[2024-01-24 13:22:01,130] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:01,132] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:01,132] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d6a9fd6-93ed-45ca-9a37-863a2519b6f7/dqc_reference
[2024-01-24 13:22:02,531] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:02,532] [INFO] Task started: Prodigal
[2024-01-24 13:22:02,532] [INFO] Running command: gunzip -c /var/lib/cwl/stgce79ea07-9100-4bfa-97e7-403a6a4015a3/GCF_900446405.1_54984_F01_genomic.fna.gz | prodigal -d GCF_900446405.1_54984_F01_genomic.fna/cds.fna -a GCF_900446405.1_54984_F01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:06,503] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:06,504] [INFO] Task started: HMMsearch
[2024-01-24 13:22:06,504] [INFO] Running command: hmmsearch --tblout GCF_900446405.1_54984_F01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d6a9fd6-93ed-45ca-9a37-863a2519b6f7/dqc_reference/reference_markers.hmm GCF_900446405.1_54984_F01_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:06,758] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:06,760] [INFO] Found 6/6 markers.
[2024-01-24 13:22:06,789] [INFO] Query marker FASTA was written to GCF_900446405.1_54984_F01_genomic.fna/markers.fasta
[2024-01-24 13:22:06,790] [INFO] Task started: Blastn
[2024-01-24 13:22:06,790] [INFO] Running command: blastn -query GCF_900446405.1_54984_F01_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d6a9fd6-93ed-45ca-9a37-863a2519b6f7/dqc_reference/reference_markers.fasta -out GCF_900446405.1_54984_F01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:07,374] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:07,377] [INFO] Selected 6 target genomes.
[2024-01-24 13:22:07,377] [INFO] Target genome list was writen to GCF_900446405.1_54984_F01_genomic.fna/target_genomes.txt
[2024-01-24 13:22:07,386] [INFO] Task started: fastANI
[2024-01-24 13:22:07,386] [INFO] Running command: fastANI --query /var/lib/cwl/stgce79ea07-9100-4bfa-97e7-403a6a4015a3/GCF_900446405.1_54984_F01_genomic.fna.gz --refList GCF_900446405.1_54984_F01_genomic.fna/target_genomes.txt --output GCF_900446405.1_54984_F01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:10,098] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:10,098] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d6a9fd6-93ed-45ca-9a37-863a2519b6f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:10,099] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d6a9fd6-93ed-45ca-9a37-863a2519b6f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:10,105] [INFO] Found 6 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:22:10,106] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:10,106] [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 helveticus	strain=NCTC12470	GCA_900446405.1	28898	28898	type	True	100.0	627	628	95	conclusive
Campylobacter helveticus	strain=ATCC 51209	GCA_002080395.1	28898	28898	type	True	99.9988	620	628	95	conclusive
Campylobacter helveticus	strain=ATCC 51209	GCA_900176295.1	28898	28898	type	True	99.9361	571	628	95	conclusive
Campylobacter upsaliensis	strain=FDAARGOS_1518	GCA_020297605.1	28080	28080	type	True	86.391	451	628	95	below_threshold
Campylobacter upsaliensis	strain=DSM 5365	GCA_000620965.1	28080	28080	type	True	86.247	433	628	95	below_threshold
Campylobacter vulpis	strain=251/13	GCA_002738305.1	1655500	1655500	type	True	84.9295	421	628	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:10,108] [INFO] DFAST Taxonomy check result was written to GCF_900446405.1_54984_F01_genomic.fna/tc_result.tsv
[2024-01-24 13:22:10,109] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:10,109] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:10,110] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d6a9fd6-93ed-45ca-9a37-863a2519b6f7/dqc_reference/checkm_data
[2024-01-24 13:22:10,111] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:10,137] [INFO] Task started: CheckM
[2024-01-24 13:22:10,137] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900446405.1_54984_F01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900446405.1_54984_F01_genomic.fna/checkm_input GCF_900446405.1_54984_F01_genomic.fna/checkm_result
[2024-01-24 13:22:29,642] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:29,643] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:29,661] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:29,661] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:29,662] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900446405.1_54984_F01_genomic.fna/markers.fasta)
[2024-01-24 13:22:29,662] [INFO] Task started: Blastn
[2024-01-24 13:22:29,662] [INFO] Running command: blastn -query GCF_900446405.1_54984_F01_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d6a9fd6-93ed-45ca-9a37-863a2519b6f7/dqc_reference/reference_markers_gtdb.fasta -out GCF_900446405.1_54984_F01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:30,519] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:30,522] [INFO] Selected 11 target genomes.
[2024-01-24 13:22:30,522] [INFO] Target genome list was writen to GCF_900446405.1_54984_F01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:30,530] [INFO] Task started: fastANI
[2024-01-24 13:22:30,530] [INFO] Running command: fastANI --query /var/lib/cwl/stgce79ea07-9100-4bfa-97e7-403a6a4015a3/GCF_900446405.1_54984_F01_genomic.fna.gz --refList GCF_900446405.1_54984_F01_genomic.fna/target_genomes_gtdb.txt --output GCF_900446405.1_54984_F01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:34,772] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:34,784] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:22:34,784] [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_002080395.1	s__Campylobacter_D helveticus	99.9988	620	628	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.44	98.95	0.97	0.95	14	conclusive
GCF_900637395.1	s__Campylobacter_D upsaliensis	86.2575	455	628	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	96.80	95.96	0.91	0.88	18	-
GCF_002738305.1	s__Campylobacter_D vulpis	84.9178	422	628	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.20	98.60	0.92	0.87	15	-
GCF_002179165.1	s__Campylobacter_D jejuni_B	78.8424	235	628	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_001492295.1	s__Campylobacter_D coli_B	78.4418	250	628	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_014305285.1	s__Campylobacter_D jejuni_D	78.2922	223	628	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_000254135.1	s__Campylobacter_D coli	78.0939	230	628	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_004378855.1	s__Campylobacter_D sp004378855	78.0281	213	628	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	77.8585	190	628	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	77.7026	206	628	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	77.6193	195	628	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 13:22:34,787] [INFO] GTDB search result was written to GCF_900446405.1_54984_F01_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:34,787] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:34,791] [INFO] DFAST_QC result json was written to GCF_900446405.1_54984_F01_genomic.fna/dqc_result.json
[2024-01-24 13:22:34,791] [INFO] DFAST_QC completed!
[2024-01-24 13:22:34,791] [INFO] Total running time: 0h0m34s