[2024-01-24 14:47:08,542] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:08,544] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:08,544] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a9b8661-8684-4a3e-9852-b01546573587/dqc_reference
[2024-01-24 14:47:09,934] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:09,935] [INFO] Task started: Prodigal
[2024-01-24 14:47:09,936] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a9965e7-693a-41d9-8955-37ca05774554/GCF_013283835.1_ASM1328383v1_genomic.fna.gz | prodigal -d GCF_013283835.1_ASM1328383v1_genomic.fna/cds.fna -a GCF_013283835.1_ASM1328383v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:15,538] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:15,538] [INFO] Task started: HMMsearch
[2024-01-24 14:47:15,538] [INFO] Running command: hmmsearch --tblout GCF_013283835.1_ASM1328383v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a9b8661-8684-4a3e-9852-b01546573587/dqc_reference/reference_markers.hmm GCF_013283835.1_ASM1328383v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:15,808] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:15,810] [INFO] Found 6/6 markers.
[2024-01-24 14:47:15,849] [INFO] Query marker FASTA was written to GCF_013283835.1_ASM1328383v1_genomic.fna/markers.fasta
[2024-01-24 14:47:15,849] [INFO] Task started: Blastn
[2024-01-24 14:47:15,850] [INFO] Running command: blastn -query GCF_013283835.1_ASM1328383v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a9b8661-8684-4a3e-9852-b01546573587/dqc_reference/reference_markers.fasta -out GCF_013283835.1_ASM1328383v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:16,487] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:16,491] [INFO] Selected 14 target genomes.
[2024-01-24 14:47:16,491] [INFO] Target genome list was writen to GCF_013283835.1_ASM1328383v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:16,515] [INFO] Task started: fastANI
[2024-01-24 14:47:16,515] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a9965e7-693a-41d9-8955-37ca05774554/GCF_013283835.1_ASM1328383v1_genomic.fna.gz --refList GCF_013283835.1_ASM1328383v1_genomic.fna/target_genomes.txt --output GCF_013283835.1_ASM1328383v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:25,675] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:25,675] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a9b8661-8684-4a3e-9852-b01546573587/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:25,676] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a9b8661-8684-4a3e-9852-b01546573587/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:25,688] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:47:25,688] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:25,688] [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	100.0	1177	1189	95	conclusive
Poseidonibacter lekithochrous	strain=LFT 1.7	GCA_001878855.1	1904463	1904463	type	True	99.973	1150	1189	95	conclusive
Malaciobacter pacificus	strain=LMG 26638	GCA_004214795.1	1080223	1080223	type	True	80.5215	460	1189	95	below_threshold
Malaciobacter pacificus	strain=CGMCC 1.11011	GCA_014636355.1	1080223	1080223	type	True	80.3838	445	1189	95	below_threshold
Arcobacter acticola	strain=KCTC 52212	GCA_013177675.1	1849015	1849015	type	True	80.1108	486	1189	95	below_threshold
Arcobacter ellisii	strain=LMG 26155	GCA_003544915.1	913109	913109	type	True	79.8891	461	1189	95	below_threshold
Arcobacter venerupis	strain=LMG 26156	GCA_013201665.1	1054033	1054033	type	True	79.75	465	1189	95	below_threshold
Halarcobacter bivalviorum	strain=LMG 26154	GCA_003346815.1	663364	663364	type	True	79.6578	431	1189	95	below_threshold
Arcobacter aquimarinus	strain=W63	GCA_013177635.1	1315211	1315211	type	True	79.5315	435	1189	95	below_threshold
Arcobacter aquimarinus	strain=CECT 8442	GCA_004115795.1	1315211	1315211	type	True	79.3379	419	1189	95	below_threshold
Arcobacter cloacae	strain=CECT 7834	GCA_004115805.1	1054034	1054034	type	True	79.1961	416	1189	95	below_threshold
[Halarcobacter] arenosus	strain=CAU 1517	GCA_005771535.1	2576037	2576037	type	True	78.9876	417	1189	95	below_threshold
Malaciobacter molluscorum	strain=CECT 7696	GCA_003544935.1	1032072	1032072	type	True	78.6772	416	1189	95	below_threshold
Malaciobacter molluscorum	strain=F98-3	GCA_002701265.1	1032072	1032072	type	True	78.4088	400	1189	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:25,690] [INFO] DFAST Taxonomy check result was written to GCF_013283835.1_ASM1328383v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:25,691] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:25,691] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:25,691] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a9b8661-8684-4a3e-9852-b01546573587/dqc_reference/checkm_data
[2024-01-24 14:47:25,692] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:25,733] [INFO] Task started: CheckM
[2024-01-24 14:47:25,734] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013283835.1_ASM1328383v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013283835.1_ASM1328383v1_genomic.fna/checkm_input GCF_013283835.1_ASM1328383v1_genomic.fna/checkm_result
[2024-01-24 14:47:50,879] [INFO] Task succeeded: CheckM
[2024-01-24 14:47:50,880] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:47:50,898] [INFO] ===== Completeness check finished =====
[2024-01-24 14:47:50,899] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:47:50,900] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013283835.1_ASM1328383v1_genomic.fna/markers.fasta)
[2024-01-24 14:47:50,900] [INFO] Task started: Blastn
[2024-01-24 14:47:50,900] [INFO] Running command: blastn -query GCF_013283835.1_ASM1328383v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a9b8661-8684-4a3e-9852-b01546573587/dqc_reference/reference_markers_gtdb.fasta -out GCF_013283835.1_ASM1328383v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:51,848] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:51,851] [INFO] Selected 17 target genomes.
[2024-01-24 14:47:51,851] [INFO] Target genome list was writen to GCF_013283835.1_ASM1328383v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:47:51,864] [INFO] Task started: fastANI
[2024-01-24 14:47:51,865] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a9965e7-693a-41d9-8955-37ca05774554/GCF_013283835.1_ASM1328383v1_genomic.fna.gz --refList GCF_013283835.1_ASM1328383v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013283835.1_ASM1328383v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:03,292] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:03,306] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:03,307] [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_013283835.1	s__Poseidonibacter lekithochrous	100.0	1177	1189	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	99.16	98.33	0.97	0.93	3	conclusive
GCA_002470185.1	s__Poseidonibacter sp002470185	93.8291	671	1189	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009208075.1	s__Poseidonibacter sp009208075	81.5514	541	1189	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	99.63	99.63	0.93	0.93	3	-
GCF_001956695.1	s__Poseidonibacter parvus	81.3732	564	1189	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	98.33	98.33	0.91	0.91	2	-
GCF_018861145.1	s__Poseidonibacter lekithochrous_A	80.9513	552	1189	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667345.1	s__Poseidonibacter antarcticus	80.9191	513	1189	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004214795.1	s__Aliarcobacter pacificus	80.5334	459	1189	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_002685075.1	s__Poseidonibacter sp002685075	80.4608	457	1189	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001895145.1	s__Halarcobacter sp001895145	79.9359	491	1189	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013201665.1	s__Aliarcobacter venerupis	79.8139	466	1189	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	100.00	100.00	0.99	0.99	2	-
GCA_004116455.1	s__Halarcobacter sp004116455	79.7764	422	1189	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	96.86	96.86	0.84	0.84	2	-
GCF_003346815.1	s__Halarcobacter bivalviorum	79.6754	428	1189	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	98.23	96.46	0.96	0.92	3	-
GCF_013201935.1	s__Aliarcobacter cloacae	79.6138	430	1189	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.96	95.91	0.93	0.87	3	-
GCF_013177635.1	s__Aliarcobacter aquimarinus	79.5918	434	1189	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_004118855.1	s__Halarcobacter sp004118855	79.2208	435	1189	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	78.998	416	1189	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	78.6649	417	1189	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	99.44	98.88	0.96	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:03,308] [INFO] GTDB search result was written to GCF_013283835.1_ASM1328383v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:03,309] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:03,312] [INFO] DFAST_QC result json was written to GCF_013283835.1_ASM1328383v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:03,312] [INFO] DFAST_QC completed!
[2024-01-24 14:48:03,313] [INFO] Total running time: 0h0m55s