[2024-01-24 13:49:45,570] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:45,576] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:45,576] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc5ed0d1-8809-4950-96a1-684f1a6f3988/dqc_reference
[2024-01-24 13:49:46,838] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:46,839] [INFO] Task started: Prodigal
[2024-01-24 13:49:46,839] [INFO] Running command: gunzip -c /var/lib/cwl/stgd2372494-1594-4cd3-bea2-7841a1e8b851/GCF_014049385.1_ASM1404938v1_genomic.fna.gz | prodigal -d GCF_014049385.1_ASM1404938v1_genomic.fna/cds.fna -a GCF_014049385.1_ASM1404938v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:51,053] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:51,053] [INFO] Task started: HMMsearch
[2024-01-24 13:49:51,053] [INFO] Running command: hmmsearch --tblout GCF_014049385.1_ASM1404938v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc5ed0d1-8809-4950-96a1-684f1a6f3988/dqc_reference/reference_markers.hmm GCF_014049385.1_ASM1404938v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:51,309] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:51,311] [INFO] Found 6/6 markers.
[2024-01-24 13:49:51,337] [INFO] Query marker FASTA was written to GCF_014049385.1_ASM1404938v1_genomic.fna/markers.fasta
[2024-01-24 13:49:51,338] [INFO] Task started: Blastn
[2024-01-24 13:49:51,338] [INFO] Running command: blastn -query GCF_014049385.1_ASM1404938v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc5ed0d1-8809-4950-96a1-684f1a6f3988/dqc_reference/reference_markers.fasta -out GCF_014049385.1_ASM1404938v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:52,018] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:52,022] [INFO] Selected 27 target genomes.
[2024-01-24 13:49:52,023] [INFO] Target genome list was writen to GCF_014049385.1_ASM1404938v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:52,033] [INFO] Task started: fastANI
[2024-01-24 13:49:52,034] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2372494-1594-4cd3-bea2-7841a1e8b851/GCF_014049385.1_ASM1404938v1_genomic.fna.gz --refList GCF_014049385.1_ASM1404938v1_genomic.fna/target_genomes.txt --output GCF_014049385.1_ASM1404938v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:04,034] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:04,035] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc5ed0d1-8809-4950-96a1-684f1a6f3988/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:04,035] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc5ed0d1-8809-4950-96a1-684f1a6f3988/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:04,045] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:04,046] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:04,046] [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
Ruoffia halotolerans	strain=INB8	GCA_014049385.1	2748684	2748684	type	True	100.0	720	722	95	conclusive
Globicatella sanguinis	strain=NBRC 15551	GCA_001552295.1	13076	13076	type	True	79.1367	71	722	95	below_threshold
Globicatella sulfidifaciens	strain=DSM 15739	GCA_900167405.1	136093	136093	type	True	78.5525	73	722	95	below_threshold
Fundicoccus ignavus	strain=DSM 109652	GCA_009659375.1	2664442	2664442	type	True	77.6473	104	722	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:04,048] [INFO] DFAST Taxonomy check result was written to GCF_014049385.1_ASM1404938v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:04,048] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:04,048] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:04,049] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc5ed0d1-8809-4950-96a1-684f1a6f3988/dqc_reference/checkm_data
[2024-01-24 13:50:04,050] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:04,075] [INFO] Task started: CheckM
[2024-01-24 13:50:04,075] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014049385.1_ASM1404938v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014049385.1_ASM1404938v1_genomic.fna/checkm_input GCF_014049385.1_ASM1404938v1_genomic.fna/checkm_result
[2024-01-24 13:50:24,148] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:24,150] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:24,169] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:24,170] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:24,170] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014049385.1_ASM1404938v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:24,171] [INFO] Task started: Blastn
[2024-01-24 13:50:24,171] [INFO] Running command: blastn -query GCF_014049385.1_ASM1404938v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc5ed0d1-8809-4950-96a1-684f1a6f3988/dqc_reference/reference_markers_gtdb.fasta -out GCF_014049385.1_ASM1404938v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:24,918] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:24,921] [INFO] Selected 18 target genomes.
[2024-01-24 13:50:24,921] [INFO] Target genome list was writen to GCF_014049385.1_ASM1404938v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:24,941] [INFO] Task started: fastANI
[2024-01-24 13:50:24,941] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2372494-1594-4cd3-bea2-7841a1e8b851/GCF_014049385.1_ASM1404938v1_genomic.fna.gz --refList GCF_014049385.1_ASM1404938v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014049385.1_ASM1404938v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:31,799] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:31,811] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:31,811] [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_014049385.1	s__Facklamia_A sp014049385	100.0	720	722	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Facklamia_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005864045.1	s__Facklamia_A tabacinasalis	94.738	590	722	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Facklamia_A	95.0	96.44	96.27	0.84	0.80	4	-
GCF_001552295.1	s__Globicatella sanguinis	79.1367	71	722	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Globicatella	95.0	97.13	96.22	0.85	0.84	3	-
GCA_015863215.1	s__DSM-111022 sp015863215	78.1645	96	722	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__DSM-111022	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009659375.1	s__Fundicoccus ignavus	77.6177	105	722	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Fundicoccus	95.0	98.16	98.10	0.87	0.87	3	-
GCA_015863195.1	s__DSM-111022 sp015863195	77.4604	81	722	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__DSM-111022	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016237705.1	s__Globicatella sp010892315	76.8719	63	722	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Globicatella	95.0	98.61	97.07	0.93	0.84	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:31,813] [INFO] GTDB search result was written to GCF_014049385.1_ASM1404938v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:31,813] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:31,816] [INFO] DFAST_QC result json was written to GCF_014049385.1_ASM1404938v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:31,816] [INFO] DFAST_QC completed!
[2024-01-24 13:50:31,816] [INFO] Total running time: 0h0m46s