[2024-01-24 13:18:55,386] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:55,387] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:55,388] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c6a09a5-8588-416a-9c86-308adc46473d/dqc_reference
[2024-01-24 13:18:56,697] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:56,698] [INFO] Task started: Prodigal
[2024-01-24 13:18:56,698] [INFO] Running command: gunzip -c /var/lib/cwl/stgc4b7ca7f-8bf6-4733-98da-919c81724b79/GCF_905120465.1_LMG_7974_genomic.fna.gz | prodigal -d GCF_905120465.1_LMG_7974_genomic.fna/cds.fna -a GCF_905120465.1_LMG_7974_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:00,621] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:00,622] [INFO] Task started: HMMsearch
[2024-01-24 13:19:00,622] [INFO] Running command: hmmsearch --tblout GCF_905120465.1_LMG_7974_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c6a09a5-8588-416a-9c86-308adc46473d/dqc_reference/reference_markers.hmm GCF_905120465.1_LMG_7974_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:00,852] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:00,853] [INFO] Found 6/6 markers.
[2024-01-24 13:19:00,877] [INFO] Query marker FASTA was written to GCF_905120465.1_LMG_7974_genomic.fna/markers.fasta
[2024-01-24 13:19:00,878] [INFO] Task started: Blastn
[2024-01-24 13:19:00,878] [INFO] Running command: blastn -query GCF_905120465.1_LMG_7974_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c6a09a5-8588-416a-9c86-308adc46473d/dqc_reference/reference_markers.fasta -out GCF_905120465.1_LMG_7974_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:01,491] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:01,504] [INFO] Selected 23 target genomes.
[2024-01-24 13:19:01,505] [INFO] Target genome list was writen to GCF_905120465.1_LMG_7974_genomic.fna/target_genomes.txt
[2024-01-24 13:19:01,541] [INFO] Task started: fastANI
[2024-01-24 13:19:01,542] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4b7ca7f-8bf6-4733-98da-919c81724b79/GCF_905120465.1_LMG_7974_genomic.fna.gz --refList GCF_905120465.1_LMG_7974_genomic.fna/target_genomes.txt --output GCF_905120465.1_LMG_7974_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:09,852] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:09,852] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c6a09a5-8588-416a-9c86-308adc46473d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:09,853] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c6a09a5-8588-416a-9c86-308adc46473d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:09,863] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:19:09,864] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:19:09,864] [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
Campylobacter mucosalis	strain=ATCC 43264	GCA_012978755.1	202	202	type	True	77.9067	178	623	95	below_threshold
Campylobacter mucosalis	strain=ATCC 43264	GCA_013372205.1	202	202	type	True	77.8669	203	623	95	below_threshold
Campylobacter showae	strain=ATCC 51146	GCA_004803815.1	204	204	suspected-type	True	77.8465	50	623	95	below_threshold
Campylobacter rectus	strain=FDAARGOS_1549	GCA_020736205.1	203	203	type	True	77.7664	57	623	95	below_threshold
Campylobacter concisus	strain=ATCC 33237	GCA_001298465.1	199	199	suspected-type	True	77.2817	129	623	95	below_threshold
Campylobacter anatolicus	strain=faydin-G140	GCA_018145655.1	2829105	2829105	type	True	77.2619	143	623	95	below_threshold
Campylobacter lanienae	strain=NCTC 13004	GCA_002139935.1	75658	75658	type	True	77.0309	65	623	95	below_threshold
Campylobacter geochelonis	strain=RC20	GCA_900063025.1	1780362	1780362	type	True	76.1149	98	623	95	below_threshold
Campylobacter geochelonis	strain=LMG 29375	GCA_013201685.1	1780362	1780362	type	True	76.0728	102	623	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:09,866] [INFO] DFAST Taxonomy check result was written to GCF_905120465.1_LMG_7974_genomic.fna/tc_result.tsv
[2024-01-24 13:19:09,866] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:09,867] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:09,867] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c6a09a5-8588-416a-9c86-308adc46473d/dqc_reference/checkm_data
[2024-01-24 13:19:09,869] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:09,894] [INFO] Task started: CheckM
[2024-01-24 13:19:09,895] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_905120465.1_LMG_7974_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_905120465.1_LMG_7974_genomic.fna/checkm_input GCF_905120465.1_LMG_7974_genomic.fna/checkm_result
[2024-01-24 13:19:29,688] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:29,690] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:29,708] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:29,709] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:29,709] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_905120465.1_LMG_7974_genomic.fna/markers.fasta)
[2024-01-24 13:19:29,710] [INFO] Task started: Blastn
[2024-01-24 13:19:29,710] [INFO] Running command: blastn -query GCF_905120465.1_LMG_7974_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c6a09a5-8588-416a-9c86-308adc46473d/dqc_reference/reference_markers_gtdb.fasta -out GCF_905120465.1_LMG_7974_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:30,515] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:30,518] [INFO] Selected 25 target genomes.
[2024-01-24 13:19:30,518] [INFO] Target genome list was writen to GCF_905120465.1_LMG_7974_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:30,550] [INFO] Task started: fastANI
[2024-01-24 13:19:30,550] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4b7ca7f-8bf6-4733-98da-919c81724b79/GCF_905120465.1_LMG_7974_genomic.fna.gz --refList GCF_905120465.1_LMG_7974_genomic.fna/target_genomes_gtdb.txt --output GCF_905120465.1_LMG_7974_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:38,055] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:38,070] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:19:38,070] [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_013372205.1	s__Campylobacter_A mucosalis	77.8669	203	623	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	98.18	96.99	0.95	0.92	7	-
GCF_902460705.1	s__Campylobacter_A concisus_Z	77.7025	118	623	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	99.93	99.93	0.97	0.97	2	-
GCF_002912895.1	s__Campylobacter_A concisus_G	77.5854	115	623	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	95.40	95.36	0.91	0.89	5	-
GCF_004803835.1	s__Campylobacter_A sp004803835	77.5773	139	623	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	99.48	98.76	0.97	0.94	10	-
GCF_001891085.1	s__Campylobacter_A concisus_O	77.4701	125	623	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	95.13	95.13	0.93	0.93	2	-
GCF_018145735.1	s__Campylobacter_A sp018145735	77.4607	139	623	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	99.06	99.05	0.97	0.96	3	-
GCF_015679985.1	s__Campylobacter_A concisus_AC	77.3595	117	623	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0251	96.37	95.15	0.93	0.89	5	-
GCF_003048615.2	s__Campylobacter_A concisus_C	77.339	121	623	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	96.12	95.77	0.93	0.88	42	-
GCF_003048835.2	s__Campylobacter_A concisus_D	77.2968	134	623	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0092	97.26	95.33	0.94	0.89	6	-
GCF_003048675.2	s__Campylobacter_A concisus_F	77.2872	123	623	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0092	95.49	95.08	0.92	0.88	22	-
GCF_002913945.1	s__Campylobacter_A concisus_P	77.2552	118	623	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002021925.1	s__Campylobacter_A pinnipediorum	77.2441	155	623	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	98.45	97.81	0.98	0.95	8	-
GCF_002022005.1	s__Campylobacter_A caledonicus	77.2256	149	623	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	99.31	99.26	0.98	0.97	3	-
GCF_902460415.1	s__Campylobacter_A concisus_Y	77.2156	128	623	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	95.32	95.32	0.92	0.92	2	-
GCF_902460875.1	s__Campylobacter_A concisus_AA	77.2045	122	623	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002913225.1	s__Campylobacter_A concisus_J	77.0051	113	623	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	95.08	95.08	0.89	0.89	2	-
GCF_002913745.1	s__Campylobacter_A concisus_R	76.9405	117	623	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	95.56	95.41	0.90	0.84	18	-
GCF_013201975.1	s__Campylobacter_A sp013201975	76.8011	99	623	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	96.07	96.03	0.84	0.80	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:38,072] [INFO] GTDB search result was written to GCF_905120465.1_LMG_7974_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:38,072] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:38,081] [INFO] DFAST_QC result json was written to GCF_905120465.1_LMG_7974_genomic.fna/dqc_result.json
[2024-01-24 13:19:38,081] [INFO] DFAST_QC completed!
[2024-01-24 13:19:38,081] [INFO] Total running time: 0h0m43s