[2024-01-24 14:55:35,210] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:35,211] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:35,211] [INFO] DQC Reference Directory: /var/lib/cwl/stge0638cb0-6708-4681-98f2-ac84affd186f/dqc_reference
[2024-01-24 14:55:36,526] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:36,527] [INFO] Task started: Prodigal
[2024-01-24 14:55:36,528] [INFO] Running command: gunzip -c /var/lib/cwl/stgff8fad70-7b0e-44e2-8658-90dfd8a685b8/GCF_014190775.1_ASM1419077v1_genomic.fna.gz | prodigal -d GCF_014190775.1_ASM1419077v1_genomic.fna/cds.fna -a GCF_014190775.1_ASM1419077v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:48,509] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:48,510] [INFO] Task started: HMMsearch
[2024-01-24 14:55:48,510] [INFO] Running command: hmmsearch --tblout GCF_014190775.1_ASM1419077v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0638cb0-6708-4681-98f2-ac84affd186f/dqc_reference/reference_markers.hmm GCF_014190775.1_ASM1419077v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:48,813] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:48,814] [INFO] Found 6/6 markers.
[2024-01-24 14:55:48,857] [INFO] Query marker FASTA was written to GCF_014190775.1_ASM1419077v1_genomic.fna/markers.fasta
[2024-01-24 14:55:48,858] [INFO] Task started: Blastn
[2024-01-24 14:55:48,858] [INFO] Running command: blastn -query GCF_014190775.1_ASM1419077v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0638cb0-6708-4681-98f2-ac84affd186f/dqc_reference/reference_markers.fasta -out GCF_014190775.1_ASM1419077v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:50,184] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:50,188] [INFO] Selected 11 target genomes.
[2024-01-24 14:55:50,188] [INFO] Target genome list was writen to GCF_014190775.1_ASM1419077v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:50,195] [INFO] Task started: fastANI
[2024-01-24 14:55:50,196] [INFO] Running command: fastANI --query /var/lib/cwl/stgff8fad70-7b0e-44e2-8658-90dfd8a685b8/GCF_014190775.1_ASM1419077v1_genomic.fna.gz --refList GCF_014190775.1_ASM1419077v1_genomic.fna/target_genomes.txt --output GCF_014190775.1_ASM1419077v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:00,412] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:00,412] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0638cb0-6708-4681-98f2-ac84affd186f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:00,413] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0638cb0-6708-4681-98f2-ac84affd186f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:00,422] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:56:00,423] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:56:00,423] [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
Leifsonia aquatica	strain=DSM 20146	GCA_014190775.1	144185	144185	type	True	100.0	1461	1464	95	inconclusive
Leifsonia aquatica	strain=ATCC 14665	GCA_000469485.1	144185	144185	type	True	99.5486	945	1464	95	inconclusive
Leifsonia naganoensis	strain=DSM 15166	GCA_013410615.1	150025	150025	type	True	97.2356	1301	1464	95	inconclusive
Leifsonia shinshuensis	strain=DSM 15165	GCA_013410375.1	150026	150026	type	True	84.1901	894	1464	95	below_threshold
Leifsonia soli	strain=DSM 23871	GCA_013408745.1	582665	582665	type	True	83.2874	848	1464	95	below_threshold
Leifsonia xyli subsp. cynodontis	strain=DSM 46306	GCA_000470775.1	31966	1575	type	True	81.8174	548	1464	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	79.3538	468	1464	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	79.2337	552	1464	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	79.2078	581	1464	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	78.8438	504	1464	95	below_threshold
Cryobacterium arcticum	strain=SK-1	GCA_003185895.1	670052	670052	type	True	78.4979	485	1464	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:00,424] [INFO] DFAST Taxonomy check result was written to GCF_014190775.1_ASM1419077v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:00,425] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:00,425] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:00,425] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0638cb0-6708-4681-98f2-ac84affd186f/dqc_reference/checkm_data
[2024-01-24 14:56:00,426] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:00,491] [INFO] Task started: CheckM
[2024-01-24 14:56:00,491] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014190775.1_ASM1419077v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014190775.1_ASM1419077v1_genomic.fna/checkm_input GCF_014190775.1_ASM1419077v1_genomic.fna/checkm_result
[2024-01-24 14:56:55,634] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:55,635] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:55,656] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:55,656] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:55,657] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014190775.1_ASM1419077v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:55,657] [INFO] Task started: Blastn
[2024-01-24 14:56:55,657] [INFO] Running command: blastn -query GCF_014190775.1_ASM1419077v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0638cb0-6708-4681-98f2-ac84affd186f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014190775.1_ASM1419077v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:57,757] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:57,761] [INFO] Selected 10 target genomes.
[2024-01-24 14:56:57,762] [INFO] Target genome list was writen to GCF_014190775.1_ASM1419077v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:57,770] [INFO] Task started: fastANI
[2024-01-24 14:56:57,771] [INFO] Running command: fastANI --query /var/lib/cwl/stgff8fad70-7b0e-44e2-8658-90dfd8a685b8/GCF_014190775.1_ASM1419077v1_genomic.fna.gz --refList GCF_014190775.1_ASM1419077v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014190775.1_ASM1419077v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:08,991] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:09,001] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:09,002] [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_014190775.1	s__Leifsonia aquatica	100.0	1459	1464	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	98.62	97.25	0.95	0.90	3	conclusive
GCA_001898805.1	s__Leifsonia sp001898805	92.8958	1213	1464	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000633535.1	s__Leifsonia aquatica_A	87.8164	1079	1464	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014217625.1	s__Leifsonia shinshuensis_A	84.2729	906	1464	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410375.1	s__Leifsonia shinshuensis	84.1791	895	1464	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001647635.1	s__Leifsonia xyli_A	83.7654	820	1464	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664105.1	s__Leifsonia sp003664105	83.7516	827	1464	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408745.1	s__Leifsonia soli	83.3364	843	1464	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	98.25	98.25	0.89	0.89	2	-
GCF_012317045.1	s__Leifsonia sp002105485	83.1868	863	1464	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	98.03	98.03	0.91	0.91	2	-
GCF_001428745.1	s__Leifsonia sp001428745	82.7755	870	1464	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:57:09,005] [INFO] GTDB search result was written to GCF_014190775.1_ASM1419077v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:09,006] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:09,010] [INFO] DFAST_QC result json was written to GCF_014190775.1_ASM1419077v1_genomic.fna/dqc_result.json
[2024-01-24 14:57:09,010] [INFO] DFAST_QC completed!
[2024-01-24 14:57:09,010] [INFO] Total running time: 0h1m34s