INFO] Selected 18 target genomes.
[2024-01-24 14:23:44,121] [INFO] Target genome list was writen to GCF_014653695.1_ASM1465369v1_genomic.fna/target_genomes.txt
[2024-01-24 14:23:44,126] [INFO] Task started: fastANI
[2024-01-24 14:23:44,126] [INFO] Running command: fastANI --query /var/lib/cwl/stg41662865-ae60-4f29-b1be-9e85542420b4/GCF_014653695.1_ASM1465369v1_genomic.fna.gz --refList GCF_014653695.1_ASM1465369v1_genomic.fna/target_genomes.txt --output GCF_014653695.1_ASM1465369v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:24:32,516] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:32,517] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f9ad02f-ac84-4562-aa9e-d37d1f2a57f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:24:32,518] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f9ad02f-ac84-4562-aa9e-d37d1f2a57f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:24:32,617] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:24:32,618] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:24:32,619] [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
Lentzea cavernae	strain=CGMCC 4.7367	GCA_014653695.1	2020703	2020703	type	True	100.0	3227	3229	95	conclusive
Lentzea albida	strain=DSM 44437	GCA_900111005.1	65499	65499	type	True	91.5219	2510	3229	95	below_threshold
Lentzea pudingi	strain=CGMCC 4.7319	GCA_014646255.1	1789439	1789439	type	True	90.7488	2341	3229	95	below_threshold
Lentzea flaviverrucosa	strain=DSM 44664	GCA_003350445.1	200379	200379	type	True	90.5835	2391	3229	95	below_threshold
Lentzea waywayandensis	strain=DSM 44232	GCA_900115955.1	84724	84724	type	True	90.4906	2411	3229	95	below_threshold
Lentzea albidocapillata	strain=NRRL B-24057	GCA_000719115.1	40571	40571	type	True	90.4384	2167	3229	95	below_threshold
Lentzea albidocapillata	strain=DSM 44073	GCA_900176525.1	40571	40571	type	True	90.4375	2173	3229	95	below_threshold
Lentzea californiensis	strain=DSM 43393	GCA_024648825.1	438851	438851	type	True	90.4283	2404	3229	95	below_threshold
Lentzea albidocapillata subsp. violacea	strain=DSM 44796	GCA_900100275.1	128104	40571	type	True	90.3312	2153	3229	95	below_threshold
Lentzea jiangxiensis	strain=CGMCC 4.6609	GCA_900104175.1	641025	641025	type	True	89.3108	2199	3229	95	below_threshold
Lentzea alba	strain=NEAU-D13	GCA_011067745.1	2714351	2714351	type	True	88.0989	2198	3229	95	below_threshold
Lentzea aerocolonigenes	strain=DSM 40034	GCA_024171805.1	68170	68170	type	True	87.9937	2199	3229	95	below_threshold
Lentzea xinjiangensis	strain=CGMCC 4.3525	GCA_900110955.1	402600	402600	type	True	87.7423	2115	3229	95	below_threshold
Lentzea flava	strain=DSM 43885	GCA_024171845.1	103732	103732	type	True	87.4668	2120	3229	95	below_threshold
Lentzea terrae	strain=NEAU-LZS 42	GCA_003265345.1	2200761	2200761	type	True	87.3275	2194	3229	95	below_threshold
Lentzea guizhouensis	strain=DHS C013	GCA_001701025.1	1586287	1586287	type	True	86.7223	2273	3229	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	82.2531	1647	3229	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	78.1539	1167	3229	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:24:32,621] [INFO] DFAST Taxonomy check result was written to GCF_014653695.1_ASM1465369v1_genomic.fna/tc_result.tsv
[2024-01-24 14:24:32,621] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:24:32,622] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:24:32,622] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f9ad02f-ac84-4562-aa9e-d37d1f2a57f8/dqc_reference/checkm_data
[2024-01-24 14:24:32,628] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:24:32,739] [INFO] Task started: CheckM
[2024-01-24 14:24:32,740] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014653695.1_ASM1465369v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014653695.1_ASM1465369v1_genomic.fna/checkm_input GCF_014653695.1_ASM1465369v1_genomic.fna/checkm_result
[2024-01-24 14:26:56,994] [INFO] Task succeeded: CheckM
[2024-01-24 14:26:56,996] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:26:57,017] [INFO] ===== Completeness check finished =====
[2024-01-24 14:26:57,017] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:26:57,018] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014653695.1_ASM1465369v1_genomic.fna/markers.fasta)
[2024-01-24 14:26:57,018] [INFO] Task started: Blastn
[2024-01-24 14:26:57,018] [INFO] Running command: blastn -query GCF_014653695.1_ASM1465369v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f9ad02f-ac84-4562-aa9e-d37d1f2a57f8/dqc_reference/reference_markers_gtdb.fasta -out GCF_014653695.1_ASM1465369v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:27:00,662] [INFO] Task succeeded: Blastn
[2024-01-24 14:27:00,665] [INFO] Selected 13 target genomes.
[2024-01-24 14:27:00,665] [INFO] Target genome list was writen to GCF_014653695.1_ASM1465369v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:27:00,672] [INFO] Task started: fastANI
[2024-01-24 14:27:00,672] [INFO] Running command: fastANI --query /var/lib/cwl/stg41662865-ae60-4f29-b1be-9e85542420b4/GCF_014653695.1_ASM1465369v1_genomic.fna.gz --refList GCF_014653695.1_ASM1465369v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014653695.1_ASM1465369v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:27:37,273] [INFO] Task succeeded: fastANI
[2024-01-24 14:27:37,325] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:27:37,325] [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_014653695.1	s__Lentzea cavernae	100.0	3227	3229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900111005.1	s__Lentzea albida	91.5123	2512	3229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646255.1	s__Lentzea pudingi	90.7896	2335	3229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350445.1	s__Lentzea flaviverrucosa	90.559	2394	3229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900115955.1	s__Lentzea waywayandensis	90.4904	2411	3229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719115.1	s__Lentzea albidocapillata	90.4393	2167	3229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	96.6655	99.99	99.99	1.00	1.00	2	-
GCF_900100275.1	s__Lentzea violacea	90.3239	2154	3229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	96.6655	N/A	N/A	N/A	N/A	1	-
GCF_900104175.1	s__Lentzea jiangxiensis	89.3243	2197	3229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011067745.1	s__Lentzea alba	88.0695	2203	3229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110955.1	s__Lentzea xinjiangensis	87.74	2116	3229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000955955.1	s__Lentzea aerocolonigenes_A	87.2719	2069	3229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907955.1	s__Lentzea nigeriaca	87.2525	2069	3229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001701025.1	s__Lentzea guizhouensis	86.7267	2271	3229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:27:37,327] [INFO] GTDB search result was written to GCF_014653695.1_ASM1465369v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:27:37,327] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:27:37,331] [INFO] DFAST_QC result json was written to GCF_014653695.1_ASM1465369v1_genomic.fna/dqc_result.json
[2024-01-24 14:27:37,332] [INFO] DFAST_QC completed!
[2024-01-24 14:27:37,332] [INFO] Total running time: 0h4m39s