[2023-06-04 22:13:14,123] [INFO] DFAST_QC pipeline started.
[2023-06-04 22:13:14,125] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 22:13:14,126] [INFO] DQC Reference Directory: /var/lib/cwl/stg16e72e96-668d-4fb8-958e-499ff6fae90f/dqc_reference
[2023-06-04 22:13:15,978] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 22:13:15,979] [INFO] Task started: Prodigal
[2023-06-04 22:13:15,979] [INFO] Running command: gunzip -c /var/lib/cwl/stg59c73210-1db4-45de-b62e-d8c418c32cbc/GCA_934692235.1_ERR7745335_bin.520_genomic.fna.gz | prodigal -d GCA_934692235.1_ERR7745335_bin.520_genomic.fna/cds.fna -a GCA_934692235.1_ERR7745335_bin.520_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 22:13:20,899] [INFO] Task succeeded: Prodigal
[2023-06-04 22:13:20,900] [INFO] Task started: HMMsearch
[2023-06-04 22:13:20,900] [INFO] Running command: hmmsearch --tblout GCA_934692235.1_ERR7745335_bin.520_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg16e72e96-668d-4fb8-958e-499ff6fae90f/dqc_reference/reference_markers.hmm GCA_934692235.1_ERR7745335_bin.520_genomic.fna/protein.faa > /dev/null
[2023-06-04 22:13:21,137] [INFO] Task succeeded: HMMsearch
[2023-06-04 22:13:21,139] [INFO] Found 6/6 markers.
[2023-06-04 22:13:21,163] [INFO] Query marker FASTA was written to GCA_934692235.1_ERR7745335_bin.520_genomic.fna/markers.fasta
[2023-06-04 22:13:21,163] [INFO] Task started: Blastn
[2023-06-04 22:13:21,163] [INFO] Running command: blastn -query GCA_934692235.1_ERR7745335_bin.520_genomic.fna/markers.fasta -db /var/lib/cwl/stg16e72e96-668d-4fb8-958e-499ff6fae90f/dqc_reference/reference_markers.fasta -out GCA_934692235.1_ERR7745335_bin.520_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 22:13:21,743] [INFO] Task succeeded: Blastn
[2023-06-04 22:13:21,748] [INFO] Selected 18 target genomes.
[2023-06-04 22:13:21,749] [INFO] Target genome list was writen to GCA_934692235.1_ERR7745335_bin.520_genomic.fna/target_genomes.txt
[2023-06-04 22:13:21,753] [INFO] Task started: fastANI
[2023-06-04 22:13:21,753] [INFO] Running command: fastANI --query /var/lib/cwl/stg59c73210-1db4-45de-b62e-d8c418c32cbc/GCA_934692235.1_ERR7745335_bin.520_genomic.fna.gz --refList GCA_934692235.1_ERR7745335_bin.520_genomic.fna/target_genomes.txt --output GCA_934692235.1_ERR7745335_bin.520_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 22:13:26,429] [INFO] Task succeeded: fastANI
[2023-06-04 22:13:26,430] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg16e72e96-668d-4fb8-958e-499ff6fae90f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 22:13:26,431] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg16e72e96-668d-4fb8-958e-499ff6fae90f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 22:13:26,444] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 22:13:26,444] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 22:13:26,444] [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 troglodytis	strain=MIT 05-9149A	GCA_006864425.1	654363	654363	type	True	78.4681	250	638	95	below_threshold
Campylobacter upsaliensis	strain=FDAARGOS_1518	GCA_020297605.1	28080	28080	type	True	76.8687	95	638	95	below_threshold
Campylobacter vulpis	strain=251/13	GCA_002738305.1	1655500	1655500	type	True	76.8076	78	638	95	below_threshold
Campylobacter upsaliensis	strain=NCTC11541	GCA_900637395.1	28080	28080	type	True	76.7915	97	638	95	below_threshold
Campylobacter coli	strain=LMG6440	GCA_003590975.1	195	195	type	True	76.6666	51	638	95	below_threshold
Campylobacter upsaliensis	strain=DSM 5365	GCA_000620965.1	28080	28080	type	True	76.6461	89	638	95	below_threshold
Campylobacter helveticus	strain=NCTC12470	GCA_900446405.1	28898	28898	type	True	76.5263	102	638	95	below_threshold
Campylobacter helveticus	strain=ATCC 51209	GCA_002080395.1	28898	28898	type	True	76.506	103	638	95	below_threshold
Campylobacter coli	strain=CCUG 11283	GCA_008802085.1	195	195	type	True	76.4489	50	638	95	below_threshold
Campylobacter jejuni subsp. jejuni	strain=CCUG 11284	GCA_008802045.1	32022	197	type	True	76.3388	50	638	95	below_threshold
Campylobacter avium	strain=LMG 24591	GCA_002238335.1	522485	522485	type	True	76.2005	95	638	95	below_threshold
Campylobacter helveticus	strain=ATCC 51209	GCA_900176295.1	28898	28898	type	True	76.1973	102	638	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 22:13:26,446] [INFO] DFAST Taxonomy check result was written to GCA_934692235.1_ERR7745335_bin.520_genomic.fna/tc_result.tsv
[2023-06-04 22:13:26,447] [INFO] ===== Taxonomy check completed =====
[2023-06-04 22:13:26,447] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 22:13:26,447] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg16e72e96-668d-4fb8-958e-499ff6fae90f/dqc_reference/checkm_data
[2023-06-04 22:13:26,448] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 22:13:26,470] [INFO] Task started: CheckM
[2023-06-04 22:13:26,470] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934692235.1_ERR7745335_bin.520_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934692235.1_ERR7745335_bin.520_genomic.fna/checkm_input GCA_934692235.1_ERR7745335_bin.520_genomic.fna/checkm_result
[2023-06-04 22:13:47,391] [INFO] Task succeeded: CheckM
[2023-06-04 22:13:47,393] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 22:13:47,412] [INFO] ===== Completeness check finished =====
[2023-06-04 22:13:47,413] [INFO] ===== Start GTDB Search =====
[2023-06-04 22:13:47,413] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934692235.1_ERR7745335_bin.520_genomic.fna/markers.fasta)
[2023-06-04 22:13:47,414] [INFO] Task started: Blastn
[2023-06-04 22:13:47,414] [INFO] Running command: blastn -query GCA_934692235.1_ERR7745335_bin.520_genomic.fna/markers.fasta -db /var/lib/cwl/stg16e72e96-668d-4fb8-958e-499ff6fae90f/dqc_reference/reference_markers_gtdb.fasta -out GCA_934692235.1_ERR7745335_bin.520_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 22:13:48,204] [INFO] Task succeeded: Blastn
[2023-06-04 22:13:48,208] [INFO] Selected 14 target genomes.
[2023-06-04 22:13:48,208] [INFO] Target genome list was writen to GCA_934692235.1_ERR7745335_bin.520_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 22:13:48,219] [INFO] Task started: fastANI
[2023-06-04 22:13:48,219] [INFO] Running command: fastANI --query /var/lib/cwl/stg59c73210-1db4-45de-b62e-d8c418c32cbc/GCA_934692235.1_ERR7745335_bin.520_genomic.fna.gz --refList GCA_934692235.1_ERR7745335_bin.520_genomic.fna/target_genomes_gtdb.txt --output GCA_934692235.1_ERR7745335_bin.520_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 22:13:53,144] [INFO] Task succeeded: fastANI
[2023-06-04 22:13:53,160] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 22:13:53,160] [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
GCA_900539255.1	s__Campylobacter_D sp900539255	96.4606	526	638	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	96.67	96.67	0.83	0.83	2	conclusive
GCA_900772495.1	s__Campylobacter_D sp900772495	93.6966	400	638	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_006864425.1	s__Campylobacter_D troglodytis	78.4367	252	638	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_006864535.1	s__Campylobacter_D sp006864535	77.2239	136	638	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	98.50	97.50	0.96	0.93	3	-
GCF_002738305.1	s__Campylobacter_D vulpis	76.8141	79	638	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_006864365.1	s__Campylobacter_D sp006864365	76.7877	107	638	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	76.72	56	638	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_006864455.1	s__Campylobacter_D sp006864455	76.6434	120	638	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_002238335.1	s__Campylobacter_D avium	76.2005	95	638	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.95	99.95	0.99	0.99	2	-
GCF_004378855.1	s__Campylobacter_D sp004378855	76.0794	57	638	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 22:13:53,162] [INFO] GTDB search result was written to GCA_934692235.1_ERR7745335_bin.520_genomic.fna/result_gtdb.tsv
[2023-06-04 22:13:53,163] [INFO] ===== GTDB Search completed =====
[2023-06-04 22:13:53,166] [INFO] DFAST_QC result json was written to GCA_934692235.1_ERR7745335_bin.520_genomic.fna/dqc_result.json
[2023-06-04 22:13:53,166] [INFO] DFAST_QC completed!
[2023-06-04 22:13:53,166] [INFO] Total running time: 0h0m39s