[2024-01-24 15:02:07,444] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:07,447] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:07,447] [INFO] DQC Reference Directory: /var/lib/cwl/stg688e2bfc-ca2b-4b98-a81d-f2f9fd1bee12/dqc_reference
[2024-01-24 15:02:09,599] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:09,600] [INFO] Task started: Prodigal
[2024-01-24 15:02:09,600] [INFO] Running command: gunzip -c /var/lib/cwl/stg97b9443e-218d-4755-ba7e-9fbe2a43ab5c/GCF_004116565.1_ASM411656v1_genomic.fna.gz | prodigal -d GCF_004116565.1_ASM411656v1_genomic.fna/cds.fna -a GCF_004116565.1_ASM411656v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:14,738] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:14,739] [INFO] Task started: HMMsearch
[2024-01-24 15:02:14,739] [INFO] Running command: hmmsearch --tblout GCF_004116565.1_ASM411656v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg688e2bfc-ca2b-4b98-a81d-f2f9fd1bee12/dqc_reference/reference_markers.hmm GCF_004116565.1_ASM411656v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:14,971] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:14,972] [INFO] Found 6/6 markers.
[2024-01-24 15:02:14,999] [INFO] Query marker FASTA was written to GCF_004116565.1_ASM411656v1_genomic.fna/markers.fasta
[2024-01-24 15:02:14,999] [INFO] Task started: Blastn
[2024-01-24 15:02:15,000] [INFO] Running command: blastn -query GCF_004116565.1_ASM411656v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg688e2bfc-ca2b-4b98-a81d-f2f9fd1bee12/dqc_reference/reference_markers.fasta -out GCF_004116565.1_ASM411656v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:17,013] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:17,017] [INFO] Selected 13 target genomes.
[2024-01-24 15:02:17,017] [INFO] Target genome list was writen to GCF_004116565.1_ASM411656v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:17,076] [INFO] Task started: fastANI
[2024-01-24 15:02:17,076] [INFO] Running command: fastANI --query /var/lib/cwl/stg97b9443e-218d-4755-ba7e-9fbe2a43ab5c/GCF_004116565.1_ASM411656v1_genomic.fna.gz --refList GCF_004116565.1_ASM411656v1_genomic.fna/target_genomes.txt --output GCF_004116565.1_ASM411656v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:24,860] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:24,860] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg688e2bfc-ca2b-4b98-a81d-f2f9fd1bee12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:24,860] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg688e2bfc-ca2b-4b98-a81d-f2f9fd1bee12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:24,871] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:02:24,871] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:24,871] [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
Halarcobacter ebronensis	strain=CECT 8441	GCA_004116565.1	1462615	1462615	type	True	100.0	1018	1020	95	conclusive
Halarcobacter ebronensis	strain=LMG 27922	GCA_013201825.1	1462615	1462615	type	True	99.9931	1018	1020	95	conclusive
Halarcobacter anaerophilus	strain=DSM 24636	GCA_004116345.1	877500	877500	type	True	80.3762	585	1020	95	below_threshold
Halarcobacter anaerophilus	strain=DSM 24636	GCA_006459125.1	877500	877500	type	True	80.3457	586	1020	95	below_threshold
[Halarcobacter] arenosus	strain=CAU 1517	GCA_005771535.1	2576037	2576037	type	True	79.969	532	1020	95	below_threshold
Halarcobacter bivalviorum	strain=LMG 26154	GCA_003346815.1	663364	663364	type	True	79.944	484	1020	95	below_threshold
Malaciobacter molluscorum	strain=CECT 7696	GCA_003544935.1	1032072	1032072	type	True	79.2228	424	1020	95	below_threshold
Malaciobacter molluscorum	strain=F98-3	GCA_002701265.1	1032072	1032072	type	True	79.1813	427	1020	95	below_threshold
Aliarcobacter butzleri	strain=RM4018	GCA_000014025.1	28197	28197	type	True	78.8573	335	1020	95	below_threshold
Arcobacter nitrofigilis	strain=DSM 7299	GCA_000092245.1	28199	28199	type	True	78.8047	402	1020	95	below_threshold
Aliarcobacter skirrowii	strain=LMG 6621	GCA_024584055.1	28200	28200	type	True	78.6626	266	1020	95	below_threshold
Arcobacter cloacae	strain=LMG 26153	GCA_013201935.1	1054034	1054034	type	True	78.6394	376	1020	95	below_threshold
Arcobacter cloacae	strain=CECT 7834	GCA_004115805.1	1054034	1054034	type	True	78.6346	370	1020	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:24,873] [INFO] DFAST Taxonomy check result was written to GCF_004116565.1_ASM411656v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:24,874] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:24,874] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:24,875] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg688e2bfc-ca2b-4b98-a81d-f2f9fd1bee12/dqc_reference/checkm_data
[2024-01-24 15:02:24,876] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:24,913] [INFO] Task started: CheckM
[2024-01-24 15:02:24,914] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004116565.1_ASM411656v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004116565.1_ASM411656v1_genomic.fna/checkm_input GCF_004116565.1_ASM411656v1_genomic.fna/checkm_result
[2024-01-24 15:02:47,711] [INFO] Task succeeded: CheckM
[2024-01-24 15:02:47,713] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:02:47,736] [INFO] ===== Completeness check finished =====
[2024-01-24 15:02:47,736] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:02:47,737] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004116565.1_ASM411656v1_genomic.fna/markers.fasta)
[2024-01-24 15:02:47,737] [INFO] Task started: Blastn
[2024-01-24 15:02:47,737] [INFO] Running command: blastn -query GCF_004116565.1_ASM411656v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg688e2bfc-ca2b-4b98-a81d-f2f9fd1bee12/dqc_reference/reference_markers_gtdb.fasta -out GCF_004116565.1_ASM411656v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:48,560] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:48,565] [INFO] Selected 16 target genomes.
[2024-01-24 15:02:48,565] [INFO] Target genome list was writen to GCF_004116565.1_ASM411656v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:02:48,588] [INFO] Task started: fastANI
[2024-01-24 15:02:48,589] [INFO] Running command: fastANI --query /var/lib/cwl/stg97b9443e-218d-4755-ba7e-9fbe2a43ab5c/GCF_004116565.1_ASM411656v1_genomic.fna.gz --refList GCF_004116565.1_ASM411656v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004116565.1_ASM411656v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:02:58,270] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:58,284] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:02:58,285] [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_013201825.1	s__Halarcobacter ebronensis	99.9931	1018	1020	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	98.25	96.51	0.95	0.90	3	conclusive
GCF_006459125.1	s__Halarcobacter anaerophilus	80.3453	586	1020	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	98.86	97.73	0.95	0.89	3	-
GCA_003252105.1	s__Halarcobacter sp003252105	80.1571	492	1020	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005771535.1	s__Halarcobacter arenosus	79.9757	531	1020	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003346815.1	s__Halarcobacter bivalviorum	79.9746	481	1020	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	98.23	96.46	0.96	0.92	3	-
GCA_004118855.1	s__Halarcobacter sp004118855	79.9529	474	1020	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004116455.1	s__Halarcobacter sp004116455	79.4633	458	1020	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	96.86	96.86	0.84	0.84	2	-
GCA_001895145.1	s__Halarcobacter sp001895145	79.4582	458	1020	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373175.1	s__Halarcobacter sp013373175	79.4507	456	1020	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003544935.1	s__Malaciobacter molluscorum	79.2288	423	1020	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	99.44	98.88	0.96	0.91	3	-
GCA_002869535.1	s__Arcobacter sp002869535	78.9395	360	1020	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Arcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003063295.1	s__Aliarcobacter lacus	78.9197	327	1020	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187115.1	s__Aliarcobacter butzleri	78.8087	338	1020	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.53	96.98	0.89	0.81	50	-
GCF_000092245.1	s__Arcobacter nitrofigilis	78.8049	402	1020	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Arcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013201935.1	s__Aliarcobacter cloacae	78.6671	373	1020	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.96	95.91	0.93	0.87	3	-
GCF_003660105.1	s__Aliarcobacter cryaerophilus	78.0462	281	1020	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.99	99.99	1.00	0.99	3	-
--------------------------------------------------------------------------------
[2024-01-24 15:02:58,286] [INFO] GTDB search result was written to GCF_004116565.1_ASM411656v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:02:58,290] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:02:58,302] [INFO] DFAST_QC result json was written to GCF_004116565.1_ASM411656v1_genomic.fna/dqc_result.json
[2024-01-24 15:02:58,303] [INFO] DFAST_QC completed!
[2024-01-24 15:02:58,303] [INFO] Total running time: 0h0m51s