[2023-06-28 21:01:57,616] [INFO] DFAST_QC pipeline started.
[2023-06-28 21:01:57,621] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 21:01:57,622] [INFO] DQC Reference Directory: /var/lib/cwl/stg05785bc3-4a89-4850-b144-d0a2c16d8fcb/dqc_reference
[2023-06-28 21:01:59,024] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 21:01:59,025] [INFO] Task started: Prodigal
[2023-06-28 21:01:59,026] [INFO] Running command: gunzip -c /var/lib/cwl/stg6ab621a8-2878-463c-8bd2-7b5034820914/GCA_020161175.1_ASM2016117v1_genomic.fna.gz | prodigal -d GCA_020161175.1_ASM2016117v1_genomic.fna/cds.fna -a GCA_020161175.1_ASM2016117v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 21:02:05,591] [INFO] Task succeeded: Prodigal
[2023-06-28 21:02:05,592] [INFO] Task started: HMMsearch
[2023-06-28 21:02:05,592] [INFO] Running command: hmmsearch --tblout GCA_020161175.1_ASM2016117v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05785bc3-4a89-4850-b144-d0a2c16d8fcb/dqc_reference/reference_markers.hmm GCA_020161175.1_ASM2016117v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 21:02:05,878] [INFO] Task succeeded: HMMsearch
[2023-06-28 21:02:05,880] [INFO] Found 6/6 markers.
[2023-06-28 21:02:05,907] [INFO] Query marker FASTA was written to GCA_020161175.1_ASM2016117v1_genomic.fna/markers.fasta
[2023-06-28 21:02:05,908] [INFO] Task started: Blastn
[2023-06-28 21:02:05,908] [INFO] Running command: blastn -query GCA_020161175.1_ASM2016117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05785bc3-4a89-4850-b144-d0a2c16d8fcb/dqc_reference/reference_markers.fasta -out GCA_020161175.1_ASM2016117v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:02:06,888] [INFO] Task succeeded: Blastn
[2023-06-28 21:02:06,894] [INFO] Selected 20 target genomes.
[2023-06-28 21:02:06,894] [INFO] Target genome list was writen to GCA_020161175.1_ASM2016117v1_genomic.fna/target_genomes.txt
[2023-06-28 21:02:06,900] [INFO] Task started: fastANI
[2023-06-28 21:02:06,900] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ab621a8-2878-463c-8bd2-7b5034820914/GCA_020161175.1_ASM2016117v1_genomic.fna.gz --refList GCA_020161175.1_ASM2016117v1_genomic.fna/target_genomes.txt --output GCA_020161175.1_ASM2016117v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 21:02:19,493] [INFO] Task succeeded: fastANI
[2023-06-28 21:02:19,493] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05785bc3-4a89-4850-b144-d0a2c16d8fcb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 21:02:19,494] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05785bc3-4a89-4850-b144-d0a2c16d8fcb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 21:02:19,517] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 21:02:19,517] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 21:02:19,517] [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 chironomi	strain=DSM 19883	GCA_000421845.1	491918	491918	type	True	79.6163	319	700	95	below_threshold
Leucobacter soli	strain=CIP 111803	GCA_910593785.1	2812850	2812850	type	True	79.5108	297	700	95	below_threshold
Leucobacter muris	strain=DSM 101948	GCA_004028235.1	1935379	1935379	type	True	79.4557	314	700	95	below_threshold
Leucobacter celer subsp. astrifaciens	strain=CBX151	GCA_001273835.1	1461260	668625	type	True	79.4054	302	700	95	below_threshold
Leucobacter ruminantium	strain=A2	GCA_017565705.1	1289170	1289170	type	True	79.2717	311	700	95	below_threshold
Leucobacter aridicollis	strain=L-9	GCA_016758215.1	283878	283878	type	True	78.9249	246	700	95	below_threshold
Leucobacter zeae	strain=CC-MF41	GCA_016758175.1	1257004	1257004	type	True	78.916	303	700	95	below_threshold
Leucobacter aridicollis	strain=DSM 17380	GCA_013409595.1	283878	283878	type	True	78.8974	248	700	95	below_threshold
Leucobacter chromiisoli	strain=CSA1	GCA_016522505.1	2796471	2796471	type	True	78.8392	292	700	95	below_threshold
Leucobacter chromiiresistens	strain=DSM 22788	GCA_900102345.1	1079994	1079994	type	True	78.7546	287	700	95	below_threshold
Leucobacter japonicus	strain=CBX130	GCA_001273855.1	1461259	1461259	type	True	78.7482	249	700	95	below_threshold
Leucobacter chromiiresistens	strain=JG 31	GCA_000231305.1	1079994	1079994	type	True	78.7368	282	700	95	below_threshold
Leucobacter luti	strain=RF6	GCA_016758235.1	340320	340320	suspected-type	True	78.6007	290	700	95	below_threshold
Leucobacter luti	strain=RF6	GCA_004217175.1	340320	340320	suspected-type	True	78.5255	291	700	95	below_threshold
Leucobacter salsicius	strain=M1-8	GCA_000350525.1	664638	664638	type	True	78.1963	251	700	95	below_threshold
Leucobacter tardus	strain=K 70/01	GCA_017583045.1	501483	501483	type	True	78.0841	219	700	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	77.2349	179	700	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	77.1668	157	700	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	77.0512	144	700	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	76.8672	172	700	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 21:02:19,519] [INFO] DFAST Taxonomy check result was written to GCA_020161175.1_ASM2016117v1_genomic.fna/tc_result.tsv
[2023-06-28 21:02:19,520] [INFO] ===== Taxonomy check completed =====
[2023-06-28 21:02:19,520] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 21:02:19,520] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05785bc3-4a89-4850-b144-d0a2c16d8fcb/dqc_reference/checkm_data
[2023-06-28 21:02:19,521] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 21:02:19,550] [INFO] Task started: CheckM
[2023-06-28 21:02:19,550] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020161175.1_ASM2016117v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020161175.1_ASM2016117v1_genomic.fna/checkm_input GCA_020161175.1_ASM2016117v1_genomic.fna/checkm_result
[2023-06-28 21:02:44,278] [INFO] Task succeeded: CheckM
[2023-06-28 21:02:44,279] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.74%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 21:02:44,300] [INFO] ===== Completeness check finished =====
[2023-06-28 21:02:44,300] [INFO] ===== Start GTDB Search =====
[2023-06-28 21:02:44,301] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020161175.1_ASM2016117v1_genomic.fna/markers.fasta)
[2023-06-28 21:02:44,301] [INFO] Task started: Blastn
[2023-06-28 21:02:44,301] [INFO] Running command: blastn -query GCA_020161175.1_ASM2016117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05785bc3-4a89-4850-b144-d0a2c16d8fcb/dqc_reference/reference_markers_gtdb.fasta -out GCA_020161175.1_ASM2016117v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:02:45,584] [INFO] Task succeeded: Blastn
[2023-06-28 21:02:45,588] [INFO] Selected 15 target genomes.
[2023-06-28 21:02:45,588] [INFO] Target genome list was writen to GCA_020161175.1_ASM2016117v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 21:02:45,607] [INFO] Task started: fastANI
[2023-06-28 21:02:45,607] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ab621a8-2878-463c-8bd2-7b5034820914/GCA_020161175.1_ASM2016117v1_genomic.fna.gz --refList GCA_020161175.1_ASM2016117v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020161175.1_ASM2016117v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 21:02:53,880] [INFO] Task succeeded: fastANI
[2023-06-28 21:02:53,896] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 21:02:53,896] [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
GCA_002336855.1	s__Leucobacter sp002336855	95.7153	523	700	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016771945.1	s__Leucobacter sulfamidivorax	79.8551	340	700	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421845.1	s__Leucobacter chironomi	79.6244	318	700	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_910593785.1	s__Leucobacter sp910593785	79.4771	299	700	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	79.476	312	700	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	98.77	98.77	0.90	0.90	2	-
GCF_001273835.1	s__Leucobacter celer	79.3647	305	700	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	79.2491	313	700	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000980875.1	s__Leucobacter sp000980875	79.1519	301	700	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000633415.1	s__Leucobacter sp000633415	79.1335	290	700	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002752355.1	s__Leucobacter sp002752355	79.0727	308	700	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	99.99	99.99	0.99	0.98	9	-
GCF_003917135.1	s__Leucobacter chromiireducens_A	79.0706	297	700	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016522505.1	s__Leucobacter sp016522505	78.8393	292	700	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102345.1	s__Leucobacter chromiiresistens	78.7764	285	700	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	99.76	99.76	0.96	0.96	2	-
GCF_001477055.1	s__Leucobacter chromiiresistens_A	78.6719	255	700	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 21:02:53,898] [INFO] GTDB search result was written to GCA_020161175.1_ASM2016117v1_genomic.fna/result_gtdb.tsv
[2023-06-28 21:02:53,899] [INFO] ===== GTDB Search completed =====
[2023-06-28 21:02:53,903] [INFO] DFAST_QC result json was written to GCA_020161175.1_ASM2016117v1_genomic.fna/dqc_result.json
[2023-06-28 21:02:53,903] [INFO] DFAST_QC completed!
[2023-06-28 21:02:53,904] [INFO] Total running time: 0h0m56s