[2024-01-24 13:25:28,303] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:28,304] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:28,304] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ee5e788-5304-4f78-a56e-1250690a81ad/dqc_reference
[2024-01-24 13:25:29,694] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:29,695] [INFO] Task started: Prodigal
[2024-01-24 13:25:29,696] [INFO] Running command: gunzip -c /var/lib/cwl/stg64c50f1a-ec86-4615-b7dd-34999a09b9ca/GCF_009668025.1_ASM966802v1_genomic.fna.gz | prodigal -d GCF_009668025.1_ASM966802v1_genomic.fna/cds.fna -a GCF_009668025.1_ASM966802v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:09,165] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:09,166] [INFO] Task started: HMMsearch
[2024-01-24 13:26:09,166] [INFO] Running command: hmmsearch --tblout GCF_009668025.1_ASM966802v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ee5e788-5304-4f78-a56e-1250690a81ad/dqc_reference/reference_markers.hmm GCF_009668025.1_ASM966802v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:09,515] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:09,517] [INFO] Found 6/6 markers.
[2024-01-24 13:26:09,579] [INFO] Query marker FASTA was written to GCF_009668025.1_ASM966802v1_genomic.fna/markers.fasta
[2024-01-24 13:26:09,579] [INFO] Task started: Blastn
[2024-01-24 13:26:09,579] [INFO] Running command: blastn -query GCF_009668025.1_ASM966802v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ee5e788-5304-4f78-a56e-1250690a81ad/dqc_reference/reference_markers.fasta -out GCF_009668025.1_ASM966802v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:10,173] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:10,176] [INFO] Selected 10 target genomes.
[2024-01-24 13:26:10,177] [INFO] Target genome list was writen to GCF_009668025.1_ASM966802v1_genomic.fna/target_genomes.txt
[2024-01-24 13:26:10,181] [INFO] Task started: fastANI
[2024-01-24 13:26:10,182] [INFO] Running command: fastANI --query /var/lib/cwl/stg64c50f1a-ec86-4615-b7dd-34999a09b9ca/GCF_009668025.1_ASM966802v1_genomic.fna.gz --refList GCF_009668025.1_ASM966802v1_genomic.fna/target_genomes.txt --output GCF_009668025.1_ASM966802v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:24,832] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:24,833] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ee5e788-5304-4f78-a56e-1250690a81ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:24,833] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ee5e788-5304-4f78-a56e-1250690a81ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:24,844] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:26:24,844] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:24,844] [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
Larkinella terrae	strain=KCTC 52001	GCA_009668025.1	2025311	2025311	type	True	100.0	2603	2604	95	conclusive
Larkinella rosea	strain=KCTC52004	GCA_003858635.1	2025312	2025312	type	True	86.4322	2090	2604	95	below_threshold
Larkinella humicola	strain=MA1	GCA_008727875.1	2607654	2607654	type	True	81.8326	1661	2604	95	below_threshold
Larkinella punicea	strain=ZZJ9	GCA_003334855.1	2315727	2315727	type	True	81.8236	1641	2604	95	below_threshold
Larkinella knui	strain=KCTC42998	GCA_003858645.1	2025310	2025310	type	True	81.4875	1650	2604	95	below_threshold
Larkinella arboricola	strain=DSM 21851	GCA_003259745.1	643671	643671	type	True	79.8624	1246	2604	95	below_threshold
Telluribacter humicola	strain=KCTC 42819	GCA_017355935.1	1720261	1720261	type	True	75.6836	57	2604	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:24,846] [INFO] DFAST Taxonomy check result was written to GCF_009668025.1_ASM966802v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:24,846] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:24,847] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:24,847] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ee5e788-5304-4f78-a56e-1250690a81ad/dqc_reference/checkm_data
[2024-01-24 13:26:24,848] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:24,917] [INFO] Task started: CheckM
[2024-01-24 13:26:24,917] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009668025.1_ASM966802v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009668025.1_ASM966802v1_genomic.fna/checkm_input GCF_009668025.1_ASM966802v1_genomic.fna/checkm_result
[2024-01-24 13:28:08,789] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:08,791] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:08,811] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:08,812] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:08,812] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009668025.1_ASM966802v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:08,813] [INFO] Task started: Blastn
[2024-01-24 13:28:08,813] [INFO] Running command: blastn -query GCF_009668025.1_ASM966802v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ee5e788-5304-4f78-a56e-1250690a81ad/dqc_reference/reference_markers_gtdb.fasta -out GCF_009668025.1_ASM966802v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:09,641] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:09,645] [INFO] Selected 8 target genomes.
[2024-01-24 13:28:09,645] [INFO] Target genome list was writen to GCF_009668025.1_ASM966802v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:09,709] [INFO] Task started: fastANI
[2024-01-24 13:28:09,709] [INFO] Running command: fastANI --query /var/lib/cwl/stg64c50f1a-ec86-4615-b7dd-34999a09b9ca/GCF_009668025.1_ASM966802v1_genomic.fna.gz --refList GCF_009668025.1_ASM966802v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009668025.1_ASM966802v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:28:24,432] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:24,447] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:28:24,447] [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_009668025.1	s__Larkinella terrae	100.0	2603	2604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003858635.1	s__Larkinella rosea	86.4276	2091	2604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008727875.1	s__Larkinella sp008727875	81.8417	1658	2604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003334855.1	s__Larkinella punicea	81.8401	1635	2604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006149005.1	s__Larkinella sp006149005	81.787	1620	2604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003858645.1	s__Larkinella knui	81.4888	1648	2604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366505.1	s__Larkinella sp004366505	80.285	1316	2604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259745.1	s__Larkinella arboricola	79.8577	1248	2604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:28:24,449] [INFO] GTDB search result was written to GCF_009668025.1_ASM966802v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:28:24,449] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:28:24,454] [INFO] DFAST_QC result json was written to GCF_009668025.1_ASM966802v1_genomic.fna/dqc_result.json
[2024-01-24 13:28:24,455] [INFO] DFAST_QC completed!
[2024-01-24 13:28:24,455] [INFO] Total running time: 0h2m56s