[2024-01-24 12:27:19,526] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:27:19,529] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:27:19,529] [INFO] DQC Reference Directory: /var/lib/cwl/stgc85c0e14-31c7-4d2d-8a25-8a033ab3a19e/dqc_reference
[2024-01-24 12:27:20,750] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:27:20,751] [INFO] Task started: Prodigal
[2024-01-24 12:27:20,751] [INFO] Running command: gunzip -c /var/lib/cwl/stg68eb6d5c-d13b-4f51-a995-a565103ab2cf/GCF_002021985.1_ASM202198v1_genomic.fna.gz | prodigal -d GCF_002021985.1_ASM202198v1_genomic.fna/cds.fna -a GCF_002021985.1_ASM202198v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:27:23,828] [INFO] Task succeeded: Prodigal
[2024-01-24 12:27:23,829] [INFO] Task started: HMMsearch
[2024-01-24 12:27:23,829] [INFO] Running command: hmmsearch --tblout GCF_002021985.1_ASM202198v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc85c0e14-31c7-4d2d-8a25-8a033ab3a19e/dqc_reference/reference_markers.hmm GCF_002021985.1_ASM202198v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:27:24,071] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:27:24,073] [INFO] Found 6/6 markers.
[2024-01-24 12:27:24,095] [INFO] Query marker FASTA was written to GCF_002021985.1_ASM202198v1_genomic.fna/markers.fasta
[2024-01-24 12:27:24,096] [INFO] Task started: Blastn
[2024-01-24 12:27:24,096] [INFO] Running command: blastn -query GCF_002021985.1_ASM202198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc85c0e14-31c7-4d2d-8a25-8a033ab3a19e/dqc_reference/reference_markers.fasta -out GCF_002021985.1_ASM202198v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:27:24,675] [INFO] Task succeeded: Blastn
[2024-01-24 12:27:24,681] [INFO] Selected 21 target genomes.
[2024-01-24 12:27:24,682] [INFO] Target genome list was writen to GCF_002021985.1_ASM202198v1_genomic.fna/target_genomes.txt
[2024-01-24 12:27:24,768] [INFO] Task started: fastANI
[2024-01-24 12:27:24,768] [INFO] Running command: fastANI --query /var/lib/cwl/stg68eb6d5c-d13b-4f51-a995-a565103ab2cf/GCF_002021985.1_ASM202198v1_genomic.fna.gz --refList GCF_002021985.1_ASM202198v1_genomic.fna/target_genomes.txt --output GCF_002021985.1_ASM202198v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:27:30,443] [INFO] Task succeeded: fastANI
[2024-01-24 12:27:30,443] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc85c0e14-31c7-4d2d-8a25-8a033ab3a19e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:27:30,444] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc85c0e14-31c7-4d2d-8a25-8a033ab3a19e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:27:30,458] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:27:30,458] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:27:30,459] [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	77.9818	126	568	95	below_threshold
Campylobacter concisus	strain=ATCC 33237	GCA_001298465.1	199	199	suspected-type	True	77.8801	102	568	95	below_threshold
Campylobacter avium	strain=LMG 24591	GCA_002238335.1	522485	522485	type	True	77.6495	52	568	95	below_threshold
Campylobacter mucosalis	strain=ATCC 43264	GCA_012978755.1	202	202	type	True	77.4812	120	568	95	below_threshold
Campylobacter jejuni	strain=NCTC11351	GCA_001457695.1	197	197	type	True	77.3544	71	568	95	below_threshold
Campylobacter blaseri	strain=LMG 30333	GCA_013201895.1	2042961	2042961	type	True	77.333	118	568	95	below_threshold
Campylobacter volucris	strain=LMG 24380	GCA_008245045.1	1031542	1031542	type	True	77.2364	95	568	95	below_threshold
Campylobacter anatolicus	strain=faydin-G140	GCA_018145655.1	2829105	2829105	type	True	77.1385	121	568	95	below_threshold
Campylobacter blaseri	strain=17S00004-5	GCA_003015205.1	2042961	2042961	type	True	76.9503	115	568	95	below_threshold
Campylobacter jejuni subsp. jejuni	strain=ATCC 33560	GCA_000254515.2	32022	197	type	True	76.3815	58	568	95	below_threshold
Campylobacter jejuni subsp. jejuni	strain=CCUG 11284	GCA_008802045.1	32022	197	type	True	76.3631	63	568	95	below_threshold
Campylobacter hyointestinalis subsp. lawsonii	strain=CCUG 34538	GCA_008802075.1	91353	198	type	True	76.2854	89	568	95	below_threshold
Campylobacter hyointestinalis subsp. lawsonii	strain=CHY5	GCA_003289475.1	91353	198	type	True	76.2251	85	568	95	below_threshold
Campylobacter portucalensis	strain=FMV-PI01	GCA_009690845.1	2608384	2608384	type	True	76.1758	93	568	95	below_threshold
Campylobacter bilis	strain=VicNov18	GCA_016806695.1	2691918	2691918	type	True	76.164	55	568	95	below_threshold
Halarcobacter ebronensis	strain=LMG 27922	GCA_013201825.1	1462615	1462615	type	True	76.1527	51	568	95	below_threshold
Campylobacter aviculae	strain=MIT17-670	GCA_005406215.1	2510190	2510190	type	True	76.1306	65	568	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:27:30,461] [INFO] DFAST Taxonomy check result was written to GCF_002021985.1_ASM202198v1_genomic.fna/tc_result.tsv
[2024-01-24 12:27:30,461] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:27:30,461] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:27:30,462] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc85c0e14-31c7-4d2d-8a25-8a033ab3a19e/dqc_reference/checkm_data
[2024-01-24 12:27:30,462] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:27:30,490] [INFO] Task started: CheckM
[2024-01-24 12:27:30,490] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002021985.1_ASM202198v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002021985.1_ASM202198v1_genomic.fna/checkm_input GCF_002021985.1_ASM202198v1_genomic.fna/checkm_result
[2024-01-24 12:27:47,330] [INFO] Task succeeded: CheckM
[2024-01-24 12:27:47,332] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:27:47,353] [INFO] ===== Completeness check finished =====
[2024-01-24 12:27:47,353] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:27:47,354] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002021985.1_ASM202198v1_genomic.fna/markers.fasta)
[2024-01-24 12:27:47,354] [INFO] Task started: Blastn
[2024-01-24 12:27:47,354] [INFO] Running command: blastn -query GCF_002021985.1_ASM202198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc85c0e14-31c7-4d2d-8a25-8a033ab3a19e/dqc_reference/reference_markers_gtdb.fasta -out GCF_002021985.1_ASM202198v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:27:48,166] [INFO] Task succeeded: Blastn
[2024-01-24 12:27:48,170] [INFO] Selected 16 target genomes.
[2024-01-24 12:27:48,171] [INFO] Target genome list was writen to GCF_002021985.1_ASM202198v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:27:48,219] [INFO] Task started: fastANI
[2024-01-24 12:27:48,219] [INFO] Running command: fastANI --query /var/lib/cwl/stg68eb6d5c-d13b-4f51-a995-a565103ab2cf/GCF_002021985.1_ASM202198v1_genomic.fna.gz --refList GCF_002021985.1_ASM202198v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002021985.1_ASM202198v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:27:53,617] [INFO] Task succeeded: fastANI
[2024-01-24 12:27:53,633] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:27:53,633] [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_002022005.1	s__Campylobacter_A caledonicus	99.2605	554	568	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	99.31	99.26	0.98	0.97	3	conclusive
GCF_002021925.1	s__Campylobacter_A pinnipediorum	94.8027	515	568	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_004803835.1	s__Campylobacter_A sp004803835	78.1959	126	568	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_013372205.1	s__Campylobacter_A mucosalis	77.9823	125	568	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_013201975.1	s__Campylobacter_A sp013201975	77.8321	80	568	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	96.07	96.03	0.84	0.80	3	-
GCF_002913745.1	s__Campylobacter_A concisus_R	77.483	70	568	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_902460845.1	s__Campylobacter_A concisus_X	77.4758	98	568	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	99.79	99.67	0.94	0.93	3	-
GCF_018145735.1	s__Campylobacter_A sp018145735	77.4391	113	568	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_013201895.1	s__Campylobacter_B blaseri	77.4339	117	568	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B	95.0	100.00	100.00	1.00	1.00	3	-
GCA_902387145.1	s__Campylobacter_A sp902387145	77.3297	96	568	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000163995.1	s__Campylobacter_D jejuni_A	76.7935	58	568	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014305285.1	s__Campylobacter_D jejuni_D	76.5039	67	568	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.99	99.99	0.99	0.99	2	-
GCA_018375265.1	s__Campylobacter_A concisus_AB	76.4851	59	568	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	95.35	95.14	0.82	0.77	23	-
GCF_009690845.1	s__Campylobacter_B portucalensis	76.1758	93	568	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:27:53,635] [INFO] GTDB search result was written to GCF_002021985.1_ASM202198v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:27:53,636] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:27:53,639] [INFO] DFAST_QC result json was written to GCF_002021985.1_ASM202198v1_genomic.fna/dqc_result.json
[2024-01-24 12:27:53,639] [INFO] DFAST_QC completed!
[2024-01-24 12:27:53,639] [INFO] Total running time: 0h0m34s