[2024-01-24 10:47:06,584] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,589] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,589] [INFO] DQC Reference Directory: /var/lib/cwl/stg576bab7b-f2eb-44a1-ada8-6981539a8ab9/dqc_reference
[2024-01-24 10:47:12,682] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,824] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,825] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b984714-acb7-492d-b20a-d724b6c492ea/GCF_003590975.1_ASM359097v1_genomic.fna.gz | prodigal -d GCF_003590975.1_ASM359097v1_genomic.fna/cds.fna -a GCF_003590975.1_ASM359097v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:16,291] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:16,291] [INFO] Task started: HMMsearch
[2024-01-24 10:47:16,292] [INFO] Running command: hmmsearch --tblout GCF_003590975.1_ASM359097v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg576bab7b-f2eb-44a1-ada8-6981539a8ab9/dqc_reference/reference_markers.hmm GCF_003590975.1_ASM359097v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:16,604] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:16,605] [INFO] Found 6/6 markers.
[2024-01-24 10:47:16,639] [INFO] Query marker FASTA was written to GCF_003590975.1_ASM359097v1_genomic.fna/markers.fasta
[2024-01-24 10:47:16,639] [INFO] Task started: Blastn
[2024-01-24 10:47:16,639] [INFO] Running command: blastn -query GCF_003590975.1_ASM359097v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg576bab7b-f2eb-44a1-ada8-6981539a8ab9/dqc_reference/reference_markers.fasta -out GCF_003590975.1_ASM359097v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:19,611] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:19,617] [INFO] Selected 8 target genomes.
[2024-01-24 10:47:19,618] [INFO] Target genome list was writen to GCF_003590975.1_ASM359097v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:20,413] [INFO] Task started: fastANI
[2024-01-24 10:47:20,414] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b984714-acb7-492d-b20a-d724b6c492ea/GCF_003590975.1_ASM359097v1_genomic.fna.gz --refList GCF_003590975.1_ASM359097v1_genomic.fna/target_genomes.txt --output GCF_003590975.1_ASM359097v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:24,208] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:24,209] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg576bab7b-f2eb-44a1-ada8-6981539a8ab9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:24,210] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg576bab7b-f2eb-44a1-ada8-6981539a8ab9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:24,228] [INFO] Found 8 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 10:47:24,229] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:24,229] [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 coli	strain=LMG6440	GCA_003590975.1	195	195	type	True	100.0	621	623	95	conclusive
Campylobacter coli	strain=CCUG 11283	GCA_008802085.1	195	195	type	True	99.9896	616	623	95	conclusive
Campylobacter coli	strain=NCTC11366	GCA_900446355.1	195	195	type	True	99.9843	620	623	95	conclusive
Campylobacter coli	strain=LMG 9860	GCA_000254135.2	195	195	type	True	99.9006	539	623	95	conclusive
Campylobacter jejuni subsp. jejuni	strain=CCUG 11284	GCA_008802045.1	32022	197	type	True	85.8007	451	623	95	below_threshold
Campylobacter hepaticus	strain=HV10	GCA_001687475.2	1813019	1813019	type	True	81.3914	386	623	95	below_threshold
Campylobacter taeniopygiae	strain=MIT10-5678	GCA_005406225.1	2510188	2510188	type	True	81.0597	360	623	95	below_threshold
Campylobacter aviculae	strain=MIT17-670	GCA_005406215.1	2510190	2510190	type	True	80.8528	377	623	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:24,232] [INFO] DFAST Taxonomy check result was written to GCF_003590975.1_ASM359097v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:24,232] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:24,233] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:24,233] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg576bab7b-f2eb-44a1-ada8-6981539a8ab9/dqc_reference/checkm_data
[2024-01-24 10:47:24,234] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:24,258] [INFO] Task started: CheckM
[2024-01-24 10:47:24,259] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003590975.1_ASM359097v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003590975.1_ASM359097v1_genomic.fna/checkm_input GCF_003590975.1_ASM359097v1_genomic.fna/checkm_result
[2024-01-24 10:47:44,591] [INFO] Task succeeded: CheckM
[2024-01-24 10:47:44,593] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:47:44,614] [INFO] ===== Completeness check finished =====
[2024-01-24 10:47:44,614] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:47:44,615] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003590975.1_ASM359097v1_genomic.fna/markers.fasta)
[2024-01-24 10:47:44,615] [INFO] Task started: Blastn
[2024-01-24 10:47:44,616] [INFO] Running command: blastn -query GCF_003590975.1_ASM359097v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg576bab7b-f2eb-44a1-ada8-6981539a8ab9/dqc_reference/reference_markers_gtdb.fasta -out GCF_003590975.1_ASM359097v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:47,748] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:47,752] [INFO] Selected 11 target genomes.
[2024-01-24 10:47:47,753] [INFO] Target genome list was writen to GCF_003590975.1_ASM359097v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:47:47,812] [INFO] Task started: fastANI
[2024-01-24 10:47:47,813] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b984714-acb7-492d-b20a-d724b6c492ea/GCF_003590975.1_ASM359097v1_genomic.fna.gz --refList GCF_003590975.1_ASM359097v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003590975.1_ASM359097v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:47:52,973] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:52,984] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:47:52,984] [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_000254135.1	s__Campylobacter_D coli	99.9006	539	623	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	98.69	96.32	0.91	0.84	983	conclusive
GCF_001492295.1	s__Campylobacter_D coli_B	93.4336	535	623	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	98.63	98.33	0.93	0.85	59	-
GCF_000470055.1	s__Campylobacter_D coli_A	92.0312	483	623	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_001457695.1	s__Campylobacter_D jejuni	85.656	471	623	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	97.50	95.69	0.92	0.84	1918	-
GCA_000163995.1	s__Campylobacter_D jejuni_A	84.3433	444	623	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	83.7936	432	623	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	81.4093	385	623	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_004378855.1	s__Campylobacter_D sp004378855	81.2501	330	623	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	80.8698	376	623	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	80.7996	369	623	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	80.6208	344	623	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 10:47:52,988] [INFO] GTDB search result was written to GCF_003590975.1_ASM359097v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:47:52,989] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:47:52,995] [INFO] DFAST_QC result json was written to GCF_003590975.1_ASM359097v1_genomic.fna/dqc_result.json
[2024-01-24 10:47:52,996] [INFO] DFAST_QC completed!
[2024-01-24 10:47:52,996] [INFO] Total running time: 0h0m46s