[2024-01-24 12:57:49,594] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:57:49,595] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:57:49,595] [INFO] DQC Reference Directory: /var/lib/cwl/stg25445ec7-6e2d-48f4-83b5-8702326c0935/dqc_reference
[2024-01-24 12:57:50,755] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:57:50,755] [INFO] Task started: Prodigal
[2024-01-24 12:57:50,756] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d10ba73-6bb0-4e7b-9282-85ea448f849b/GCF_004299785.2_ASM429978v2_genomic.fna.gz | prodigal -d GCF_004299785.2_ASM429978v2_genomic.fna/cds.fna -a GCF_004299785.2_ASM429978v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:57:53,852] [INFO] Task succeeded: Prodigal
[2024-01-24 12:57:53,852] [INFO] Task started: HMMsearch
[2024-01-24 12:57:53,852] [INFO] Running command: hmmsearch --tblout GCF_004299785.2_ASM429978v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25445ec7-6e2d-48f4-83b5-8702326c0935/dqc_reference/reference_markers.hmm GCF_004299785.2_ASM429978v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:57:54,028] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:57:54,029] [INFO] Found 6/6 markers.
[2024-01-24 12:57:54,049] [INFO] Query marker FASTA was written to GCF_004299785.2_ASM429978v2_genomic.fna/markers.fasta
[2024-01-24 12:57:54,049] [INFO] Task started: Blastn
[2024-01-24 12:57:54,049] [INFO] Running command: blastn -query GCF_004299785.2_ASM429978v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg25445ec7-6e2d-48f4-83b5-8702326c0935/dqc_reference/reference_markers.fasta -out GCF_004299785.2_ASM429978v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:57:54,617] [INFO] Task succeeded: Blastn
[2024-01-24 12:57:54,620] [INFO] Selected 6 target genomes.
[2024-01-24 12:57:54,620] [INFO] Target genome list was writen to GCF_004299785.2_ASM429978v2_genomic.fna/target_genomes.txt
[2024-01-24 12:57:54,622] [INFO] Task started: fastANI
[2024-01-24 12:57:54,622] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d10ba73-6bb0-4e7b-9282-85ea448f849b/GCF_004299785.2_ASM429978v2_genomic.fna.gz --refList GCF_004299785.2_ASM429978v2_genomic.fna/target_genomes.txt --output GCF_004299785.2_ASM429978v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:57:57,503] [INFO] Task succeeded: fastANI
[2024-01-24 12:57:57,503] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25445ec7-6e2d-48f4-83b5-8702326c0935/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:57:57,504] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25445ec7-6e2d-48f4-83b5-8702326c0935/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:57:57,510] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:57:57,511] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:57:57,511] [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] porcinus	strain=CCUG 56899	GCA_004299785.2	1935204	1935204	type	True	100.0	671	672	95	conclusive
[Arcobacter] porcinus	strain=LMG 24487	GCA_024584075.1	1935204	1935204	type	True	98.4128	541	672	95	conclusive
Aliarcobacter thereius	strain=LMG 24486	GCA_004214815.1	544718	544718	type	True	93.2429	549	672	95	below_threshold
Aliarcobacter thereius	strain=LMG 24486	GCA_001695395.1	544718	544718	type	True	93.2007	552	672	95	below_threshold
Aliarcobacter thereius	strain=LMG 24486	GCA_024584025.1	544718	544718	type	True	93.169	545	672	95	below_threshold
Aliarcobacter thereius	strain=DSM 23385	GCA_005818985.1	544718	544718	type	True	93.1319	541	672	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:57:57,513] [INFO] DFAST Taxonomy check result was written to GCF_004299785.2_ASM429978v2_genomic.fna/tc_result.tsv
[2024-01-24 12:57:57,513] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:57:57,513] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:57:57,514] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25445ec7-6e2d-48f4-83b5-8702326c0935/dqc_reference/checkm_data
[2024-01-24 12:57:57,514] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:57:57,535] [INFO] Task started: CheckM
[2024-01-24 12:57:57,535] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004299785.2_ASM429978v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004299785.2_ASM429978v2_genomic.fna/checkm_input GCF_004299785.2_ASM429978v2_genomic.fna/checkm_result
[2024-01-24 12:58:13,695] [INFO] Task succeeded: CheckM
[2024-01-24 12:58:13,696] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:58:13,717] [INFO] ===== Completeness check finished =====
[2024-01-24 12:58:13,717] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:58:13,717] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004299785.2_ASM429978v2_genomic.fna/markers.fasta)
[2024-01-24 12:58:13,718] [INFO] Task started: Blastn
[2024-01-24 12:58:13,718] [INFO] Running command: blastn -query GCF_004299785.2_ASM429978v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg25445ec7-6e2d-48f4-83b5-8702326c0935/dqc_reference/reference_markers_gtdb.fasta -out GCF_004299785.2_ASM429978v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:58:14,496] [INFO] Task succeeded: Blastn
[2024-01-24 12:58:14,499] [INFO] Selected 14 target genomes.
[2024-01-24 12:58:14,499] [INFO] Target genome list was writen to GCF_004299785.2_ASM429978v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:58:14,503] [INFO] Task started: fastANI
[2024-01-24 12:58:14,503] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d10ba73-6bb0-4e7b-9282-85ea448f849b/GCF_004299785.2_ASM429978v2_genomic.fna.gz --refList GCF_004299785.2_ASM429978v2_genomic.fna/target_genomes_gtdb.txt --output GCF_004299785.2_ASM429978v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:58:21,319] [INFO] Task succeeded: fastANI
[2024-01-24 12:58:21,330] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:58:21,331] [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_004299785.2	s__Aliarcobacter porcinus	100.0	672	672	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.76	98.06	0.91	0.88	6	conclusive
GCF_004214815.1	s__Aliarcobacter thereius	93.1655	550	672	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.14	98.62	0.93	0.89	8	-
GCF_003544835.1	s__Aliarcobacter skirrowii	83.8569	465	672	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.32	95.07	0.91	0.85	16	-
GCF_014352935.1	s__Aliarcobacter cryaerophilus_A	82.9429	441	672	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.54	96.41	0.86	0.82	23	-
GCF_002993025.1	s__Aliarcobacter cryaerophilus_B	82.7391	428	672	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.88	97.88	0.90	0.90	2	-
GCF_003355515.1	s__Aliarcobacter trophiarum	82.487	414	672	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.76	99.53	0.96	0.92	3	-
GCF_016106035.1	s__Aliarcobacter sp016106035	82.3851	432	672	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013201705.1	s__Aliarcobacter faecis	82.3265	443	672	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.88	99.77	0.97	0.95	3	-
GCA_003316695.1	s__Aliarcobacter sp003316695	81.8635	416	672	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.67	97.67	0.88	0.88	2	-
GCF_013372265.1	s__Aliarcobacter cibarius	81.7385	406	672	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.17	98.67	0.91	0.84	6	-
GCF_013201625.1	s__Aliarcobacter lanthieri	81.6452	432	672	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.15	95.77	0.93	0.89	6	-
GCF_900187115.1	s__Aliarcobacter butzleri	81.1068	408	672	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.53	96.98	0.89	0.81	50	-
GCF_003063295.1	s__Aliarcobacter lacus	80.7239	384	672	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013201665.1	s__Aliarcobacter venerupis	79.7874	360	672	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:58:21,332] [INFO] GTDB search result was written to GCF_004299785.2_ASM429978v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:58:21,333] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:58:21,336] [INFO] DFAST_QC result json was written to GCF_004299785.2_ASM429978v2_genomic.fna/dqc_result.json
[2024-01-24 12:58:21,336] [INFO] DFAST_QC completed!
[2024-01-24 12:58:21,336] [INFO] Total running time: 0h0m32s