[2024-01-25 17:34:07,126] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:34:07,129] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:34:07,130] [INFO] DQC Reference Directory: /var/lib/cwl/stg6e0f43f0-5694-4429-929a-c496c2afe22a/dqc_reference
[2024-01-25 17:34:09,026] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:34:09,030] [INFO] Task started: Prodigal
[2024-01-25 17:34:09,031] [INFO] Running command: gunzip -c /var/lib/cwl/stg4fc469eb-df38-4382-ab57-9c6a818edf45/GCF_016758235.1_ASM1675823v1_genomic.fna.gz | prodigal -d GCF_016758235.1_ASM1675823v1_genomic.fna/cds.fna -a GCF_016758235.1_ASM1675823v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:34:19,482] [INFO] Task succeeded: Prodigal
[2024-01-25 17:34:19,482] [INFO] Task started: HMMsearch
[2024-01-25 17:34:19,482] [INFO] Running command: hmmsearch --tblout GCF_016758235.1_ASM1675823v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6e0f43f0-5694-4429-929a-c496c2afe22a/dqc_reference/reference_markers.hmm GCF_016758235.1_ASM1675823v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:34:19,740] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:34:19,741] [INFO] Found 6/6 markers.
[2024-01-25 17:34:19,768] [INFO] Query marker FASTA was written to GCF_016758235.1_ASM1675823v1_genomic.fna/markers.fasta
[2024-01-25 17:34:19,768] [INFO] Task started: Blastn
[2024-01-25 17:34:19,768] [INFO] Running command: blastn -query GCF_016758235.1_ASM1675823v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e0f43f0-5694-4429-929a-c496c2afe22a/dqc_reference/reference_markers.fasta -out GCF_016758235.1_ASM1675823v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:34:20,730] [INFO] Task succeeded: Blastn
[2024-01-25 17:34:20,733] [INFO] Selected 19 target genomes.
[2024-01-25 17:34:20,733] [INFO] Target genome list was writen to GCF_016758235.1_ASM1675823v1_genomic.fna/target_genomes.txt
[2024-01-25 17:34:20,751] [INFO] Task started: fastANI
[2024-01-25 17:34:20,751] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fc469eb-df38-4382-ab57-9c6a818edf45/GCF_016758235.1_ASM1675823v1_genomic.fna.gz --refList GCF_016758235.1_ASM1675823v1_genomic.fna/target_genomes.txt --output GCF_016758235.1_ASM1675823v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:34:34,621] [INFO] Task succeeded: fastANI
[2024-01-25 17:34:34,622] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6e0f43f0-5694-4429-929a-c496c2afe22a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:34:34,622] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6e0f43f0-5694-4429-929a-c496c2afe22a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:34:34,635] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:34:34,635] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:34:34,635] [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
Leucobacter luti	strain=RF6	GCA_016758235.1	340320	340320	suspected-type	True	100.0	1204	1204	95	conclusive
Leucobacter luti	strain=RF6	GCA_004217175.1	340320	340320	suspected-type	True	99.9963	1197	1204	95	conclusive
Leucobacter chironomi	strain=DSM 19883	GCA_000421845.1	491918	491918	type	True	81.828	582	1204	95	below_threshold
Leucobacter muris	strain=DSM 101948	GCA_004028235.1	1935379	1935379	type	True	81.4887	581	1204	95	below_threshold
Leucobacter ruminantium	strain=A2	GCA_017565705.1	1289170	1289170	type	True	81.0927	504	1204	95	below_threshold
Leucobacter chromiiresistens	strain=JG 31	GCA_000231305.1	1079994	1079994	type	True	80.997	564	1204	95	below_threshold
Leucobacter chromiiresistens	strain=DSM 22788	GCA_900102345.1	1079994	1079994	type	True	80.9739	568	1204	95	below_threshold
Leucobacter zeae	strain=CC-MF41	GCA_016758175.1	1257004	1257004	type	True	80.843	584	1204	95	below_threshold
Leucobacter massiliensis	strain=122RC15	GCA_002982315.1	1686285	1686285	type	True	80.8121	495	1204	95	below_threshold
Leucobacter japonicus	strain=CBX130	GCA_001273855.1	1461259	1461259	type	True	80.3636	511	1204	95	below_threshold
Leucobacter soli	strain=CIP 111803	GCA_910593785.1	2812850	2812850	type	True	80.1941	429	1204	95	below_threshold
Leucobacter musarum subsp. musarum	strain=CBX152	GCA_001273845.1	1461261	1930747	type	True	80.1361	492	1204	95	below_threshold
Leucobacter aridicollis	strain=DSM 17380	GCA_013409595.1	283878	283878	type	True	80.0759	462	1204	95	below_threshold
Leucobacter salsicius	strain=M1-8	GCA_000350525.1	664638	664638	type	True	79.5338	446	1204	95	below_threshold
Leucobacter viscericola	strain=HDW9C	GCA_011299575.1	2714935	2714935	type	True	79.0493	415	1204	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	77.7553	309	1204	95	below_threshold
Curtobacterium citreum	strain=LMG8786T	GCA_024997915.1	2036	2036	type	True	77.5099	253	1204	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	77.5037	264	1204	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	76.1941	219	1204	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:34:34,636] [INFO] DFAST Taxonomy check result was written to GCF_016758235.1_ASM1675823v1_genomic.fna/tc_result.tsv
[2024-01-25 17:34:34,637] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:34:34,637] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:34:34,637] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6e0f43f0-5694-4429-929a-c496c2afe22a/dqc_reference/checkm_data
[2024-01-25 17:34:34,638] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:34:34,675] [INFO] Task started: CheckM
[2024-01-25 17:34:34,675] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016758235.1_ASM1675823v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016758235.1_ASM1675823v1_genomic.fna/checkm_input GCF_016758235.1_ASM1675823v1_genomic.fna/checkm_result
[2024-01-25 17:35:08,260] [INFO] Task succeeded: CheckM
[2024-01-25 17:35:08,261] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:35:08,278] [INFO] ===== Completeness check finished =====
[2024-01-25 17:35:08,278] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:35:08,278] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016758235.1_ASM1675823v1_genomic.fna/markers.fasta)
[2024-01-25 17:35:08,278] [INFO] Task started: Blastn
[2024-01-25 17:35:08,278] [INFO] Running command: blastn -query GCF_016758235.1_ASM1675823v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e0f43f0-5694-4429-929a-c496c2afe22a/dqc_reference/reference_markers_gtdb.fasta -out GCF_016758235.1_ASM1675823v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:09,814] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:09,817] [INFO] Selected 12 target genomes.
[2024-01-25 17:35:09,817] [INFO] Target genome list was writen to GCF_016758235.1_ASM1675823v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:35:09,824] [INFO] Task started: fastANI
[2024-01-25 17:35:09,824] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fc469eb-df38-4382-ab57-9c6a818edf45/GCF_016758235.1_ASM1675823v1_genomic.fna.gz --refList GCF_016758235.1_ASM1675823v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016758235.1_ASM1675823v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:35:19,163] [INFO] Task succeeded: fastANI
[2024-01-25 17:35:19,171] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:35:19,171] [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_004217175.1	s__Leucobacter luti	99.9963	1197	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000633415.1	s__Leucobacter sp000633415	82.9505	683	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003917135.1	s__Leucobacter chromiireducens_A	82.9501	724	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016758195.1	s__Leucobacter solipictus	82.0406	688	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004028235.1	s__Leucobacter muris	81.4886	581	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	98.77	98.77	0.90	0.90	2	-
GCF_003569785.1	s__Leucobacter sp003569785	81.219	580	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017565705.1	s__Leucobacter ruminantium	81.1216	502	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900163635.1	s__Leucobacter sp900163635	81.0072	592	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016522535.1	s__Leucobacter sp016522535	80.9416	499	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016758175.1	s__Leucobacter zeae	80.8821	579	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339635.1	s__Leucobacter luti_A	80.7758	676	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	98.22	98.22	0.92	0.92	2	-
GCF_000980875.1	s__Leucobacter sp000980875	80.5514	518	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:35:19,172] [INFO] GTDB search result was written to GCF_016758235.1_ASM1675823v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:35:19,172] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:35:19,176] [INFO] DFAST_QC result json was written to GCF_016758235.1_ASM1675823v1_genomic.fna/dqc_result.json
[2024-01-25 17:35:19,177] [INFO] DFAST_QC completed!
[2024-01-25 17:35:19,177] [INFO] Total running time: 0h1m12s