[2024-01-24 14:13:01,345] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:13:01,347] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:13:01,348] [INFO] DQC Reference Directory: /var/lib/cwl/stgdbb65b2a-7084-451b-a56b-52de0734b9da/dqc_reference
[2024-01-24 14:13:02,585] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:13:02,586] [INFO] Task started: Prodigal
[2024-01-24 14:13:02,587] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ecb0863-d77d-4507-8059-919c4012c503/GCF_002104335.1_ASM210433v1_genomic.fna.gz | prodigal -d GCF_002104335.1_ASM210433v1_genomic.fna/cds.fna -a GCF_002104335.1_ASM210433v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:06,348] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:06,349] [INFO] Task started: HMMsearch
[2024-01-24 14:13:06,349] [INFO] Running command: hmmsearch --tblout GCF_002104335.1_ASM210433v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdbb65b2a-7084-451b-a56b-52de0734b9da/dqc_reference/reference_markers.hmm GCF_002104335.1_ASM210433v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:06,591] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:06,592] [INFO] Found 6/6 markers.
[2024-01-24 14:13:06,618] [INFO] Query marker FASTA was written to GCF_002104335.1_ASM210433v1_genomic.fna/markers.fasta
[2024-01-24 14:13:06,618] [INFO] Task started: Blastn
[2024-01-24 14:13:06,618] [INFO] Running command: blastn -query GCF_002104335.1_ASM210433v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbb65b2a-7084-451b-a56b-52de0734b9da/dqc_reference/reference_markers.fasta -out GCF_002104335.1_ASM210433v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:07,196] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:07,200] [INFO] Selected 11 target genomes.
[2024-01-24 14:13:07,201] [INFO] Target genome list was writen to GCF_002104335.1_ASM210433v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:07,253] [INFO] Task started: fastANI
[2024-01-24 14:13:07,254] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ecb0863-d77d-4507-8059-919c4012c503/GCF_002104335.1_ASM210433v1_genomic.fna.gz --refList GCF_002104335.1_ASM210433v1_genomic.fna/target_genomes.txt --output GCF_002104335.1_ASM210433v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:11,170] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:11,170] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdbb65b2a-7084-451b-a56b-52de0734b9da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:11,170] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdbb65b2a-7084-451b-a56b-52de0734b9da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:11,180] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:13:11,181] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:11,181] [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 cuniculorum	strain=LMG 24588	GCA_002104335.1	374106	374106	type	True	100.0	644	644	95	conclusive
Campylobacter cuniculorum	strain=DSM 23162	GCA_000621005.1	374106	374106	type	True	99.9402	596	644	95	conclusive
Campylobacter jejuni	strain=NCTC11351	GCA_001457695.1	197	197	type	True	79.3522	309	644	95	below_threshold
Campylobacter jejuni subsp. jejuni	strain=ATCC 33560	GCA_000254515.2	32022	197	type	True	79.0809	267	644	95	below_threshold
Campylobacter jejuni subsp. jejuni	strain=CCUG 11284	GCA_008802045.1	32022	197	type	True	79.0666	295	644	95	below_threshold
Campylobacter taeniopygiae	strain=MIT10-5678	GCA_005406225.1	2510188	2510188	type	True	78.6146	259	644	95	below_threshold
Campylobacter coli	strain=LMG6440	GCA_003590975.1	195	195	type	True	78.5935	293	644	95	below_threshold
Campylobacter coli	strain=LMG 9860	GCA_000254135.2	195	195	type	True	78.5083	287	644	95	below_threshold
Campylobacter hepaticus	strain=HV10	GCA_001687475.2	1813019	1813019	type	True	78.1829	265	644	95	below_threshold
Campylobacter aviculae	strain=MIT17-670	GCA_005406215.1	2510190	2510190	type	True	78.1294	257	644	95	below_threshold
Campylobacter novaezeelandiae	strain=B423b	GCA_004323845.1	2267891	2267891	type	True	77.8907	231	644	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:11,183] [INFO] DFAST Taxonomy check result was written to GCF_002104335.1_ASM210433v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:11,183] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:11,183] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:11,183] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdbb65b2a-7084-451b-a56b-52de0734b9da/dqc_reference/checkm_data
[2024-01-24 14:13:11,185] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:11,211] [INFO] Task started: CheckM
[2024-01-24 14:13:11,211] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002104335.1_ASM210433v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002104335.1_ASM210433v1_genomic.fna/checkm_input GCF_002104335.1_ASM210433v1_genomic.fna/checkm_result
[2024-01-24 14:13:31,086] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:31,087] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:31,114] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:31,115] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:31,115] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002104335.1_ASM210433v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:31,116] [INFO] Task started: Blastn
[2024-01-24 14:13:31,116] [INFO] Running command: blastn -query GCF_002104335.1_ASM210433v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbb65b2a-7084-451b-a56b-52de0734b9da/dqc_reference/reference_markers_gtdb.fasta -out GCF_002104335.1_ASM210433v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:31,993] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:31,997] [INFO] Selected 15 target genomes.
[2024-01-24 14:13:31,997] [INFO] Target genome list was writen to GCF_002104335.1_ASM210433v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:32,011] [INFO] Task started: fastANI
[2024-01-24 14:13:32,011] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ecb0863-d77d-4507-8059-919c4012c503/GCF_002104335.1_ASM210433v1_genomic.fna.gz --refList GCF_002104335.1_ASM210433v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002104335.1_ASM210433v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:37,633] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:37,647] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:37,647] [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_002104335.1	s__Campylobacter_D cuniculorum	100.0	644	644	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.99	99.99	1.00	1.00	3	conclusive
GCF_001457695.1	s__Campylobacter_D jejuni	79.3326	307	644	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	97.50	95.69	0.92	0.84	1918	-
GCF_001492295.1	s__Campylobacter_D coli_B	78.9229	299	644	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	98.63	98.33	0.93	0.85	59	-
GCA_000163995.1	s__Campylobacter_D jejuni_A	78.8725	285	644	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002179165.1	s__Campylobacter_D jejuni_B	78.8206	285	644	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005406225.1	s__Campylobacter_D taeniopygiae	78.6309	258	644	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	78.5926	276	644	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004378855.1	s__Campylobacter_D sp004378855	78.3828	266	644	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001687475.2	s__Campylobacter_D hepaticus	78.3021	266	644	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.94	99.56	0.99	0.97	33	-
GCF_005406205.1	s__Campylobacter_D estrildidarum	78.2987	235	644	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016598935.1	s__Campylobacter_D sp016598935	78.156	235	644	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005406215.1	s__Campylobacter_D aviculae	78.1206	257	644	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004323845.1	s__Campylobacter_D novaezeelandiae	77.885	232	644	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	98.63	98.04	0.93	0.83	5	-
GCF_006864455.1	s__Campylobacter_D sp006864455	77.4358	156	644	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:37,649] [INFO] GTDB search result was written to GCF_002104335.1_ASM210433v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:37,649] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:37,653] [INFO] DFAST_QC result json was written to GCF_002104335.1_ASM210433v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:37,653] [INFO] DFAST_QC completed!
[2024-01-24 14:13:37,653] [INFO] Total running time: 0h0m36s