[2024-01-24 10:57:12,181] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:12,184] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:12,184] [INFO] DQC Reference Directory: /var/lib/cwl/stgdfaa813d-c959-4afb-9435-809db528bde3/dqc_reference
[2024-01-24 10:57:13,593] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:13,594] [INFO] Task started: Prodigal
[2024-01-24 10:57:13,594] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a23bba4-b48e-4976-b3cb-1ae2a6ca9e00/GCF_013372125.1_ASM1337212v1_genomic.fna.gz | prodigal -d GCF_013372125.1_ASM1337212v1_genomic.fna/cds.fna -a GCF_013372125.1_ASM1337212v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:18,254] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:18,254] [INFO] Task started: HMMsearch
[2024-01-24 10:57:18,255] [INFO] Running command: hmmsearch --tblout GCF_013372125.1_ASM1337212v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdfaa813d-c959-4afb-9435-809db528bde3/dqc_reference/reference_markers.hmm GCF_013372125.1_ASM1337212v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:18,504] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:18,505] [INFO] Found 6/6 markers.
[2024-01-24 10:57:18,525] [INFO] Query marker FASTA was written to GCF_013372125.1_ASM1337212v1_genomic.fna/markers.fasta
[2024-01-24 10:57:18,526] [INFO] Task started: Blastn
[2024-01-24 10:57:18,526] [INFO] Running command: blastn -query GCF_013372125.1_ASM1337212v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdfaa813d-c959-4afb-9435-809db528bde3/dqc_reference/reference_markers.fasta -out GCF_013372125.1_ASM1337212v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:19,146] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:19,149] [INFO] Selected 7 target genomes.
[2024-01-24 10:57:19,149] [INFO] Target genome list was writen to GCF_013372125.1_ASM1337212v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:19,212] [INFO] Task started: fastANI
[2024-01-24 10:57:19,212] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a23bba4-b48e-4976-b3cb-1ae2a6ca9e00/GCF_013372125.1_ASM1337212v1_genomic.fna.gz --refList GCF_013372125.1_ASM1337212v1_genomic.fna/target_genomes.txt --output GCF_013372125.1_ASM1337212v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:23,212] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:23,213] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdfaa813d-c959-4afb-9435-809db528bde3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:23,213] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdfaa813d-c959-4afb-9435-809db528bde3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:23,223] [INFO] Found 7 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 10:57:23,224] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:23,224] [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 curvus	strain=ATCC 35224	GCA_013372125.1	200	200	suspected-type	True	100.0	657	658	95	conclusive
Campylobacter curvus	strain=FDAARGOS_1547	GCA_020736225.1	200	200	suspected-type	True	99.9987	656	658	95	conclusive
Campylobacter curvus	strain=DSM 6644	GCA_000376325.1	200	200	suspected-type	True	99.9828	648	658	95	conclusive
Campylobacter curvus	strain=ATCC 35224	GCA_012978875.1	200	200	suspected-type	True	99.9785	636	658	95	conclusive
Campylobacter massiliensis	strain=Marseille-Q3452	GCA_014253065.1	2762557	2762557	type	True	78.6776	253	658	95	below_threshold
Campylobacter showae	strain=ATCC 51146	GCA_004803815.1	204	204	suspected-type	True	78.5816	253	658	95	below_threshold
Campylobacter concisus	strain=ATCC 33237	GCA_001298465.1	199	199	suspected-type	True	78.4774	242	658	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:23,225] [INFO] DFAST Taxonomy check result was written to GCF_013372125.1_ASM1337212v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:23,226] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:23,226] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:23,226] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdfaa813d-c959-4afb-9435-809db528bde3/dqc_reference/checkm_data
[2024-01-24 10:57:23,227] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:23,254] [INFO] Task started: CheckM
[2024-01-24 10:57:23,254] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013372125.1_ASM1337212v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013372125.1_ASM1337212v1_genomic.fna/checkm_input GCF_013372125.1_ASM1337212v1_genomic.fna/checkm_result
[2024-01-24 10:57:44,630] [INFO] Task succeeded: CheckM
[2024-01-24 10:57:44,632] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:57:44,645] [INFO] ===== Completeness check finished =====
[2024-01-24 10:57:44,645] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:57:44,646] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013372125.1_ASM1337212v1_genomic.fna/markers.fasta)
[2024-01-24 10:57:44,646] [INFO] Task started: Blastn
[2024-01-24 10:57:44,646] [INFO] Running command: blastn -query GCF_013372125.1_ASM1337212v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdfaa813d-c959-4afb-9435-809db528bde3/dqc_reference/reference_markers_gtdb.fasta -out GCF_013372125.1_ASM1337212v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:45,628] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:45,632] [INFO] Selected 19 target genomes.
[2024-01-24 10:57:45,632] [INFO] Target genome list was writen to GCF_013372125.1_ASM1337212v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:57:45,646] [INFO] Task started: fastANI
[2024-01-24 10:57:45,647] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a23bba4-b48e-4976-b3cb-1ae2a6ca9e00/GCF_013372125.1_ASM1337212v1_genomic.fna.gz --refList GCF_013372125.1_ASM1337212v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013372125.1_ASM1337212v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:57:53,697] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:53,713] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:57:53,714] [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_013372125.1	s__Campylobacter_A curvus	100.0	657	658	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	96.39	95.49	0.91	0.89	16	conclusive
GCF_900699785.1	s__Campylobacter_A showae_D	78.7713	242	658	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	99.98	99.98	0.99	0.99	3	-
GCF_014253065.1	s__Campylobacter_A sp014253065	78.7587	257	658	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_900573985.1	s__Campylobacter_A showae_E	78.5895	260	658	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_004803815.1	s__Campylobacter_A showae	78.5858	251	658	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_003048375.1	s__Campylobacter_A concisus_T	78.5788	282	658	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	95.30	95.13	0.90	0.85	33	-
GCF_003048835.2	s__Campylobacter_A concisus_D	78.5588	279	658	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_015230015.1	s__Campylobacter_A concisus_AF	78.4997	269	658	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_000344295.2	s__Campylobacter_A showae_B	78.4775	213	658	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_003048405.1	s__Campylobacter_A concisus_Q	78.4516	249	658	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	97.74	96.49	0.97	0.95	3	-
GCF_000466685.1	s__Campylobacter_A concisus_A	78.4293	287	658	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_902460415.1	s__Campylobacter_A concisus_Y	78.4263	233	658	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_000313615.1	s__Campylobacter_A showae_A	78.4151	236	658	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	96.64	96.14	0.94	0.93	5	-
GCF_002913225.1	s__Campylobacter_A concisus_J	78.3971	280	658	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_004803795.1	s__Campylobacter_A rectus	78.3521	229	658	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	97.92	96.44	0.98	0.96	4	-
GCF_003048675.2	s__Campylobacter_A concisus_F	78.3341	296	658	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_002912895.1	s__Campylobacter_A concisus_G	78.2821	230	658	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_018375265.1	s__Campylobacter_A concisus_AB	78.2165	167	658	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_018145735.1	s__Campylobacter_A sp018145735	77.5365	154	658	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	99.06	99.05	0.97	0.96	3	-
--------------------------------------------------------------------------------
[2024-01-24 10:57:53,715] [INFO] GTDB search result was written to GCF_013372125.1_ASM1337212v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:57:53,716] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:57:53,720] [INFO] DFAST_QC result json was written to GCF_013372125.1_ASM1337212v1_genomic.fna/dqc_result.json
[2024-01-24 10:57:53,720] [INFO] DFAST_QC completed!
[2024-01-24 10:57:53,720] [INFO] Total running time: 0h0m42s