[2024-01-24 11:26:21,951] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:21,953] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:21,953] [INFO] DQC Reference Directory: /var/lib/cwl/stgb741834c-3eca-424e-903a-35e2b33d9c83/dqc_reference
[2024-01-24 11:26:23,211] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:23,212] [INFO] Task started: Prodigal
[2024-01-24 11:26:23,212] [INFO] Running command: gunzip -c /var/lib/cwl/stga5f1aff7-64b7-4a50-9056-e92d1b28b77f/GCF_022919175.1_ASM2291917v1_genomic.fna.gz | prodigal -d GCF_022919175.1_ASM2291917v1_genomic.fna/cds.fna -a GCF_022919175.1_ASM2291917v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:33,062] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:33,063] [INFO] Task started: HMMsearch
[2024-01-24 11:26:33,063] [INFO] Running command: hmmsearch --tblout GCF_022919175.1_ASM2291917v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb741834c-3eca-424e-903a-35e2b33d9c83/dqc_reference/reference_markers.hmm GCF_022919175.1_ASM2291917v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:33,363] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:33,364] [INFO] Found 6/6 markers.
[2024-01-24 11:26:33,393] [INFO] Query marker FASTA was written to GCF_022919175.1_ASM2291917v1_genomic.fna/markers.fasta
[2024-01-24 11:26:33,394] [INFO] Task started: Blastn
[2024-01-24 11:26:33,394] [INFO] Running command: blastn -query GCF_022919175.1_ASM2291917v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb741834c-3eca-424e-903a-35e2b33d9c83/dqc_reference/reference_markers.fasta -out GCF_022919175.1_ASM2291917v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:34,462] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:34,465] [INFO] Selected 20 target genomes.
[2024-01-24 11:26:34,465] [INFO] Target genome list was writen to GCF_022919175.1_ASM2291917v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:34,482] [INFO] Task started: fastANI
[2024-01-24 11:26:34,482] [INFO] Running command: fastANI --query /var/lib/cwl/stga5f1aff7-64b7-4a50-9056-e92d1b28b77f/GCF_022919175.1_ASM2291917v1_genomic.fna.gz --refList GCF_022919175.1_ASM2291917v1_genomic.fna/target_genomes.txt --output GCF_022919175.1_ASM2291917v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:47,771] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:47,772] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb741834c-3eca-424e-903a-35e2b33d9c83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:47,772] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb741834c-3eca-424e-903a-35e2b33d9c83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:47,788] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:26:47,788] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:26:47,788] [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	81.7148	558	1112	95	below_threshold
Leucobacter muris	strain=DSM 101948	GCA_004028235.1	1935379	1935379	type	True	81.7124	600	1112	95	below_threshold
Leucobacter ruminantium	strain=A2	GCA_017565705.1	1289170	1289170	type	True	81.5084	517	1112	95	below_threshold
Leucobacter celer subsp. astrifaciens	strain=CBX151	GCA_001273835.1	1461260	668625	type	True	81.4359	670	1112	95	below_threshold
Leucobacter chromiiresistens	strain=JG 31	GCA_000231305.1	1079994	1079994	type	True	81.3978	545	1112	95	below_threshold
Leucobacter chromiiresistens	strain=DSM 22788	GCA_900102345.1	1079994	1079994	type	True	81.3874	565	1112	95	below_threshold
Leucobacter triazinivorans	strain=JW-1	GCA_004208635.1	1784719	1784719	type	True	81.1479	588	1112	95	below_threshold
Leucobacter zeae	strain=CC-MF41	GCA_016758175.1	1257004	1257004	type	True	81.1238	580	1112	95	below_threshold
Leucobacter chromiisoli	strain=CSA1	GCA_016522505.1	2796471	2796471	type	True	81.0341	498	1112	95	below_threshold
Leucobacter luti	strain=RF6	GCA_004217175.1	340320	340320	suspected-type	True	80.978	593	1112	95	below_threshold
Leucobacter luti	strain=RF6	GCA_016758235.1	340320	340320	suspected-type	True	80.9713	591	1112	95	below_threshold
Leucobacter massiliensis	strain=122RC15	GCA_002982315.1	1686285	1686285	type	True	80.786	531	1112	95	below_threshold
Leucobacter soli	strain=CIP 111803	GCA_910593785.1	2812850	2812850	type	True	80.3321	438	1112	95	below_threshold
Leucobacter japonicus	strain=CBX130	GCA_001273855.1	1461259	1461259	type	True	80.3097	510	1112	95	below_threshold
Leucobacter musarum subsp. musarum	strain=CBX152	GCA_001273845.1	1461261	1930747	type	True	80.1998	483	1112	95	below_threshold
Leucobacter viscericola	strain=HDW9C	GCA_011299575.1	2714935	2714935	type	True	80.1553	456	1112	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	78.1255	308	1112	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	77.9157	283	1112	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	77.8023	256	1112	95	below_threshold
Curtobacterium citreum	strain=LMG8786T	GCA_024997915.1	2036	2036	type	True	77.6282	268	1112	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:47,790] [INFO] DFAST Taxonomy check result was written to GCF_022919175.1_ASM2291917v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:47,791] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:47,792] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:47,792] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb741834c-3eca-424e-903a-35e2b33d9c83/dqc_reference/checkm_data
[2024-01-24 11:26:47,793] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:47,827] [INFO] Task started: CheckM
[2024-01-24 11:26:47,827] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022919175.1_ASM2291917v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022919175.1_ASM2291917v1_genomic.fna/checkm_input GCF_022919175.1_ASM2291917v1_genomic.fna/checkm_result
[2024-01-24 11:27:26,657] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:26,659] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:26,679] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:26,679] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:26,680] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022919175.1_ASM2291917v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:26,680] [INFO] Task started: Blastn
[2024-01-24 11:27:26,680] [INFO] Running command: blastn -query GCF_022919175.1_ASM2291917v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb741834c-3eca-424e-903a-35e2b33d9c83/dqc_reference/reference_markers_gtdb.fasta -out GCF_022919175.1_ASM2291917v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:28,244] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:28,248] [INFO] Selected 17 target genomes.
[2024-01-24 11:27:28,249] [INFO] Target genome list was writen to GCF_022919175.1_ASM2291917v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:28,258] [INFO] Task started: fastANI
[2024-01-24 11:27:28,259] [INFO] Running command: fastANI --query /var/lib/cwl/stga5f1aff7-64b7-4a50-9056-e92d1b28b77f/GCF_022919175.1_ASM2291917v1_genomic.fna.gz --refList GCF_022919175.1_ASM2291917v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022919175.1_ASM2291917v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:39,781] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:39,795] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:27:39,795] [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_004028235.1	s__Leucobacter muris	81.7217	599	1112	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	98.77	98.77	0.90	0.90	2	-
GCF_000421845.1	s__Leucobacter chironomi	81.7148	558	1112	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	81.4865	518	1112	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	81.4832	564	1112	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001273835.1	s__Leucobacter celer	81.4362	670	1112	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001477055.1	s__Leucobacter chromiiresistens_A	81.2855	499	1112	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	81.1767	554	1112	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003569785.1	s__Leucobacter sp003569785	81.1637	570	1112	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	81.1426	579	1112	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004208635.1	s__Leucobacter triazinivorans	81.1154	586	1112	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	81.0461	497	1112	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	80.9349	474	1112	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217175.1	s__Leucobacter luti	80.9233	598	1112	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000980875.1	s__Leucobacter sp000980875	80.7876	498	1112	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	80.5636	515	1112	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	99.99	99.99	0.99	0.98	9	-
GCF_001273845.1	s__Leucobacter musarum	80.2022	482	1112	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	95.38	95.38	0.87	0.87	2	-
GCF_011299575.1	s__Leucobacter viscericola	80.1427	457	1112	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:39,797] [INFO] GTDB search result was written to GCF_022919175.1_ASM2291917v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:39,797] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:39,801] [INFO] DFAST_QC result json was written to GCF_022919175.1_ASM2291917v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:39,801] [INFO] DFAST_QC completed!
[2024-01-24 11:27:39,801] [INFO] Total running time: 0h1m18s