[2024-01-24 14:14:20,549] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:20,552] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:20,553] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a6ca9bb-b436-406b-9940-061810069613/dqc_reference
[2024-01-24 14:14:21,916] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:21,917] [INFO] Task started: Prodigal
[2024-01-24 14:14:21,917] [INFO] Running command: gunzip -c /var/lib/cwl/stge7f066c7-fdca-4698-8c95-e30db5139136/GCF_013409595.1_ASM1340959v1_genomic.fna.gz | prodigal -d GCF_013409595.1_ASM1340959v1_genomic.fna/cds.fna -a GCF_013409595.1_ASM1340959v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:32,366] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:32,367] [INFO] Task started: HMMsearch
[2024-01-24 14:14:32,367] [INFO] Running command: hmmsearch --tblout GCF_013409595.1_ASM1340959v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a6ca9bb-b436-406b-9940-061810069613/dqc_reference/reference_markers.hmm GCF_013409595.1_ASM1340959v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:32,676] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:32,677] [INFO] Found 6/6 markers.
[2024-01-24 14:14:32,706] [INFO] Query marker FASTA was written to GCF_013409595.1_ASM1340959v1_genomic.fna/markers.fasta
[2024-01-24 14:14:32,707] [INFO] Task started: Blastn
[2024-01-24 14:14:32,707] [INFO] Running command: blastn -query GCF_013409595.1_ASM1340959v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a6ca9bb-b436-406b-9940-061810069613/dqc_reference/reference_markers.fasta -out GCF_013409595.1_ASM1340959v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:33,663] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:33,667] [INFO] Selected 16 target genomes.
[2024-01-24 14:14:33,667] [INFO] Target genome list was writen to GCF_013409595.1_ASM1340959v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:33,676] [INFO] Task started: fastANI
[2024-01-24 14:14:33,676] [INFO] Running command: fastANI --query /var/lib/cwl/stge7f066c7-fdca-4698-8c95-e30db5139136/GCF_013409595.1_ASM1340959v1_genomic.fna.gz --refList GCF_013409595.1_ASM1340959v1_genomic.fna/target_genomes.txt --output GCF_013409595.1_ASM1340959v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:44,881] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:44,881] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a6ca9bb-b436-406b-9940-061810069613/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:44,882] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a6ca9bb-b436-406b-9940-061810069613/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:44,895] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:14:44,895] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:44,896] [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 aridicollis	strain=DSM 17380	GCA_013409595.1	283878	283878	type	True	100.0	1190	1191	95	conclusive
Leucobacter aridicollis	strain=L-9	GCA_016758215.1	283878	283878	type	True	99.9897	1182	1191	95	conclusive
Leucobacter komagatae	strain=DSM 8803	GCA_006716085.1	55969	55969	type	True	86.6766	878	1191	95	below_threshold
Leucobacter chironomi	strain=DSM 19883	GCA_000421845.1	491918	491918	type	True	80.3772	438	1191	95	below_threshold
Leucobacter muris	strain=DSM 101948	GCA_004028235.1	1935379	1935379	type	True	80.1224	474	1191	95	below_threshold
Leucobacter zeae	strain=CC-MF41	GCA_016758175.1	1257004	1257004	type	True	79.9974	476	1191	95	below_threshold
Leucobacter ruminantium	strain=A2	GCA_017565705.1	1289170	1289170	type	True	79.9188	441	1191	95	below_threshold
Leucobacter celer subsp. astrifaciens	strain=CBX151	GCA_001273835.1	1461260	668625	type	True	79.8374	460	1191	95	below_threshold
Leucobacter chromiisoli	strain=CSA1	GCA_016522505.1	2796471	2796471	type	True	79.5898	416	1191	95	below_threshold
Leucobacter japonicus	strain=CBX130	GCA_001273855.1	1461259	1461259	type	True	79.4201	371	1191	95	below_threshold
Leucobacter musarum subsp. musarum	strain=CBX152	GCA_001273845.1	1461261	1930747	type	True	79.3413	367	1191	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	77.8163	281	1191	95	below_threshold
Leucobacter chinensis	strain=NC76-1	GCA_019049105.1	2851010	2851010	type	True	77.808	208	1191	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	77.7145	305	1191	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	77.656	240	1191	95	below_threshold
Curtobacterium allii	strain=20TX0166	GCA_021271025.1	2878384	2878384	type	True	77.2588	224	1191	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:44,897] [INFO] DFAST Taxonomy check result was written to GCF_013409595.1_ASM1340959v1_genomic.fna/tc_result.tsv
[2024-01-24 14:14:44,898] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:44,898] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:44,898] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a6ca9bb-b436-406b-9940-061810069613/dqc_reference/checkm_data
[2024-01-24 14:14:44,900] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:44,951] [INFO] Task started: CheckM
[2024-01-24 14:14:44,951] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013409595.1_ASM1340959v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013409595.1_ASM1340959v1_genomic.fna/checkm_input GCF_013409595.1_ASM1340959v1_genomic.fna/checkm_result
[2024-01-24 14:15:19,074] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:19,079] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:19,096] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:19,096] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:19,096] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013409595.1_ASM1340959v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:19,097] [INFO] Task started: Blastn
[2024-01-24 14:15:19,097] [INFO] Running command: blastn -query GCF_013409595.1_ASM1340959v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a6ca9bb-b436-406b-9940-061810069613/dqc_reference/reference_markers_gtdb.fasta -out GCF_013409595.1_ASM1340959v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:20,472] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:20,475] [INFO] Selected 15 target genomes.
[2024-01-24 14:15:20,475] [INFO] Target genome list was writen to GCF_013409595.1_ASM1340959v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:20,485] [INFO] Task started: fastANI
[2024-01-24 14:15:20,485] [INFO] Running command: fastANI --query /var/lib/cwl/stge7f066c7-fdca-4698-8c95-e30db5139136/GCF_013409595.1_ASM1340959v1_genomic.fna.gz --refList GCF_013409595.1_ASM1340959v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013409595.1_ASM1340959v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:30,760] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:30,774] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:30,774] [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_013409595.1	s__Leucobacter aridicollis	100.0	1191	1191	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	98.50	96.99	0.93	0.86	3	conclusive
GCF_006716085.1	s__Leucobacter komagatae	86.6927	877	1191	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001482305.1	s__Leucobacter sp001482305	82.3869	669	1191	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000834055.1	s__Leucobacter komagatae_A	81.8237	626	1191	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017990305.1	s__Leucobacter sp017990305	81.514	389	1191	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	80.4748	517	1191	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	80.3998	496	1191	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	80.3507	442	1191	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	80.0828	474	1191	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	98.77	98.77	0.90	0.90	2	-
GCF_016758175.1	s__Leucobacter zeae	80.021	474	1191	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	80.0184	454	1191	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	99.99	99.99	0.99	0.98	9	-
GCF_017565705.1	s__Leucobacter ruminantium	79.9506	438	1191	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	79.9504	412	1191	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014529985.1	s__Leucobacter sp014529985	79.0139	280	1191	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004339635.1	s__Leucobacter luti_A	78.3941	318	1191	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	98.22	98.22	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:30,776] [INFO] GTDB search result was written to GCF_013409595.1_ASM1340959v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:30,777] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:30,781] [INFO] DFAST_QC result json was written to GCF_013409595.1_ASM1340959v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:30,782] [INFO] DFAST_QC completed!
[2024-01-24 14:15:30,782] [INFO] Total running time: 0h1m10s