[2024-01-24 14:31:14,894] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:14,896] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:14,897] [INFO] DQC Reference Directory: /var/lib/cwl/stg2befe942-62ab-46ec-a9e3-ddc4bb87b826/dqc_reference
[2024-01-24 14:31:16,222] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:16,223] [INFO] Task started: Prodigal
[2024-01-24 14:31:16,223] [INFO] Running command: gunzip -c /var/lib/cwl/stg70c1b5fc-8d37-4359-870b-4870978e0841/GCF_001273845.1_CBX152_1.1_genomic.fna.gz | prodigal -d GCF_001273845.1_CBX152_1.1_genomic.fna/cds.fna -a GCF_001273845.1_CBX152_1.1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:27,151] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:27,151] [INFO] Task started: HMMsearch
[2024-01-24 14:31:27,152] [INFO] Running command: hmmsearch --tblout GCF_001273845.1_CBX152_1.1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2befe942-62ab-46ec-a9e3-ddc4bb87b826/dqc_reference/reference_markers.hmm GCF_001273845.1_CBX152_1.1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:27,471] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:27,473] [INFO] Found 6/6 markers.
[2024-01-24 14:31:27,510] [INFO] Query marker FASTA was written to GCF_001273845.1_CBX152_1.1_genomic.fna/markers.fasta
[2024-01-24 14:31:27,510] [INFO] Task started: Blastn
[2024-01-24 14:31:27,510] [INFO] Running command: blastn -query GCF_001273845.1_CBX152_1.1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2befe942-62ab-46ec-a9e3-ddc4bb87b826/dqc_reference/reference_markers.fasta -out GCF_001273845.1_CBX152_1.1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:28,508] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:28,512] [INFO] Selected 16 target genomes.
[2024-01-24 14:31:28,513] [INFO] Target genome list was writen to GCF_001273845.1_CBX152_1.1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:28,524] [INFO] Task started: fastANI
[2024-01-24 14:31:28,524] [INFO] Running command: fastANI --query /var/lib/cwl/stg70c1b5fc-8d37-4359-870b-4870978e0841/GCF_001273845.1_CBX152_1.1_genomic.fna.gz --refList GCF_001273845.1_CBX152_1.1_genomic.fna/target_genomes.txt --output GCF_001273845.1_CBX152_1.1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:40,476] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:40,477] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2befe942-62ab-46ec-a9e3-ddc4bb87b826/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:40,477] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2befe942-62ab-46ec-a9e3-ddc4bb87b826/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:40,490] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:31:40,490] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:31:40,490] [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 musarum subsp. musarum	strain=CBX152	GCA_001273845.1	1461261	1930747	type	True	100.0	1124	1127	95	inconclusive
Leucobacter japonicus	strain=CBX130	GCA_001273855.1	1461259	1461259	type	True	95.3756	975	1127	95	inconclusive
Leucobacter chromiiresistens	strain=DSM 22788	GCA_900102345.1	1079994	1079994	type	True	82.335	687	1127	95	below_threshold
Leucobacter chromiiresistens	strain=JG 31	GCA_000231305.1	1079994	1079994	type	True	82.2609	663	1127	95	below_threshold
Leucobacter chironomi	strain=DSM 19883	GCA_000421845.1	491918	491918	type	True	80.8276	490	1127	95	below_threshold
Leucobacter muris	strain=DSM 101948	GCA_004028235.1	1935379	1935379	type	True	80.6771	520	1127	95	below_threshold
Leucobacter celer subsp. astrifaciens	strain=CBX151	GCA_001273835.1	1461260	668625	type	True	80.4674	549	1127	95	below_threshold
Leucobacter zeae	strain=CC-MF41	GCA_016758175.1	1257004	1257004	type	True	80.2852	526	1127	95	below_threshold
Leucobacter luti	strain=RF6	GCA_004217175.1	340320	340320	suspected-type	True	80.0646	493	1127	95	below_threshold
Leucobacter luti	strain=RF6	GCA_016758235.1	340320	340320	suspected-type	True	80.0534	499	1127	95	below_threshold
Leucobacter soli	strain=CIP 111803	GCA_910593785.1	2812850	2812850	type	True	79.2806	355	1127	95	below_threshold
Leucobacter salsicius	strain=M1-8	GCA_000350525.1	664638	664638	type	True	79.1337	365	1127	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	77.6957	243	1127	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	77.5093	287	1127	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	77.4325	263	1127	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	77.3579	227	1127	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:40,492] [INFO] DFAST Taxonomy check result was written to GCF_001273845.1_CBX152_1.1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:40,493] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:40,493] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:40,493] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2befe942-62ab-46ec-a9e3-ddc4bb87b826/dqc_reference/checkm_data
[2024-01-24 14:31:40,494] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:40,529] [INFO] Task started: CheckM
[2024-01-24 14:31:40,529] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001273845.1_CBX152_1.1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001273845.1_CBX152_1.1_genomic.fna/checkm_input GCF_001273845.1_CBX152_1.1_genomic.fna/checkm_result
[2024-01-24 14:32:17,334] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:17,335] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:17,354] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:17,355] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:17,355] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001273845.1_CBX152_1.1_genomic.fna/markers.fasta)
[2024-01-24 14:32:17,355] [INFO] Task started: Blastn
[2024-01-24 14:32:17,356] [INFO] Running command: blastn -query GCF_001273845.1_CBX152_1.1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2befe942-62ab-46ec-a9e3-ddc4bb87b826/dqc_reference/reference_markers_gtdb.fasta -out GCF_001273845.1_CBX152_1.1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:18,694] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:18,699] [INFO] Selected 12 target genomes.
[2024-01-24 14:32:18,699] [INFO] Target genome list was writen to GCF_001273845.1_CBX152_1.1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:18,708] [INFO] Task started: fastANI
[2024-01-24 14:32:18,708] [INFO] Running command: fastANI --query /var/lib/cwl/stg70c1b5fc-8d37-4359-870b-4870978e0841/GCF_001273845.1_CBX152_1.1_genomic.fna.gz --refList GCF_001273845.1_CBX152_1.1_genomic.fna/target_genomes_gtdb.txt --output GCF_001273845.1_CBX152_1.1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:26,906] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:26,920] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:26,920] [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_001273845.1	s__Leucobacter musarum	100.0	1124	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	95.38	95.38	0.87	0.87	2	conclusive
GCF_900102345.1	s__Leucobacter chromiiresistens	82.3447	686	1127	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	82.295	575	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016597785.1	s__Leucobacter sp001373475	81.5235	644	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	98.62	98.46	0.91	0.89	3	-
GCF_000421845.1	s__Leucobacter chironomi	80.8077	492	1127	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	80.6574	522	1127	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	80.437	553	1127	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	80.4295	473	1127	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	80.2751	527	1127	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	80.2648	498	1127	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	80.1853	397	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016758255.1	s__Leucobacter chromiireducens	79.8432	421	1127	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 14:32:26,922] [INFO] GTDB search result was written to GCF_001273845.1_CBX152_1.1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:26,923] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:26,927] [INFO] DFAST_QC result json was written to GCF_001273845.1_CBX152_1.1_genomic.fna/dqc_result.json
[2024-01-24 14:32:26,927] [INFO] DFAST_QC completed!
[2024-01-24 14:32:26,927] [INFO] Total running time: 0h1m12s