[2024-01-24 13:21:41,043] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:41,048] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:41,048] [INFO] DQC Reference Directory: /var/lib/cwl/stgd85767f6-54e2-46cf-b802-732656f5f8ad/dqc_reference
[2024-01-24 13:21:42,260] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:42,262] [INFO] Task started: Prodigal
[2024-01-24 13:21:42,262] [INFO] Running command: gunzip -c /var/lib/cwl/stge9375100-6e57-4ccf-ba59-e199f841ba26/GCF_005406215.1_ASM540621v1_genomic.fna.gz | prodigal -d GCF_005406215.1_ASM540621v1_genomic.fna/cds.fna -a GCF_005406215.1_ASM540621v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:21:45,134] [INFO] Task succeeded: Prodigal
[2024-01-24 13:21:45,134] [INFO] Task started: HMMsearch
[2024-01-24 13:21:45,134] [INFO] Running command: hmmsearch --tblout GCF_005406215.1_ASM540621v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd85767f6-54e2-46cf-b802-732656f5f8ad/dqc_reference/reference_markers.hmm GCF_005406215.1_ASM540621v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:21:45,364] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:21:45,365] [INFO] Found 6/6 markers.
[2024-01-24 13:21:45,387] [INFO] Query marker FASTA was written to GCF_005406215.1_ASM540621v1_genomic.fna/markers.fasta
[2024-01-24 13:21:45,387] [INFO] Task started: Blastn
[2024-01-24 13:21:45,388] [INFO] Running command: blastn -query GCF_005406215.1_ASM540621v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd85767f6-54e2-46cf-b802-732656f5f8ad/dqc_reference/reference_markers.fasta -out GCF_005406215.1_ASM540621v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:46,051] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:46,055] [INFO] Selected 12 target genomes.
[2024-01-24 13:21:46,055] [INFO] Target genome list was writen to GCF_005406215.1_ASM540621v1_genomic.fna/target_genomes.txt
[2024-01-24 13:21:46,066] [INFO] Task started: fastANI
[2024-01-24 13:21:46,067] [INFO] Running command: fastANI --query /var/lib/cwl/stge9375100-6e57-4ccf-ba59-e199f841ba26/GCF_005406215.1_ASM540621v1_genomic.fna.gz --refList GCF_005406215.1_ASM540621v1_genomic.fna/target_genomes.txt --output GCF_005406215.1_ASM540621v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:21:50,430] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:50,430] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd85767f6-54e2-46cf-b802-732656f5f8ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:21:50,431] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd85767f6-54e2-46cf-b802-732656f5f8ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:21:50,444] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:21:50,445] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:21:50,445] [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 aviculae	strain=MIT17-670	GCA_005406215.1	2510190	2510190	type	True	100.0	542	542	95	conclusive
Campylobacter taeniopygiae	strain=MIT10-5678	GCA_005406225.1	2510188	2510188	type	True	89.4046	449	542	95	below_threshold
Campylobacter jejuni subsp. jejuni	strain=ATCC 33560	GCA_000254515.2	32022	197	type	True	81.1221	336	542	95	below_threshold
Campylobacter coli	strain=LMG 9860	GCA_000254135.2	195	195	type	True	81.014	360	542	95	below_threshold
Campylobacter coli	strain=CCUG 11283	GCA_008802085.1	195	195	type	True	81.0117	375	542	95	below_threshold
Campylobacter jejuni	strain=NCTC11351	GCA_001457695.1	197	197	type	True	80.9988	379	542	95	below_threshold
Campylobacter jejuni subsp. jejuni	strain=CCUG 11284	GCA_008802045.1	32022	197	type	True	80.9348	373	542	95	below_threshold
Campylobacter coli	strain=LMG6440	GCA_003590975.1	195	195	type	True	80.9287	379	542	95	below_threshold
Campylobacter hepaticus	strain=HV10	GCA_001687475.2	1813019	1813019	type	True	80.0529	355	542	95	below_threshold
Campylobacter helveticus	strain=ATCC 51209	GCA_002080395.1	28898	28898	type	True	77.9333	182	542	95	below_threshold
Campylobacter helveticus	strain=NCTC12470	GCA_900446405.1	28898	28898	type	True	77.9133	183	542	95	below_threshold
Campylobacter helveticus	strain=ATCC 51209	GCA_900176295.1	28898	28898	type	True	77.8355	181	542	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:21:50,448] [INFO] DFAST Taxonomy check result was written to GCF_005406215.1_ASM540621v1_genomic.fna/tc_result.tsv
[2024-01-24 13:21:50,449] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:21:50,449] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:21:50,450] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd85767f6-54e2-46cf-b802-732656f5f8ad/dqc_reference/checkm_data
[2024-01-24 13:21:50,451] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:21:50,483] [INFO] Task started: CheckM
[2024-01-24 13:21:50,484] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005406215.1_ASM540621v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005406215.1_ASM540621v1_genomic.fna/checkm_input GCF_005406215.1_ASM540621v1_genomic.fna/checkm_result
[2024-01-24 13:22:07,419] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:07,420] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:07,464] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:07,465] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:07,465] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005406215.1_ASM540621v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:07,465] [INFO] Task started: Blastn
[2024-01-24 13:22:07,465] [INFO] Running command: blastn -query GCF_005406215.1_ASM540621v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd85767f6-54e2-46cf-b802-732656f5f8ad/dqc_reference/reference_markers_gtdb.fasta -out GCF_005406215.1_ASM540621v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:08,318] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:08,322] [INFO] Selected 10 target genomes.
[2024-01-24 13:22:08,322] [INFO] Target genome list was writen to GCF_005406215.1_ASM540621v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:08,339] [INFO] Task started: fastANI
[2024-01-24 13:22:08,339] [INFO] Running command: fastANI --query /var/lib/cwl/stge9375100-6e57-4ccf-ba59-e199f841ba26/GCF_005406215.1_ASM540621v1_genomic.fna.gz --refList GCF_005406215.1_ASM540621v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005406215.1_ASM540621v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:12,753] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:12,764] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:22:12,764] [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_005406215.1	s__Campylobacter_D aviculae	100.0	542	542	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005406225.1	s__Campylobacter_D taeniopygiae	89.4376	448	542	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_005406205.1	s__Campylobacter_D estrildidarum	88.8309	465	542	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	86.897	424	542	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_000254135.1	s__Campylobacter_D coli	81.0324	359	542	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	98.69	96.32	0.91	0.84	983	-
GCF_001492295.1	s__Campylobacter_D coli_B	80.9844	369	542	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	80.7951	385	542	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_000470055.1	s__Campylobacter_D coli_A	80.7256	357	542	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	97.85	97.41	0.95	0.91	86	-
GCF_001687475.2	s__Campylobacter_D hepaticus	80.0844	353	542	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_002080395.1	s__Campylobacter_D helveticus	77.9598	179	542	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.44	98.95	0.97	0.95	14	-
--------------------------------------------------------------------------------
[2024-01-24 13:22:12,768] [INFO] GTDB search result was written to GCF_005406215.1_ASM540621v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:12,769] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:12,776] [INFO] DFAST_QC result json was written to GCF_005406215.1_ASM540621v1_genomic.fna/dqc_result.json
[2024-01-24 13:22:12,777] [INFO] DFAST_QC completed!
[2024-01-24 13:22:12,777] [INFO] Total running time: 0h0m32s