[2024-01-24 11:35:11,984] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:11,987] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:11,987] [INFO] DQC Reference Directory: /var/lib/cwl/stgd89a38bd-87c5-4133-8e82-fa6ef8386f88/dqc_reference
[2024-01-24 11:35:14,487] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:14,488] [INFO] Task started: Prodigal
[2024-01-24 11:35:14,488] [INFO] Running command: gunzip -c /var/lib/cwl/stg9d9500f7-bb7b-4736-a784-fc01c3475760/GCF_025061645.1_ASM2506164v1_genomic.fna.gz | prodigal -d GCF_025061645.1_ASM2506164v1_genomic.fna/cds.fna -a GCF_025061645.1_ASM2506164v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:36:03,942] [INFO] Task succeeded: Prodigal
[2024-01-24 11:36:03,943] [INFO] Task started: HMMsearch
[2024-01-24 11:36:03,943] [INFO] Running command: hmmsearch --tblout GCF_025061645.1_ASM2506164v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd89a38bd-87c5-4133-8e82-fa6ef8386f88/dqc_reference/reference_markers.hmm GCF_025061645.1_ASM2506164v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:36:04,394] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:36:04,395] [INFO] Found 6/6 markers.
[2024-01-24 11:36:04,483] [INFO] Query marker FASTA was written to GCF_025061645.1_ASM2506164v1_genomic.fna/markers.fasta
[2024-01-24 11:36:04,484] [INFO] Task started: Blastn
[2024-01-24 11:36:04,484] [INFO] Running command: blastn -query GCF_025061645.1_ASM2506164v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd89a38bd-87c5-4133-8e82-fa6ef8386f88/dqc_reference/reference_markers.fasta -out GCF_025061645.1_ASM2506164v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:05,772] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:05,795] [INFO] Selected 23 target genomes.
[2024-01-24 11:36:05,796] [INFO] Target genome list was writen to GCF_025061645.1_ASM2506164v1_genomic.fna/target_genomes.txt
[2024-01-24 11:36:05,804] [INFO] Task started: fastANI
[2024-01-24 11:36:05,804] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d9500f7-bb7b-4736-a784-fc01c3475760/GCF_025061645.1_ASM2506164v1_genomic.fna.gz --refList GCF_025061645.1_ASM2506164v1_genomic.fna/target_genomes.txt --output GCF_025061645.1_ASM2506164v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:36:54,181] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:54,182] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd89a38bd-87c5-4133-8e82-fa6ef8386f88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:36:54,183] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd89a38bd-87c5-4133-8e82-fa6ef8386f88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:36:54,203] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:36:54,203] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:36:54,203] [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
Saccharothrix carnea	strain=CGMCC 4.7097	GCA_003014735.1	1280637	1280637	type	True	80.996	1612	3642	95	below_threshold
Saccharothrix coeruleofusca	strain=JCM 3313	GCA_014648515.1	33919	33919	type	True	80.9619	1532	3642	95	below_threshold
Saccharothrix texasensis	strain=DSM 44231	GCA_003752005.1	103734	103734	type	True	80.824	1724	3642	95	below_threshold
Saccharothrix deserti	strain=BMP B8144	GCA_009769385.1	2593674	2593674	type	True	80.7254	1665	3642	95	below_threshold
Saccharothrix saharensis	strain=DSM 45456	GCA_006716745.1	571190	571190	type	True	80.6954	1711	3642	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	80.4872	1513	3642	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_000716755.1	103733	103733	type	True	80.4331	1737	3642	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_009498035.1	103733	103733	type	True	80.4175	1777	3642	95	below_threshold
Saccharothrix obliqua	strain=SC076	GCA_019375475.1	2861747	2861747	type	True	80.2197	1403	3642	95	below_threshold
Lentzea jiangxiensis	strain=CGMCC 4.6609	GCA_900104175.1	641025	641025	type	True	80.1926	1464	3642	95	below_threshold
Lentzea californiensis	strain=DSM 43393	GCA_024648825.1	438851	438851	type	True	80.1646	1482	3642	95	below_threshold
Lentzea albidocapillata	strain=NRRL B-24057	GCA_000719115.1	40571	40571	type	True	80.101	1358	3642	95	below_threshold
Lentzea cavernae	strain=CGMCC 4.7367	GCA_014653695.1	2020703	2020703	type	True	80.075	1614	3642	95	below_threshold
Lentzea pudingi	strain=CGMCC 4.7319	GCA_014646255.1	1789439	1789439	type	True	80.0406	1495	3642	95	below_threshold
Lentzea xinjiangensis	strain=CGMCC 4.3525	GCA_900110955.1	402600	402600	type	True	80.0092	1562	3642	95	below_threshold
Lentzea albidocapillata	strain=DSM 44073	GCA_900176525.1	40571	40571	type	True	79.9681	1382	3642	95	below_threshold
Lentzea flaviverrucosa	strain=DSM 44664	GCA_003350445.1	200379	200379	type	True	79.9612	1513	3642	95	below_threshold
Lentzea waywayandensis	strain=DSM 44232	GCA_900115955.1	84724	84724	type	True	79.945	1599	3642	95	below_threshold
Lentzea kentuckyensis	strain=NRRL B-24416	GCA_002150765.1	360086	360086	type	True	79.9026	1504	3642	95	below_threshold
Lentzea flava	strain=JCM 3296	GCA_014648475.1	103732	103732	type	True	79.8842	1474	3642	95	below_threshold
Saccharothrix violaceirubra	strain=DSM 45084	GCA_014203755.1	413306	413306	type	True	79.839	1279	3642	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	77.7567	986	3642	95	below_threshold
Prauserella aidingensis	strain=DSM 45266	GCA_024171865.1	387890	387890	type	True	77.3454	780	3642	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:36:54,205] [INFO] DFAST Taxonomy check result was written to GCF_025061645.1_ASM2506164v1_genomic.fna/tc_result.tsv
[2024-01-24 11:36:54,206] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:36:54,206] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:36:54,207] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd89a38bd-87c5-4133-8e82-fa6ef8386f88/dqc_reference/checkm_data
[2024-01-24 11:36:54,209] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:36:54,303] [INFO] Task started: CheckM
[2024-01-24 11:36:54,304] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025061645.1_ASM2506164v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025061645.1_ASM2506164v1_genomic.fna/checkm_input GCF_025061645.1_ASM2506164v1_genomic.fna/checkm_result
[2024-01-24 11:39:36,740] [INFO] Task succeeded: CheckM
[2024-01-24 11:39:36,742] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:39:36,775] [INFO] ===== Completeness check finished =====
[2024-01-24 11:39:36,775] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:39:36,775] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025061645.1_ASM2506164v1_genomic.fna/markers.fasta)
[2024-01-24 11:39:36,776] [INFO] Task started: Blastn
[2024-01-24 11:39:36,776] [INFO] Running command: blastn -query GCF_025061645.1_ASM2506164v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd89a38bd-87c5-4133-8e82-fa6ef8386f88/dqc_reference/reference_markers_gtdb.fasta -out GCF_025061645.1_ASM2506164v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:39:38,726] [INFO] Task succeeded: Blastn
[2024-01-24 11:39:38,730] [INFO] Selected 20 target genomes.
[2024-01-24 11:39:38,731] [INFO] Target genome list was writen to GCF_025061645.1_ASM2506164v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:39:38,743] [INFO] Task started: fastANI
[2024-01-24 11:39:38,743] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d9500f7-bb7b-4736-a784-fc01c3475760/GCF_025061645.1_ASM2506164v1_genomic.fna.gz --refList GCF_025061645.1_ASM2506164v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025061645.1_ASM2506164v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:40:22,673] [INFO] Task succeeded: fastANI
[2024-01-24 11:40:22,693] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:40:22,693] [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_003002815.1	s__Umezawaea tangerina	86.7779	2489	3642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Umezawaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016464305.1	s__REN6 sp016464305	81.0929	1389	3642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__REN6	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003752005.1	s__Actinosynnema texasense	80.8583	1717	3642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	98.51	98.51	0.92	0.92	2	-
GCF_000716595.1	s__Actinosynnema sp000716595	80.8465	1587	3642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280085.1	s__Actinosynnema sp001280085	80.8352	1753	3642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009769385.1	s__Actinosynnema deserti	80.7302	1662	3642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716745.1	s__Actinosynnema saharense	80.7196	1704	3642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007845675.1	s__Lentzea sp007845675	80.5188	1508	3642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009498035.1	s__Actinosynnema syringae	80.4372	1769	3642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	99.98	99.98	1.00	1.00	2	-
GCF_900104175.1	s__Lentzea jiangxiensis	80.1816	1467	3642	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	80.0835	1361	3642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	96.6655	99.99	99.99	1.00	1.00	2	-
GCF_900110955.1	s__Lentzea xinjiangensis	80.0729	1543	3642	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	80.0078	1505	3642	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	79.9956	1505	3642	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	79.9229	1604	3642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648475.1	s__Lentzea flava	79.9059	1468	3642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002150765.1	s__Lentzea kentuckyensis	79.9039	1502	3642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203755.1	s__Actinosynnema violaceirubrum	79.8286	1284	3642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000955955.1	s__Lentzea aerocolonigenes_A	79.7163	1394	3642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119165.1	s__Amycolatopsis australiensis	77.9432	1243	3642	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 11:40:22,697] [INFO] GTDB search result was written to GCF_025061645.1_ASM2506164v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:40:22,703] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:40:22,711] [INFO] DFAST_QC result json was written to GCF_025061645.1_ASM2506164v1_genomic.fna/dqc_result.json
[2024-01-24 11:40:22,711] [INFO] DFAST_QC completed!
[2024-01-24 11:40:22,711] [INFO] Total running time: 0h5m11s