[2024-01-24 14:06:14,217] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:14,219] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:14,219] [INFO] DQC Reference Directory: /var/lib/cwl/stg954caea8-f4ca-4f41-8de9-7e6eab853e9c/dqc_reference
[2024-01-24 14:06:15,532] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:15,533] [INFO] Task started: Prodigal
[2024-01-24 14:06:15,533] [INFO] Running command: gunzip -c /var/lib/cwl/stg2ba460e8-0c82-48da-87fd-4000f05bc610/GCF_003063245.1_ASM306324v1_genomic.fna.gz | prodigal -d GCF_003063245.1_ASM306324v1_genomic.fna/cds.fna -a GCF_003063245.1_ASM306324v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:19,448] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:19,449] [INFO] Task started: HMMsearch
[2024-01-24 14:06:19,449] [INFO] Running command: hmmsearch --tblout GCF_003063245.1_ASM306324v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg954caea8-f4ca-4f41-8de9-7e6eab853e9c/dqc_reference/reference_markers.hmm GCF_003063245.1_ASM306324v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:19,690] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:19,691] [INFO] Found 6/6 markers.
[2024-01-24 14:06:19,732] [INFO] Query marker FASTA was written to GCF_003063245.1_ASM306324v1_genomic.fna/markers.fasta
[2024-01-24 14:06:19,733] [INFO] Task started: Blastn
[2024-01-24 14:06:19,733] [INFO] Running command: blastn -query GCF_003063245.1_ASM306324v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg954caea8-f4ca-4f41-8de9-7e6eab853e9c/dqc_reference/reference_markers.fasta -out GCF_003063245.1_ASM306324v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:20,387] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:20,390] [INFO] Selected 9 target genomes.
[2024-01-24 14:06:20,390] [INFO] Target genome list was writen to GCF_003063245.1_ASM306324v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:20,394] [INFO] Task started: fastANI
[2024-01-24 14:06:20,394] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ba460e8-0c82-48da-87fd-4000f05bc610/GCF_003063245.1_ASM306324v1_genomic.fna.gz --refList GCF_003063245.1_ASM306324v1_genomic.fna/target_genomes.txt --output GCF_003063245.1_ASM306324v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:26,575] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:26,576] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg954caea8-f4ca-4f41-8de9-7e6eab853e9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:26,576] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg954caea8-f4ca-4f41-8de9-7e6eab853e9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:26,585] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:26,585] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:26,585] [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
Arcobacter caeni	strain=RW17-10	GCA_003063245.1	1912877	1912877	type	True	100.0	779	779	95	conclusive
Arcobacter suis	strain=CECT7833	GCA_004023465.1	1278212	1278212	type	True	88.2201	617	779	95	below_threshold
Arcobacter suis	strain=CECT 7833	GCA_003544815.1	1278212	1278212	type	True	88.1781	637	779	95	below_threshold
Arcobacter venerupis	strain=CECT7836	GCA_004023405.1	1054033	1054033	type	True	86.5159	597	779	95	below_threshold
Arcobacter venerupis	strain=LMG 26156	GCA_013201665.1	1054033	1054033	type	True	86.4639	615	779	95	below_threshold
Arcobacter ellisii	strain=LMG 26155	GCA_003544915.1	913109	913109	type	True	83.9581	590	779	95	below_threshold
Arcobacter ellisii	strain=CECT 7837	GCA_004115815.1	913109	913109	type	True	83.9556	565	779	95	below_threshold
Arcobacter cloacae	strain=CECT 7834	GCA_004115805.1	1054034	1054034	type	True	83.8917	546	779	95	below_threshold
Arcobacter cloacae	strain=LMG 26153	GCA_013201935.1	1054034	1054034	type	True	83.8879	559	779	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:26,587] [INFO] DFAST Taxonomy check result was written to GCF_003063245.1_ASM306324v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:26,588] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:26,588] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:26,588] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg954caea8-f4ca-4f41-8de9-7e6eab853e9c/dqc_reference/checkm_data
[2024-01-24 14:06:26,590] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:26,623] [INFO] Task started: CheckM
[2024-01-24 14:06:26,623] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003063245.1_ASM306324v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003063245.1_ASM306324v1_genomic.fna/checkm_input GCF_003063245.1_ASM306324v1_genomic.fna/checkm_result
[2024-01-24 14:06:47,021] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:47,022] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:47,036] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:47,036] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:47,036] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003063245.1_ASM306324v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:47,037] [INFO] Task started: Blastn
[2024-01-24 14:06:47,037] [INFO] Running command: blastn -query GCF_003063245.1_ASM306324v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg954caea8-f4ca-4f41-8de9-7e6eab853e9c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003063245.1_ASM306324v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:47,887] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:47,890] [INFO] Selected 10 target genomes.
[2024-01-24 14:06:47,891] [INFO] Target genome list was writen to GCF_003063245.1_ASM306324v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:47,900] [INFO] Task started: fastANI
[2024-01-24 14:06:47,900] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ba460e8-0c82-48da-87fd-4000f05bc610/GCF_003063245.1_ASM306324v1_genomic.fna.gz --refList GCF_003063245.1_ASM306324v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003063245.1_ASM306324v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:54,373] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:54,381] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:54,382] [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_003063245.1	s__Aliarcobacter caeni	100.0	779	779	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003544815.1	s__Aliarcobacter suis	88.1181	640	779	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013201665.1	s__Aliarcobacter venerupis	86.4404	617	779	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	100.00	100.00	0.99	0.99	2	-
GCA_017995775.1	s__Aliarcobacter sp017995775	86.0672	497	779	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.13	99.13	0.84	0.84	2	-
GCA_018816105.1	s__Aliarcobacter sp018816105	84.2327	517	779	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013177675.1	s__Aliarcobacter acticola	83.9713	565	779	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003544915.1	s__Aliarcobacter ellisii	83.914	593	779	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.73	97.46	0.92	0.84	3	-
GCF_013201935.1	s__Aliarcobacter cloacae	83.8879	559	779	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.96	95.91	0.93	0.87	3	-
GCF_013201725.1	s__Aliarcobacter defluvii	83.5849	561	779	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.85	98.15	0.93	0.88	4	-
GCF_013177635.1	s__Aliarcobacter aquimarinus	83.5045	555	779	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:54,383] [INFO] GTDB search result was written to GCF_003063245.1_ASM306324v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:54,384] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:54,387] [INFO] DFAST_QC result json was written to GCF_003063245.1_ASM306324v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:54,387] [INFO] DFAST_QC completed!
[2024-01-24 14:06:54,388] [INFO] Total running time: 0h0m40s