[2024-01-24 12:14:33,685] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:33,686] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:33,687] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d695ebe-cc36-48a7-85d6-ad334f508954/dqc_reference
[2024-01-24 12:14:34,965] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:34,966] [INFO] Task started: Prodigal
[2024-01-24 12:14:34,966] [INFO] Running command: gunzip -c /var/lib/cwl/stgecc4f4f8-4cc1-4958-ac8a-eaace574c64c/GCF_024343775.1_ASM2434377v1_genomic.fna.gz | prodigal -d GCF_024343775.1_ASM2434377v1_genomic.fna/cds.fna -a GCF_024343775.1_ASM2434377v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:59,648] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:59,649] [INFO] Task started: HMMsearch
[2024-01-24 12:14:59,649] [INFO] Running command: hmmsearch --tblout GCF_024343775.1_ASM2434377v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d695ebe-cc36-48a7-85d6-ad334f508954/dqc_reference/reference_markers.hmm GCF_024343775.1_ASM2434377v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:59,995] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:59,996] [INFO] Found 6/6 markers.
[2024-01-24 12:15:00,047] [INFO] Query marker FASTA was written to GCF_024343775.1_ASM2434377v1_genomic.fna/markers.fasta
[2024-01-24 12:15:00,047] [INFO] Task started: Blastn
[2024-01-24 12:15:00,048] [INFO] Running command: blastn -query GCF_024343775.1_ASM2434377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d695ebe-cc36-48a7-85d6-ad334f508954/dqc_reference/reference_markers.fasta -out GCF_024343775.1_ASM2434377v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:00,664] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:00,670] [INFO] Selected 26 target genomes.
[2024-01-24 12:15:00,671] [INFO] Target genome list was writen to GCF_024343775.1_ASM2434377v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:00,681] [INFO] Task started: fastANI
[2024-01-24 12:15:00,681] [INFO] Running command: fastANI --query /var/lib/cwl/stgecc4f4f8-4cc1-4958-ac8a-eaace574c64c/GCF_024343775.1_ASM2434377v1_genomic.fna.gz --refList GCF_024343775.1_ASM2434377v1_genomic.fna/target_genomes.txt --output GCF_024343775.1_ASM2434377v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:19,969] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:19,969] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d695ebe-cc36-48a7-85d6-ad334f508954/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:19,970] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d695ebe-cc36-48a7-85d6-ad334f508954/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:19,977] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:19,977] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:19,977] [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
Lacihabitans soyangensis	strain=KCTC23259	GCA_024343775.1	869394	869394	type	True	100.0	1776	1781	95	conclusive
Emticicia aquatilis	strain=CGMCC 1.15958	GCA_014644295.1	1537369	1537369	type	True	77.7743	135	1781	95	below_threshold
Leadbetterella byssophila	strain=DSM 17132	GCA_000166395.1	316068	316068	type	True	77.1984	77	1781	95	below_threshold
Arcticibacterium luteifluviistationis	strain=SM1504	GCA_003258705.1	1784714	1784714	type	True	76.1349	71	1781	95	below_threshold
Emticicia agri	strain=17J42-9	GCA_004168285.1	2492393	2492393	type	True	75.7653	73	1781	95	below_threshold
Emticicia aquatica	strain=CECT 8858, type strain	GCA_923079645.1	1681835	1681835	type	True	75.7269	99	1781	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:19,979] [INFO] DFAST Taxonomy check result was written to GCF_024343775.1_ASM2434377v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:19,980] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:19,980] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:19,980] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d695ebe-cc36-48a7-85d6-ad334f508954/dqc_reference/checkm_data
[2024-01-24 12:15:19,982] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:20,040] [INFO] Task started: CheckM
[2024-01-24 12:15:20,040] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024343775.1_ASM2434377v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024343775.1_ASM2434377v1_genomic.fna/checkm_input GCF_024343775.1_ASM2434377v1_genomic.fna/checkm_result
[2024-01-24 12:16:29,194] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:29,195] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:29,221] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:29,222] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:29,222] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024343775.1_ASM2434377v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:29,222] [INFO] Task started: Blastn
[2024-01-24 12:16:29,223] [INFO] Running command: blastn -query GCF_024343775.1_ASM2434377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d695ebe-cc36-48a7-85d6-ad334f508954/dqc_reference/reference_markers_gtdb.fasta -out GCF_024343775.1_ASM2434377v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:29,940] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:29,944] [INFO] Selected 26 target genomes.
[2024-01-24 12:16:29,944] [INFO] Target genome list was writen to GCF_024343775.1_ASM2434377v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:29,972] [INFO] Task started: fastANI
[2024-01-24 12:16:29,972] [INFO] Running command: fastANI --query /var/lib/cwl/stgecc4f4f8-4cc1-4958-ac8a-eaace574c64c/GCF_024343775.1_ASM2434377v1_genomic.fna.gz --refList GCF_024343775.1_ASM2434377v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024343775.1_ASM2434377v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:51,230] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:51,246] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:16:51,246] [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_002256295.1	s__Leadbetterella sp002256295	82.8897	889	1781	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Leadbetterella	95.0	97.02	97.02	0.83	0.83	2	-
GCF_014644295.1	s__Emticicia aquatilis	77.7743	135	1781	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Emticicia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016722655.1	s__Leadbetterella sp016722655	77.509	255	1781	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Leadbetterella	95.0	99.38	99.07	0.96	0.94	5	-
GCF_000166395.1	s__Leadbetterella byssophila	77.1944	77	1781	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Leadbetterella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009905725.1	s__Leadbetterella sp002483125	76.5462	87	1781	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Leadbetterella	95.0	98.11	98.11	0.94	0.94	2	-
GCA_000263195.1	s__Emticicia oligotrophica	76.5182	97	1781	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Emticicia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258705.1	s__Arcticibacterium luteifluviistationis	76.2997	72	1781	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Arcticibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900230115.1	s__TFI-002 sp900230115	76.2829	77	1781	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__TFI-002	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002855535.1	s__Emticicia sp002855535	76.0102	59	1781	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Emticicia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000427405.1	s__Flectobacillus major	75.7372	64	1781	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Flectobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003418935.1	s__Emticicia sp003418935	75.5228	87	1781	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Emticicia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013912375.1	s__Emticicia sp013912375	75.4174	67	1781	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Emticicia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:51,248] [INFO] GTDB search result was written to GCF_024343775.1_ASM2434377v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:51,248] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:51,251] [INFO] DFAST_QC result json was written to GCF_024343775.1_ASM2434377v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:51,252] [INFO] DFAST_QC completed!
[2024-01-24 12:16:51,252] [INFO] Total running time: 0h2m18s