[2024-01-24 11:59:05,175] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:05,177] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:05,177] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c5232bf-0472-4526-9d85-794c36aece1e/dqc_reference
[2024-01-24 11:59:06,336] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:06,337] [INFO] Task started: Prodigal
[2024-01-24 11:59:06,337] [INFO] Running command: gunzip -c /var/lib/cwl/stg1df7c465-0cd6-4a82-a07c-9775d86e3038/GCF_003711085.1_ASM371108v1_genomic.fna.gz | prodigal -d GCF_003711085.1_ASM371108v1_genomic.fna/cds.fna -a GCF_003711085.1_ASM371108v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:10,688] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:10,688] [INFO] Task started: HMMsearch
[2024-01-24 11:59:10,688] [INFO] Running command: hmmsearch --tblout GCF_003711085.1_ASM371108v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c5232bf-0472-4526-9d85-794c36aece1e/dqc_reference/reference_markers.hmm GCF_003711085.1_ASM371108v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:10,921] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:10,923] [INFO] Found 6/6 markers.
[2024-01-24 11:59:10,954] [INFO] Query marker FASTA was written to GCF_003711085.1_ASM371108v1_genomic.fna/markers.fasta
[2024-01-24 11:59:10,955] [INFO] Task started: Blastn
[2024-01-24 11:59:10,956] [INFO] Running command: blastn -query GCF_003711085.1_ASM371108v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c5232bf-0472-4526-9d85-794c36aece1e/dqc_reference/reference_markers.fasta -out GCF_003711085.1_ASM371108v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:11,617] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:11,621] [INFO] Selected 16 target genomes.
[2024-01-24 11:59:11,622] [INFO] Target genome list was writen to GCF_003711085.1_ASM371108v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:11,797] [INFO] Task started: fastANI
[2024-01-24 11:59:11,797] [INFO] Running command: fastANI --query /var/lib/cwl/stg1df7c465-0cd6-4a82-a07c-9775d86e3038/GCF_003711085.1_ASM371108v1_genomic.fna.gz --refList GCF_003711085.1_ASM371108v1_genomic.fna/target_genomes.txt --output GCF_003711085.1_ASM371108v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:21,270] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:21,271] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c5232bf-0472-4526-9d85-794c36aece1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:21,271] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c5232bf-0472-4526-9d85-794c36aece1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:21,290] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:59:21,290] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:59:21,290] [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
Poseidonibacter lekithochrous	strain=DSM 100870	GCA_013283835.1	1904463	1904463	type	True	81.4533	551	938	95	below_threshold
Poseidonibacter lekithochrous	strain=LFT 1.7	GCA_001878855.1	1904463	1904463	type	True	81.2256	542	938	95	below_threshold
Arcobacter acticola	strain=KCTC 52212	GCA_013177675.1	1849015	1849015	type	True	81.1909	520	938	95	below_threshold
Arcobacter suis	strain=CECT 7833	GCA_003544815.1	1278212	1278212	type	True	80.5565	460	938	95	below_threshold
Malaciobacter pacificus	strain=LMG 26638	GCA_004214795.1	1080223	1080223	type	True	80.4808	474	938	95	below_threshold
Malaciobacter pacificus	strain=CGMCC 1.11011	GCA_014636355.1	1080223	1080223	type	True	80.4621	450	938	95	below_threshold
Arcobacter caeni	strain=RW17-10	GCA_003063245.1	1912877	1912877	type	True	80.3488	460	938	95	below_threshold
Arcobacter suis	strain=CECT7833	GCA_004023465.1	1278212	1278212	type	True	80.3447	444	938	95	below_threshold
Arcobacter venerupis	strain=LMG 26156	GCA_013201665.1	1054033	1054033	type	True	80.3281	475	938	95	below_threshold
Arcobacter defluvii	strain=LMG 25694	GCA_013201725.1	873191	873191	type	True	80.2981	466	938	95	below_threshold
Arcobacter ellisii	strain=LMG 26155	GCA_003544915.1	913109	913109	type	True	80.1728	491	938	95	below_threshold
Arcobacter venerupis	strain=CECT7836	GCA_004023405.1	1054033	1054033	type	True	80.1071	459	938	95	below_threshold
Arcobacter defluvii	strain=CECT 7697	GCA_004115775.1	873191	873191	type	True	80.1	452	938	95	below_threshold
Arcobacter ellisii	strain=CECT 7837	GCA_004115815.1	913109	913109	type	True	80.0712	466	938	95	below_threshold
Arcobacter cloacae	strain=LMG 26153	GCA_013201935.1	1054034	1054034	type	True	80.0268	465	938	95	below_threshold
Arcobacter cloacae	strain=CECT 7834	GCA_004115805.1	1054034	1054034	type	True	79.829	451	938	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:21,292] [INFO] DFAST Taxonomy check result was written to GCF_003711085.1_ASM371108v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:21,293] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:21,293] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:21,293] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c5232bf-0472-4526-9d85-794c36aece1e/dqc_reference/checkm_data
[2024-01-24 11:59:21,294] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:21,325] [INFO] Task started: CheckM
[2024-01-24 11:59:21,326] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003711085.1_ASM371108v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003711085.1_ASM371108v1_genomic.fna/checkm_input GCF_003711085.1_ASM371108v1_genomic.fna/checkm_result
[2024-01-24 11:59:41,526] [INFO] Task succeeded: CheckM
[2024-01-24 11:59:41,528] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:59:41,551] [INFO] ===== Completeness check finished =====
[2024-01-24 11:59:41,552] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:59:41,552] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003711085.1_ASM371108v1_genomic.fna/markers.fasta)
[2024-01-24 11:59:41,553] [INFO] Task started: Blastn
[2024-01-24 11:59:41,553] [INFO] Running command: blastn -query GCF_003711085.1_ASM371108v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c5232bf-0472-4526-9d85-794c36aece1e/dqc_reference/reference_markers_gtdb.fasta -out GCF_003711085.1_ASM371108v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:42,384] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:42,388] [INFO] Selected 8 target genomes.
[2024-01-24 11:59:42,388] [INFO] Target genome list was writen to GCF_003711085.1_ASM371108v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:59:42,425] [INFO] Task started: fastANI
[2024-01-24 11:59:42,426] [INFO] Running command: fastANI --query /var/lib/cwl/stg1df7c465-0cd6-4a82-a07c-9775d86e3038/GCF_003711085.1_ASM371108v1_genomic.fna.gz --refList GCF_003711085.1_ASM371108v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003711085.1_ASM371108v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:59:47,912] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:47,921] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:59:47,921] [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_001956695.1	s__Poseidonibacter parvus	98.2619	853	938	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	98.33	98.33	0.91	0.91	2	conclusive
GCF_009208075.1	s__Poseidonibacter sp009208075	85.0795	644	938	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	99.63	99.63	0.93	0.93	3	-
GCF_003667345.1	s__Poseidonibacter antarcticus	84.6724	618	938	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861145.1	s__Poseidonibacter lekithochrous_A	84.4175	654	938	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002685075.1	s__Poseidonibacter sp002685075	84.1616	536	938	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479135.1	s__Poseidonibacter sp905479135	83.8314	377	938	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013283835.1	s__Poseidonibacter lekithochrous	81.4241	551	938	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	99.16	98.33	0.97	0.93	3	-
GCF_003063245.1	s__Aliarcobacter caeni	80.3778	457	938	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:59:47,923] [INFO] GTDB search result was written to GCF_003711085.1_ASM371108v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:59:47,924] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:59:47,928] [INFO] DFAST_QC result json was written to GCF_003711085.1_ASM371108v1_genomic.fna/dqc_result.json
[2024-01-24 11:59:47,928] [INFO] DFAST_QC completed!
[2024-01-24 11:59:47,928] [INFO] Total running time: 0h0m43s