[2024-01-25 17:38:20,522] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:38:20,524] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:38:20,524] [INFO] DQC Reference Directory: /var/lib/cwl/stg80ec7b30-ac0d-492a-bba6-d94931b0f31a/dqc_reference
[2024-01-25 17:38:21,667] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:38:21,668] [INFO] Task started: Prodigal
[2024-01-25 17:38:21,668] [INFO] Running command: gunzip -c /var/lib/cwl/stg2be1483b-2a02-4501-b191-a405ef30b210/GCF_030813695.1_ASM3081369v1_genomic.fna.gz | prodigal -d GCF_030813695.1_ASM3081369v1_genomic.fna/cds.fna -a GCF_030813695.1_ASM3081369v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:38:45,961] [INFO] Task succeeded: Prodigal
[2024-01-25 17:38:45,961] [INFO] Task started: HMMsearch
[2024-01-25 17:38:45,961] [INFO] Running command: hmmsearch --tblout GCF_030813695.1_ASM3081369v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80ec7b30-ac0d-492a-bba6-d94931b0f31a/dqc_reference/reference_markers.hmm GCF_030813695.1_ASM3081369v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:38:46,279] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:38:46,280] [INFO] Found 6/6 markers.
[2024-01-25 17:38:46,343] [INFO] Query marker FASTA was written to GCF_030813695.1_ASM3081369v1_genomic.fna/markers.fasta
[2024-01-25 17:38:46,343] [INFO] Task started: Blastn
[2024-01-25 17:38:46,344] [INFO] Running command: blastn -query GCF_030813695.1_ASM3081369v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80ec7b30-ac0d-492a-bba6-d94931b0f31a/dqc_reference/reference_markers.fasta -out GCF_030813695.1_ASM3081369v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:38:47,635] [INFO] Task succeeded: Blastn
[2024-01-25 17:38:47,638] [INFO] Selected 16 target genomes.
[2024-01-25 17:38:47,638] [INFO] Target genome list was writen to GCF_030813695.1_ASM3081369v1_genomic.fna/target_genomes.txt
[2024-01-25 17:38:47,642] [INFO] Task started: fastANI
[2024-01-25 17:38:47,643] [INFO] Running command: fastANI --query /var/lib/cwl/stg2be1483b-2a02-4501-b191-a405ef30b210/GCF_030813695.1_ASM3081369v1_genomic.fna.gz --refList GCF_030813695.1_ASM3081369v1_genomic.fna/target_genomes.txt --output GCF_030813695.1_ASM3081369v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:39:29,660] [INFO] Task succeeded: fastANI
[2024-01-25 17:39:29,660] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80ec7b30-ac0d-492a-bba6-d94931b0f31a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:39:29,661] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80ec7b30-ac0d-492a-bba6-d94931b0f31a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:39:29,671] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:39:29,671] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:39:29,671] [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
Kitasatospora herbaricolor	strain=JCM 4138	GCA_014648975.1	68217	68217	type	True	99.9616	3072	3193	95	conclusive
Kitasatospora indigofera	strain=JCM 4646	GCA_014655955.1	67307	67307	type	True	94.4401	2650	3193	95	below_threshold
Kitasatospora atroaurantiaca	strain=DSM 41649	GCA_007828955.1	285545	285545	type	True	84.8709	1617	3193	95	below_threshold
Kitasatospora purpeofusca	strain=NRRL B-1817	GCA_000718025.1	67352	67352	type	True	84.0916	1827	3193	95	below_threshold
Kitasatospora aureofaciens	strain=NRRL 2209	GCA_000978515.1	1894	1894	type	True	84.0587	1448	3193	95	below_threshold
Kitasatospora gansuensis	strain=DSM 44786	GCA_014203705.1	258050	258050	type	True	83.9795	1712	3193	95	below_threshold
Streptomyces rubellomurinus	strain=ATCC 31215	GCA_000961885.1	359131	359131	type	True	83.9546	1655	3193	95	below_threshold
Kitasatospora paracochleata	strain=DSM 41656	GCA_024172095.1	58354	58354	type	True	83.5704	1739	3193	95	below_threshold
Kitasatospora azatica	strain=KCTC 9699	GCA_000744785.1	58347	58347	type	True	83.188	1570	3193	95	below_threshold
Kitasatospora mediocidica	strain=KCTC 9733	GCA_000744225.1	58352	58352	type	True	83.128	1631	3193	95	below_threshold
Kitasatospora kifunensis	strain=DSM 41654	GCA_014203855.1	58351	58351	type	True	82.7326	1554	3193	95	below_threshold
Kitasatospora acidiphila	strain=MMS16-CNU292	GCA_006636205.1	2567942	2567942	type	True	82.4793	1453	3193	95	below_threshold
Kitasatospora viridis	strain=DSM 44826	GCA_007829815.1	281105	281105	type	True	82.331	1686	3193	95	below_threshold
Kitasatospora humi	strain=RB6PN24	GCA_020907985.1	2893891	2893891	type	True	82.1765	1416	3193	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	79.1798	1191	3193	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	78.939	941	3193	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:39:29,672] [INFO] DFAST Taxonomy check result was written to GCF_030813695.1_ASM3081369v1_genomic.fna/tc_result.tsv
[2024-01-25 17:39:29,673] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:39:29,673] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:39:29,673] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80ec7b30-ac0d-492a-bba6-d94931b0f31a/dqc_reference/checkm_data
[2024-01-25 17:39:29,674] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:39:29,763] [INFO] Task started: CheckM
[2024-01-25 17:39:29,764] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030813695.1_ASM3081369v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030813695.1_ASM3081369v1_genomic.fna/checkm_input GCF_030813695.1_ASM3081369v1_genomic.fna/checkm_result
[2024-01-25 17:42:28,412] [INFO] Task succeeded: CheckM
[2024-01-25 17:42:28,413] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:42:28,443] [INFO] ===== Completeness check finished =====
[2024-01-25 17:42:28,443] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:42:28,444] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030813695.1_ASM3081369v1_genomic.fna/markers.fasta)
[2024-01-25 17:42:28,445] [INFO] Task started: Blastn
[2024-01-25 17:42:28,445] [INFO] Running command: blastn -query GCF_030813695.1_ASM3081369v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80ec7b30-ac0d-492a-bba6-d94931b0f31a/dqc_reference/reference_markers_gtdb.fasta -out GCF_030813695.1_ASM3081369v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:42:30,585] [INFO] Task succeeded: Blastn
[2024-01-25 17:42:30,589] [INFO] Selected 14 target genomes.
[2024-01-25 17:42:30,589] [INFO] Target genome list was writen to GCF_030813695.1_ASM3081369v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:42:30,603] [INFO] Task started: fastANI
[2024-01-25 17:42:30,603] [INFO] Running command: fastANI --query /var/lib/cwl/stg2be1483b-2a02-4501-b191-a405ef30b210/GCF_030813695.1_ASM3081369v1_genomic.fna.gz --refList GCF_030813695.1_ASM3081369v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030813695.1_ASM3081369v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:43:09,474] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:09,483] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:43:09,483] [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_014648975.1	s__Kitasatospora herbaricolor	99.9616	3072	3193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	96.20	96.20	0.86	0.86	2	conclusive
GCF_014655955.1	s__Kitasatospora indigofera	94.4418	2650	3193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007828955.1	s__Kitasatospora atroaurantiaca	84.7893	1627	3193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002953255.1	s__Kitasatospora sp002953255	84.6039	1789	3193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	98.26	96.53	0.79	0.78	3	-
GCF_001625365.1	s__Kitasatospora sp001625365	84.4069	1769	3193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009569385.1	s__Kitasatospora kaniharaensis	84.2493	1634	3193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019192735.1	s__Kitasatospora aureofaciens_A	84.2314	1671	3193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000961885.1	s__Kitasatospora rubellomurina	83.9576	1653	3193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203705.1	s__Kitasatospora gansuensis	83.9445	1716	3193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014596465.1	s__Kitasatospora sp014596465	83.9416	1611	3193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744785.1	s__Kitasatospora azatica	83.2274	1562	3193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744225.1	s__Kitasatospora mediocidica	83.1907	1622	3193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002943525.1	s__Kitasatospora sp002943525	83.1723	1694	3193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203855.1	s__Kitasatospora kifunensis	82.7399	1549	3193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:43:09,485] [INFO] GTDB search result was written to GCF_030813695.1_ASM3081369v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:43:09,485] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:43:09,488] [INFO] DFAST_QC result json was written to GCF_030813695.1_ASM3081369v1_genomic.fna/dqc_result.json
[2024-01-25 17:43:09,488] [INFO] DFAST_QC completed!
[2024-01-25 17:43:09,489] [INFO] Total running time: 0h4m49s