[2024-01-24 13:18:59,770] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:59,771] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:59,772] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f72b5bc-f229-48ee-8598-327d10c3521a/dqc_reference
[2024-01-24 13:19:01,105] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:01,106] [INFO] Task started: Prodigal
[2024-01-24 13:19:01,106] [INFO] Running command: gunzip -c /var/lib/cwl/stgceb0b661-3002-4fc2-bd34-40758fcab32b/GCF_013201605.1_ASM1320160v1_genomic.fna.gz | prodigal -d GCF_013201605.1_ASM1320160v1_genomic.fna/cds.fna -a GCF_013201605.1_ASM1320160v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:03,970] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:03,971] [INFO] Task started: HMMsearch
[2024-01-24 13:19:03,971] [INFO] Running command: hmmsearch --tblout GCF_013201605.1_ASM1320160v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f72b5bc-f229-48ee-8598-327d10c3521a/dqc_reference/reference_markers.hmm GCF_013201605.1_ASM1320160v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:04,220] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:04,221] [INFO] Found 6/6 markers.
[2024-01-24 13:19:04,242] [INFO] Query marker FASTA was written to GCF_013201605.1_ASM1320160v1_genomic.fna/markers.fasta
[2024-01-24 13:19:04,242] [INFO] Task started: Blastn
[2024-01-24 13:19:04,243] [INFO] Running command: blastn -query GCF_013201605.1_ASM1320160v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f72b5bc-f229-48ee-8598-327d10c3521a/dqc_reference/reference_markers.fasta -out GCF_013201605.1_ASM1320160v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:04,842] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:04,855] [INFO] Selected 8 target genomes.
[2024-01-24 13:19:04,855] [INFO] Target genome list was writen to GCF_013201605.1_ASM1320160v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:04,865] [INFO] Task started: fastANI
[2024-01-24 13:19:04,865] [INFO] Running command: fastANI --query /var/lib/cwl/stgceb0b661-3002-4fc2-bd34-40758fcab32b/GCF_013201605.1_ASM1320160v1_genomic.fna.gz --refList GCF_013201605.1_ASM1320160v1_genomic.fna/target_genomes.txt --output GCF_013201605.1_ASM1320160v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:07,999] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:07,999] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f72b5bc-f229-48ee-8598-327d10c3521a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:08,000] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f72b5bc-f229-48ee-8598-327d10c3521a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:08,007] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:19:08,008] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:08,008] [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 ornithocola	strain=LMG 29815	GCA_013201605.1	1848766	1848766	type	True	100.0	545	548	95	conclusive
Campylobacter ornithocola	strain=WBE38	GCA_001705345.1	1848766	1848766	type	True	99.9348	511	548	95	conclusive
Campylobacter lari subsp. concheus	strain=CCUG 55786	GCA_008802005.1	488545	201	type	True	90.8452	436	548	95	below_threshold
Campylobacter lari subsp. concheus	strain=LMG 21009	GCA_008245025.1	488545	201	type	True	90.6782	454	548	95	below_threshold
Campylobacter lari	strain=FDAARGOS_1101	GCA_016726265.1	201	201	type	True	89.8348	453	548	95	below_threshold
Campylobacter lari	strain=NCTC11352	GCA_900446615.1	201	201	type	True	89.715	459	548	95	below_threshold
Campylobacter lari subsp. lari	strain=ATCC 35221	GCA_900111465.1	650054	201	type	True	89.666	443	548	95	below_threshold
Campylobacter subantarcticus	strain=LMG 24377	GCA_000816305.1	497724	497724	type	True	88.424	475	548	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:08,010] [INFO] DFAST Taxonomy check result was written to GCF_013201605.1_ASM1320160v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:08,013] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:08,013] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:08,013] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f72b5bc-f229-48ee-8598-327d10c3521a/dqc_reference/checkm_data
[2024-01-24 13:19:08,015] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:08,034] [INFO] Task started: CheckM
[2024-01-24 13:19:08,035] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013201605.1_ASM1320160v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013201605.1_ASM1320160v1_genomic.fna/checkm_input GCF_013201605.1_ASM1320160v1_genomic.fna/checkm_result
[2024-01-24 13:19:26,345] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:26,348] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:26,364] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:26,364] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:26,365] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013201605.1_ASM1320160v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:26,365] [INFO] Task started: Blastn
[2024-01-24 13:19:26,365] [INFO] Running command: blastn -query GCF_013201605.1_ASM1320160v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f72b5bc-f229-48ee-8598-327d10c3521a/dqc_reference/reference_markers_gtdb.fasta -out GCF_013201605.1_ASM1320160v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:27,186] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:27,189] [INFO] Selected 7 target genomes.
[2024-01-24 13:19:27,189] [INFO] Target genome list was writen to GCF_013201605.1_ASM1320160v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:27,203] [INFO] Task started: fastANI
[2024-01-24 13:19:27,203] [INFO] Running command: fastANI --query /var/lib/cwl/stgceb0b661-3002-4fc2-bd34-40758fcab32b/GCF_013201605.1_ASM1320160v1_genomic.fna.gz --refList GCF_013201605.1_ASM1320160v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013201605.1_ASM1320160v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:30,598] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:30,606] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:30,606] [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_013201605.1	s__Campylobacter_D ornithocola	100.0	546	548	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.99	99.99	0.98	0.98	2	conclusive
GCF_001017575.1	s__Campylobacter_D lari_C	91.5909	472	548	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	97.15	95.06	0.92	0.89	21	-
GCF_002179635.1	s__Campylobacter_D jejuni_C	91.3941	441	548	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	98.56	98.44	0.93	0.93	4	-
GCF_004357905.1	s__Campylobacter_D lari_D	90.8761	431	548	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_008245025.1	s__Campylobacter_D concheus	90.6395	455	548	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.27	98.88	0.96	0.94	4	-
GCF_013372185.1	s__Campylobacter_D lari	89.7414	458	548	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	98.73	98.09	0.96	0.93	13	-
GCF_000816305.1	s__Campylobacter_D subantarcticus	88.3309	474	548	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.30	98.60	0.97	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:30,608] [INFO] GTDB search result was written to GCF_013201605.1_ASM1320160v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:30,609] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:30,612] [INFO] DFAST_QC result json was written to GCF_013201605.1_ASM1320160v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:30,612] [INFO] DFAST_QC completed!
[2024-01-24 13:19:30,612] [INFO] Total running time: 0h0m31s