[2024-01-24 13:24:12,381] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:24:12,382] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:24:12,383] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a6a222c-3153-4f56-93be-f79a4ce62698/dqc_reference
[2024-01-24 13:24:13,579] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:24:13,580] [INFO] Task started: Prodigal
[2024-01-24 13:24:13,580] [INFO] Running command: gunzip -c /var/lib/cwl/stg0877cb02-7699-41b2-80b1-6e1caae6b851/GCF_030249845.1_ASM3024984v1_genomic.fna.gz | prodigal -d GCF_030249845.1_ASM3024984v1_genomic.fna/cds.fna -a GCF_030249845.1_ASM3024984v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:24:17,709] [INFO] Task succeeded: Prodigal
[2024-01-24 13:24:17,710] [INFO] Task started: HMMsearch
[2024-01-24 13:24:17,710] [INFO] Running command: hmmsearch --tblout GCF_030249845.1_ASM3024984v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a6a222c-3153-4f56-93be-f79a4ce62698/dqc_reference/reference_markers.hmm GCF_030249845.1_ASM3024984v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:24:17,890] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:24:17,891] [INFO] Found 6/6 markers.
[2024-01-24 13:24:17,914] [INFO] Query marker FASTA was written to GCF_030249845.1_ASM3024984v1_genomic.fna/markers.fasta
[2024-01-24 13:24:17,915] [INFO] Task started: Blastn
[2024-01-24 13:24:17,915] [INFO] Running command: blastn -query GCF_030249845.1_ASM3024984v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a6a222c-3153-4f56-93be-f79a4ce62698/dqc_reference/reference_markers.fasta -out GCF_030249845.1_ASM3024984v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:18,474] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:18,478] [INFO] Selected 18 target genomes.
[2024-01-24 13:24:18,478] [INFO] Target genome list was writen to GCF_030249845.1_ASM3024984v1_genomic.fna/target_genomes.txt
[2024-01-24 13:24:18,516] [INFO] Task started: fastANI
[2024-01-24 13:24:18,516] [INFO] Running command: fastANI --query /var/lib/cwl/stg0877cb02-7699-41b2-80b1-6e1caae6b851/GCF_030249845.1_ASM3024984v1_genomic.fna.gz --refList GCF_030249845.1_ASM3024984v1_genomic.fna/target_genomes.txt --output GCF_030249845.1_ASM3024984v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:24:24,311] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:24,312] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a6a222c-3153-4f56-93be-f79a4ce62698/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:24:24,312] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a6a222c-3153-4f56-93be-f79a4ce62698/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:24:24,323] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:24:24,323] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:24:24,323] [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_013372205.1	202	202	type	True	85.1292	347	715	95	below_threshold
Campylobacter mucosalis	strain=ATCC 43264	GCA_012978755.1	202	202	type	True	84.847	322	715	95	below_threshold
Campylobacter anatolicus	strain=faydin-G140	GCA_018145655.1	2829105	2829105	type	True	77.8235	160	715	95	below_threshold
Campylobacter concisus	strain=ATCC 33237	GCA_001298465.1	199	199	suspected-type	True	77.5003	167	715	95	below_threshold
Campylobacter curvus	strain=FDAARGOS_1547	GCA_020736225.1	200	200	suspected-type	True	77.3819	131	715	95	below_threshold
Campylobacter curvus	strain=DSM 6644	GCA_000376325.1	200	200	suspected-type	True	77.337	133	715	95	below_threshold
Campylobacter hyointestinalis subsp. lawsonii	strain=CHY5	GCA_013372165.1	91353	198	type	True	77.0012	85	715	95	below_threshold
Campylobacter showae	strain=ATCC 51146	GCA_004803815.1	204	204	suspected-type	True	76.9048	107	715	95	below_threshold
Campylobacter massiliensis	strain=Marseille-Q3452	GCA_014253065.1	2762557	2762557	type	True	76.6863	105	715	95	below_threshold
Campylobacter hyointestinalis subsp. lawsonii	strain=CCUG 34538	GCA_008802075.1	91353	198	type	True	76.5992	81	715	95	below_threshold
Campylobacter rectus	strain=FDAARGOS_1549	GCA_020736205.1	203	203	type	True	76.5709	103	715	95	below_threshold
Campylobacter rectus	strain=ATCC 33238	GCA_004803795.1	203	203	type	True	76.5696	103	715	95	below_threshold
Campylobacter hyointestinalis subsp. lawsonii	strain=CHY5	GCA_003289475.1	91353	198	type	True	76.4851	83	715	95	below_threshold
Campylobacter portucalensis	strain=FMV-PI01	GCA_009690845.1	2608384	2608384	type	True	75.9532	63	715	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:24:24,325] [INFO] DFAST Taxonomy check result was written to GCF_030249845.1_ASM3024984v1_genomic.fna/tc_result.tsv
[2024-01-24 13:24:24,325] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:24:24,325] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:24:24,326] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a6a222c-3153-4f56-93be-f79a4ce62698/dqc_reference/checkm_data
[2024-01-24 13:24:24,327] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:24:24,350] [INFO] Task started: CheckM
[2024-01-24 13:24:24,350] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030249845.1_ASM3024984v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030249845.1_ASM3024984v1_genomic.fna/checkm_input GCF_030249845.1_ASM3024984v1_genomic.fna/checkm_result
[2024-01-24 13:24:43,104] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:43,105] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:24:43,122] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:43,123] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:43,123] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030249845.1_ASM3024984v1_genomic.fna/markers.fasta)
[2024-01-24 13:24:43,123] [INFO] Task started: Blastn
[2024-01-24 13:24:43,123] [INFO] Running command: blastn -query GCF_030249845.1_ASM3024984v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a6a222c-3153-4f56-93be-f79a4ce62698/dqc_reference/reference_markers_gtdb.fasta -out GCF_030249845.1_ASM3024984v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:43,878] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:43,881] [INFO] Selected 22 target genomes.
[2024-01-24 13:24:43,881] [INFO] Target genome list was writen to GCF_030249845.1_ASM3024984v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:43,904] [INFO] Task started: fastANI
[2024-01-24 13:24:43,904] [INFO] Running command: fastANI --query /var/lib/cwl/stg0877cb02-7699-41b2-80b1-6e1caae6b851/GCF_030249845.1_ASM3024984v1_genomic.fna.gz --refList GCF_030249845.1_ASM3024984v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030249845.1_ASM3024984v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:50,214] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:50,226] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:24:50,227] [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	85.1105	348	715	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_003048595.2	s__Campylobacter_A concisus_L	77.5837	162	715	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	97.61	95.79	0.95	0.92	5	-
GCF_003049085.1	s__Campylobacter_A concisus_H	77.5802	159	715	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.031	N/A	N/A	N/A	N/A	1	-
GCF_002165775.1	s__Campylobacter_A concisus_E	77.5781	155	715	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003048615.2	s__Campylobacter_A concisus_C	77.5769	175	715	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_004803835.1	s__Campylobacter_A sp004803835	77.5672	160	715	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_902460705.1	s__Campylobacter_A concisus_Z	77.5399	161	715	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_003048575.1	s__Campylobacter_A concisus_U	77.534	156	715	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_000466685.1	s__Campylobacter_A concisus_A	77.4499	164	715	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	95.29	95.22	0.88	0.86	5	-
GCF_002912895.1	s__Campylobacter_A concisus_G	77.4274	155	715	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	95.40	95.36	0.91	0.89	5	-
GCA_902387145.1	s__Campylobacter_A sp902387145	77.3691	164	715	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_015679985.1	s__Campylobacter_A concisus_AC	77.3345	155	715	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_002139915.1	s__Campylobacter sp002139915	77.2179	59	715	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	97.90	97.72	0.92	0.90	37	-
GCF_004803815.1	s__Campylobacter_A showae	76.9048	107	715	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_900573985.1	s__Campylobacter_A showae_E	76.8209	112	715	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:50,228] [INFO] GTDB search result was written to GCF_030249845.1_ASM3024984v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:50,229] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:50,232] [INFO] DFAST_QC result json was written to GCF_030249845.1_ASM3024984v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:50,233] [INFO] DFAST_QC completed!
[2024-01-24 13:24:50,233] [INFO] Total running time: 0h0m38s