[2024-01-24 15:10:20,134] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:20,136] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:20,136] [INFO] DQC Reference Directory: /var/lib/cwl/stg12e61f00-6891-4925-8d7c-afb521fdaf65/dqc_reference
[2024-01-24 15:10:22,726] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:22,730] [INFO] Task started: Prodigal
[2024-01-24 15:10:22,730] [INFO] Running command: gunzip -c /var/lib/cwl/stg910d1294-cc7b-4af4-8be9-7157c022acf7/GCF_005771535.1_ASM577153v1_genomic.fna.gz | prodigal -d GCF_005771535.1_ASM577153v1_genomic.fna/cds.fna -a GCF_005771535.1_ASM577153v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:27,672] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:27,672] [INFO] Task started: HMMsearch
[2024-01-24 15:10:27,673] [INFO] Running command: hmmsearch --tblout GCF_005771535.1_ASM577153v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg12e61f00-6891-4925-8d7c-afb521fdaf65/dqc_reference/reference_markers.hmm GCF_005771535.1_ASM577153v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:27,967] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:27,968] [INFO] Found 6/6 markers.
[2024-01-24 15:10:28,011] [INFO] Query marker FASTA was written to GCF_005771535.1_ASM577153v1_genomic.fna/markers.fasta
[2024-01-24 15:10:28,012] [INFO] Task started: Blastn
[2024-01-24 15:10:28,012] [INFO] Running command: blastn -query GCF_005771535.1_ASM577153v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12e61f00-6891-4925-8d7c-afb521fdaf65/dqc_reference/reference_markers.fasta -out GCF_005771535.1_ASM577153v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:30,085] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:30,090] [INFO] Selected 17 target genomes.
[2024-01-24 15:10:30,090] [INFO] Target genome list was writen to GCF_005771535.1_ASM577153v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:30,614] [INFO] Task started: fastANI
[2024-01-24 15:10:30,615] [INFO] Running command: fastANI --query /var/lib/cwl/stg910d1294-cc7b-4af4-8be9-7157c022acf7/GCF_005771535.1_ASM577153v1_genomic.fna.gz --refList GCF_005771535.1_ASM577153v1_genomic.fna/target_genomes.txt --output GCF_005771535.1_ASM577153v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:40,031] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:40,031] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg12e61f00-6891-4925-8d7c-afb521fdaf65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:40,032] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg12e61f00-6891-4925-8d7c-afb521fdaf65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:40,050] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:10:40,050] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:10:40,050] [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] arenosus	strain=CAU 1517	GCA_005771535.1	2576037	2576037	type	True	100.0	1032	1034	95	conclusive
Halarcobacter bivalviorum	strain=CECT 7835	GCA_004116675.1	663364	663364	type	True	80.4733	500	1034	95	below_threshold
Halarcobacter bivalviorum	strain=LMG 26154	GCA_003346815.1	663364	663364	type	True	80.3975	510	1034	95	below_threshold
Malaciobacter pacificus	strain=CGMCC 1.11011	GCA_014636355.1	1080223	1080223	type	True	80.3313	411	1034	95	below_threshold
Malaciobacter pacificus	strain=LMG 26638	GCA_004214795.1	1080223	1080223	type	True	80.2257	422	1034	95	below_threshold
Halarcobacter ebronensis	strain=CECT 8441	GCA_004116565.1	1462615	1462615	type	True	80.105	509	1034	95	below_threshold
Halarcobacter ebronensis	strain=LMG 27922	GCA_013201825.1	1462615	1462615	type	True	80.0653	522	1034	95	below_threshold
Arcobacter ellisii	strain=CECT 7837	GCA_004115815.1	913109	913109	type	True	79.3807	429	1034	95	below_threshold
Arcobacter ellisii	strain=LMG 26155	GCA_003544915.1	913109	913109	type	True	79.3498	429	1034	95	below_threshold
Arcobacter defluvii	strain=CECT 7697	GCA_004115775.1	873191	873191	type	True	79.258	401	1034	95	below_threshold
Malaciobacter molluscorum	strain=CECT 7696	GCA_003544935.1	1032072	1032072	type	True	79.2308	409	1034	95	below_threshold
Arcobacter suis	strain=CECT 7833	GCA_003544815.1	1278212	1278212	type	True	79.0725	384	1034	95	below_threshold
Arcobacter suis	strain=CECT7833	GCA_004023465.1	1278212	1278212	type	True	79.0169	389	1034	95	below_threshold
Halarcobacter anaerophilus	strain=DSM 24636	GCA_006459125.1	877500	877500	type	True	78.9163	446	1034	95	below_threshold
Poseidonibacter lekithochrous	strain=DSM 100870	GCA_013283835.1	1904463	1904463	type	True	78.912	415	1034	95	below_threshold
Halarcobacter anaerophilus	strain=DSM 24636	GCA_004116345.1	877500	877500	type	True	78.9082	446	1034	95	below_threshold
Poseidonibacter lekithochrous	strain=LFT 1.7	GCA_001878855.1	1904463	1904463	type	True	78.8282	412	1034	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:10:40,052] [INFO] DFAST Taxonomy check result was written to GCF_005771535.1_ASM577153v1_genomic.fna/tc_result.tsv
[2024-01-24 15:10:40,053] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:40,053] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:40,053] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg12e61f00-6891-4925-8d7c-afb521fdaf65/dqc_reference/checkm_data
[2024-01-24 15:10:40,054] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:10:40,095] [INFO] Task started: CheckM
[2024-01-24 15:10:40,096] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005771535.1_ASM577153v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005771535.1_ASM577153v1_genomic.fna/checkm_input GCF_005771535.1_ASM577153v1_genomic.fna/checkm_result
[2024-01-24 15:11:02,529] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:02,530] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:02,563] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:02,563] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:02,564] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005771535.1_ASM577153v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:02,564] [INFO] Task started: Blastn
[2024-01-24 15:11:02,564] [INFO] Running command: blastn -query GCF_005771535.1_ASM577153v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12e61f00-6891-4925-8d7c-afb521fdaf65/dqc_reference/reference_markers_gtdb.fasta -out GCF_005771535.1_ASM577153v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:03,485] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:03,489] [INFO] Selected 13 target genomes.
[2024-01-24 15:11:03,489] [INFO] Target genome list was writen to GCF_005771535.1_ASM577153v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:03,536] [INFO] Task started: fastANI
[2024-01-24 15:11:03,537] [INFO] Running command: fastANI --query /var/lib/cwl/stg910d1294-cc7b-4af4-8be9-7157c022acf7/GCF_005771535.1_ASM577153v1_genomic.fna.gz --refList GCF_005771535.1_ASM577153v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005771535.1_ASM577153v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:14,451] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:14,464] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:14,464] [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_005771535.1	s__Halarcobacter arenosus	100.0	1032	1034	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004118855.1	s__Halarcobacter sp004118855	80.8947	505	1034	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	80.583	480	1034	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	80.5271	467	1034	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	80.5262	545	1034	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003252105.1	s__Halarcobacter sp003252105	80.4384	476	1034	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	80.3938	510	1034	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	98.23	96.46	0.96	0.92	3	-
GCF_004116625.1	s__Halarcobacter mediterraneus	80.2157	496	1034	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002869565.1	s__Halarcobacter sp002869565	80.2111	584	1034	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013201825.1	s__Halarcobacter ebronensis	80.0623	523	1034	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	98.25	96.51	0.95	0.90	3	-
GCF_009208075.1	s__Poseidonibacter sp009208075	79.2351	409	1034	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	99.63	99.63	0.93	0.93	3	-
GCF_003544815.1	s__Aliarcobacter suis	79.0495	386	1034	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013283835.1	s__Poseidonibacter lekithochrous	78.9193	413	1034	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	99.16	98.33	0.97	0.93	3	-
--------------------------------------------------------------------------------
[2024-01-24 15:11:14,466] [INFO] GTDB search result was written to GCF_005771535.1_ASM577153v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:14,467] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:14,480] [INFO] DFAST_QC result json was written to GCF_005771535.1_ASM577153v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:14,480] [INFO] DFAST_QC completed!
[2024-01-24 15:11:14,480] [INFO] Total running time: 0h0m54s