[2023-06-27 14:44:04,598] [INFO] DFAST_QC pipeline started.
[2023-06-27 14:44:04,604] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 14:44:04,604] [INFO] DQC Reference Directory: /var/lib/cwl/stg19049afa-482c-4b6b-817f-64bc28d8bdb6/dqc_reference
[2023-06-27 14:44:05,904] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 14:44:05,904] [INFO] Task started: Prodigal
[2023-06-27 14:44:05,905] [INFO] Running command: gunzip -c /var/lib/cwl/stg7553184d-1cf2-4b11-88f1-e4cae2644cea/GCA_002749345.1_ASM274934v1_genomic.fna.gz | prodigal -d GCA_002749345.1_ASM274934v1_genomic.fna/cds.fna -a GCA_002749345.1_ASM274934v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 14:44:07,722] [INFO] Task succeeded: Prodigal
[2023-06-27 14:44:07,722] [INFO] Task started: HMMsearch
[2023-06-27 14:44:07,722] [INFO] Running command: hmmsearch --tblout GCA_002749345.1_ASM274934v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19049afa-482c-4b6b-817f-64bc28d8bdb6/dqc_reference/reference_markers.hmm GCA_002749345.1_ASM274934v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 14:44:07,906] [INFO] Task succeeded: HMMsearch
[2023-06-27 14:44:07,909] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7553184d-1cf2-4b11-88f1-e4cae2644cea/GCA_002749345.1_ASM274934v1_genomic.fna.gz]
[2023-06-27 14:44:07,929] [INFO] Query marker FASTA was written to GCA_002749345.1_ASM274934v1_genomic.fna/markers.fasta
[2023-06-27 14:44:07,929] [INFO] Task started: Blastn
[2023-06-27 14:44:07,929] [INFO] Running command: blastn -query GCA_002749345.1_ASM274934v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19049afa-482c-4b6b-817f-64bc28d8bdb6/dqc_reference/reference_markers.fasta -out GCA_002749345.1_ASM274934v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 14:44:08,508] [INFO] Task succeeded: Blastn
[2023-06-27 14:44:08,512] [INFO] Selected 19 target genomes.
[2023-06-27 14:44:08,513] [INFO] Target genome list was writen to GCA_002749345.1_ASM274934v1_genomic.fna/target_genomes.txt
[2023-06-27 14:44:08,517] [INFO] Task started: fastANI
[2023-06-27 14:44:08,517] [INFO] Running command: fastANI --query /var/lib/cwl/stg7553184d-1cf2-4b11-88f1-e4cae2644cea/GCA_002749345.1_ASM274934v1_genomic.fna.gz --refList GCA_002749345.1_ASM274934v1_genomic.fna/target_genomes.txt --output GCA_002749345.1_ASM274934v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 14:44:14,736] [INFO] Task succeeded: fastANI
[2023-06-27 14:44:14,737] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19049afa-482c-4b6b-817f-64bc28d8bdb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 14:44:14,737] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19049afa-482c-4b6b-817f-64bc28d8bdb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 14:44:14,750] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 14:44:14,750] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 14:44:14,751] [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 aquimarinus	strain=W63	GCA_013177635.1	1315211	1315211	type	True	76.9157	90	329	95	below_threshold
Arcobacter aquimarinus	strain=CECT 8442	GCA_004115795.1	1315211	1315211	type	True	76.91	86	329	95	below_threshold
Aliarcobacter thereius	strain=LMG 24486	GCA_001695395.1	544718	544718	type	True	76.8427	71	329	95	below_threshold
Aliarcobacter thereius	strain=LMG 24486	GCA_024584025.1	544718	544718	type	True	76.8398	72	329	95	below_threshold
Halarcobacter bivalviorum	strain=CECT 7835	GCA_004116675.1	663364	663364	type	True	76.7994	97	329	95	below_threshold
Malaciobacter pacificus	strain=CGMCC 1.11011	GCA_014636355.1	1080223	1080223	type	True	76.7956	73	329	95	below_threshold
Malaciobacter pacificus	strain=LMG 26638	GCA_004214795.1	1080223	1080223	type	True	76.7943	75	329	95	below_threshold
Halarcobacter bivalviorum	strain=LMG 26154	GCA_003346815.1	663364	663364	type	True	76.7911	101	329	95	below_threshold
Aliarcobacter thereius	strain=LMG 24486	GCA_004214815.1	544718	544718	type	True	76.7678	73	329	95	below_threshold
Arcobacter venerupis	strain=LMG 26156	GCA_013201665.1	1054033	1054033	type	True	76.6988	94	329	95	below_threshold
Arcobacter acticola	strain=KCTC 52212	GCA_013177675.1	1849015	1849015	type	True	76.6355	87	329	95	below_threshold
Arcobacter caeni	strain=RW17-10	GCA_003063245.1	1912877	1912877	type	True	76.6267	86	329	95	below_threshold
Arcobacter venerupis	strain=CECT7836	GCA_004023405.1	1054033	1054033	type	True	76.5966	93	329	95	below_threshold
Aliarcobacter vitoriensis	strain=LMG 30050	GCA_024583985.1	2011099	2011099	type	True	76.4866	87	329	95	below_threshold
[Arcobacter] porcinus	strain=CCUG 56899	GCA_004299785.2	1935204	1935204	type	True	76.4718	81	329	95	below_threshold
Aliarcobacter vitoriensis	strain=CECT 9230	GCA_003316695.1	2011099	2011099	type	True	76.4657	88	329	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 14:44:14,753] [INFO] DFAST Taxonomy check result was written to GCA_002749345.1_ASM274934v1_genomic.fna/tc_result.tsv
[2023-06-27 14:44:14,753] [INFO] ===== Taxonomy check completed =====
[2023-06-27 14:44:14,753] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 14:44:14,754] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19049afa-482c-4b6b-817f-64bc28d8bdb6/dqc_reference/checkm_data
[2023-06-27 14:44:14,755] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 14:44:14,773] [INFO] Task started: CheckM
[2023-06-27 14:44:14,773] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002749345.1_ASM274934v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002749345.1_ASM274934v1_genomic.fna/checkm_input GCA_002749345.1_ASM274934v1_genomic.fna/checkm_result
[2023-06-27 14:44:28,514] [INFO] Task succeeded: CheckM
[2023-06-27 14:44:28,515] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.45%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 14:44:28,540] [INFO] ===== Completeness check finished =====
[2023-06-27 14:44:28,540] [INFO] ===== Start GTDB Search =====
[2023-06-27 14:44:28,541] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002749345.1_ASM274934v1_genomic.fna/markers.fasta)
[2023-06-27 14:44:28,541] [INFO] Task started: Blastn
[2023-06-27 14:44:28,541] [INFO] Running command: blastn -query GCA_002749345.1_ASM274934v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19049afa-482c-4b6b-817f-64bc28d8bdb6/dqc_reference/reference_markers_gtdb.fasta -out GCA_002749345.1_ASM274934v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 14:44:29,330] [INFO] Task succeeded: Blastn
[2023-06-27 14:44:29,334] [INFO] Selected 24 target genomes.
[2023-06-27 14:44:29,334] [INFO] Target genome list was writen to GCA_002749345.1_ASM274934v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 14:44:29,347] [INFO] Task started: fastANI
[2023-06-27 14:44:29,348] [INFO] Running command: fastANI --query /var/lib/cwl/stg7553184d-1cf2-4b11-88f1-e4cae2644cea/GCA_002749345.1_ASM274934v1_genomic.fna.gz --refList GCA_002749345.1_ASM274934v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002749345.1_ASM274934v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 14:44:38,382] [INFO] Task succeeded: fastANI
[2023-06-27 14:44:38,404] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 14:44:38,405] [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
GCA_018662405.1	s__JADHTT01 sp018662405	77.9311	65	329	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__JADHTT01	95.0	99.77	99.69	0.93	0.90	13	-
GCA_015663165.1	s__CAIJNA01 sp015663165	77.6421	85	329	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__CAIJNA01	95.0	99.59	99.59	0.85	0.85	2	-
GCF_001956695.1	s__Poseidonibacter parvus	77.4529	101	329	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	98.33	98.33	0.91	0.91	2	-
GCF_003667345.1	s__Poseidonibacter antarcticus	77.3785	83	329	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002869565.1	s__Halarcobacter sp002869565	77.2881	84	329	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861145.1	s__Poseidonibacter lekithochrous_A	77.1138	97	329	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017995775.1	s__Aliarcobacter sp017995775	76.9283	81	329	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.13	99.13	0.84	0.84	2	-
GCF_013177635.1	s__Aliarcobacter aquimarinus	76.9157	90	329	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003252105.1	s__Halarcobacter sp003252105	76.8415	92	329	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004214815.1	s__Aliarcobacter thereius	76.8005	72	329	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.14	98.62	0.93	0.89	8	-
GCF_004214795.1	s__Aliarcobacter pacificus	76.7908	75	329	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_013201665.1	s__Aliarcobacter venerupis	76.7504	93	329	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	100.00	100.00	0.99	0.99	2	-
GCA_004116495.1	s__Malaciobacter sp004116495	76.7333	91	329	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004116625.1	s__Halarcobacter mediterraneus	76.7316	96	329	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014352935.1	s__Aliarcobacter cryaerophilus_A	76.6729	83	329	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.54	96.41	0.86	0.82	23	-
GCA_018399655.1	s__CAIJNA01 sp018399655	76.6323	61	329	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__CAIJNA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013177675.1	s__Aliarcobacter acticola	76.6114	88	329	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744485.1	s__BB30 sp016744485	76.2503	63	329	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__BB30	95.0	99.52	99.52	0.89	0.89	2	-
GCA_013215945.1	s__NORP36 sp004566295	76.1458	69	329	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__NORP36	95.0	99.94	99.94	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-27 14:44:38,408] [INFO] GTDB search result was written to GCA_002749345.1_ASM274934v1_genomic.fna/result_gtdb.tsv
[2023-06-27 14:44:38,408] [INFO] ===== GTDB Search completed =====
[2023-06-27 14:44:38,413] [INFO] DFAST_QC result json was written to GCA_002749345.1_ASM274934v1_genomic.fna/dqc_result.json
[2023-06-27 14:44:38,413] [INFO] DFAST_QC completed!
[2023-06-27 14:44:38,413] [INFO] Total running time: 0h0m34s