[2024-01-24 11:20:03,799] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:03,801] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:03,801] [INFO] DQC Reference Directory: /var/lib/cwl/stg89b4d1f4-db0e-47db-8796-bfd7dff10af4/dqc_reference
[2024-01-24 11:20:04,979] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:04,980] [INFO] Task started: Prodigal
[2024-01-24 11:20:04,980] [INFO] Running command: gunzip -c /var/lib/cwl/stgd498c822-6b01-4596-932b-3978d38b14bb/GCF_006176165.1_ASM617616v1_genomic.fna.gz | prodigal -d GCF_006176165.1_ASM617616v1_genomic.fna/cds.fna -a GCF_006176165.1_ASM617616v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:07,495] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:07,495] [INFO] Task started: HMMsearch
[2024-01-24 11:20:07,495] [INFO] Running command: hmmsearch --tblout GCF_006176165.1_ASM617616v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89b4d1f4-db0e-47db-8796-bfd7dff10af4/dqc_reference/reference_markers.hmm GCF_006176165.1_ASM617616v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:07,712] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:07,713] [INFO] Found 6/6 markers.
[2024-01-24 11:20:07,731] [INFO] Query marker FASTA was written to GCF_006176165.1_ASM617616v1_genomic.fna/markers.fasta
[2024-01-24 11:20:07,732] [INFO] Task started: Blastn
[2024-01-24 11:20:07,732] [INFO] Running command: blastn -query GCF_006176165.1_ASM617616v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89b4d1f4-db0e-47db-8796-bfd7dff10af4/dqc_reference/reference_markers.fasta -out GCF_006176165.1_ASM617616v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:08,292] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:08,295] [INFO] Selected 9 target genomes.
[2024-01-24 11:20:08,296] [INFO] Target genome list was writen to GCF_006176165.1_ASM617616v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:08,347] [INFO] Task started: fastANI
[2024-01-24 11:20:08,348] [INFO] Running command: fastANI --query /var/lib/cwl/stgd498c822-6b01-4596-932b-3978d38b14bb/GCF_006176165.1_ASM617616v1_genomic.fna.gz --refList GCF_006176165.1_ASM617616v1_genomic.fna/target_genomes.txt --output GCF_006176165.1_ASM617616v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:11,963] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:11,963] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89b4d1f4-db0e-47db-8796-bfd7dff10af4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:11,964] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89b4d1f4-db0e-47db-8796-bfd7dff10af4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:11,972] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:20:11,973] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:11,973] [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 armoricus	strain=CA656	GCA_006176165.1	2505970	2505970	type	True	100.0	509	511	95	conclusive
Campylobacter armoricus	strain=CCUG 73571	GCA_013372105.1	2505970	2505970	type	True	99.9985	511	511	95	conclusive
Campylobacter ornithocola	strain=LMG 29815	GCA_013201605.1	1848766	1848766	type	True	88.8335	443	511	95	below_threshold
Campylobacter ornithocola	strain=WBE38	GCA_001705345.1	1848766	1848766	type	True	88.803	448	511	95	below_threshold
Campylobacter lari subsp. concheus	strain=LMG 21009	GCA_008245025.1	488545	201	type	True	88.4596	422	511	95	below_threshold
Campylobacter lari subsp. concheus	strain=CCUG 55786	GCA_008802005.1	488545	201	type	True	88.433	424	511	95	below_threshold
Campylobacter lari subsp. lari	strain=ATCC 35221	GCA_900111465.1	650054	201	type	True	87.8653	438	511	95	below_threshold
Campylobacter lari	strain=FDAARGOS_1101	GCA_016726265.1	201	201	type	True	87.8462	437	511	95	below_threshold
Campylobacter peloridis	strain=LMG 23910	GCA_000816785.1	488546	488546	type	True	86.3305	418	511	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:11,974] [INFO] DFAST Taxonomy check result was written to GCF_006176165.1_ASM617616v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:11,975] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:11,975] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:11,975] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89b4d1f4-db0e-47db-8796-bfd7dff10af4/dqc_reference/checkm_data
[2024-01-24 11:20:11,976] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:11,993] [INFO] Task started: CheckM
[2024-01-24 11:20:11,994] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006176165.1_ASM617616v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006176165.1_ASM617616v1_genomic.fna/checkm_input GCF_006176165.1_ASM617616v1_genomic.fna/checkm_result
[2024-01-24 11:20:28,337] [INFO] Task succeeded: CheckM
[2024-01-24 11:20:28,338] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:20:28,353] [INFO] ===== Completeness check finished =====
[2024-01-24 11:20:28,354] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:20:28,354] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006176165.1_ASM617616v1_genomic.fna/markers.fasta)
[2024-01-24 11:20:28,354] [INFO] Task started: Blastn
[2024-01-24 11:20:28,354] [INFO] Running command: blastn -query GCF_006176165.1_ASM617616v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89b4d1f4-db0e-47db-8796-bfd7dff10af4/dqc_reference/reference_markers_gtdb.fasta -out GCF_006176165.1_ASM617616v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:29,103] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:29,106] [INFO] Selected 8 target genomes.
[2024-01-24 11:20:29,106] [INFO] Target genome list was writen to GCF_006176165.1_ASM617616v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:20:29,113] [INFO] Task started: fastANI
[2024-01-24 11:20:29,113] [INFO] Running command: fastANI --query /var/lib/cwl/stgd498c822-6b01-4596-932b-3978d38b14bb/GCF_006176165.1_ASM617616v1_genomic.fna.gz --refList GCF_006176165.1_ASM617616v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006176165.1_ASM617616v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:20:32,351] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:32,358] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:20:32,359] [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_013372105.1	s__Campylobacter_D armoricus	99.9985	511	511	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.30	98.87	0.93	0.88	11	conclusive
GCF_000816245.1	s__Campylobacter_D sp000816245	90.3833	445	511	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_013201605.1	s__Campylobacter_D ornithocola	88.8335	443	511	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.99	99.99	0.98	0.98	2	-
GCF_002179635.1	s__Campylobacter_D jejuni_C	88.7334	423	511	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_001017575.1	s__Campylobacter_D lari_C	88.5359	437	511	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_004357905.1	s__Campylobacter_D lari_D	88.463	428	511	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	88.4596	422	511	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	87.722	443	511	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	98.73	98.09	0.96	0.93	13	-
--------------------------------------------------------------------------------
[2024-01-24 11:20:32,360] [INFO] GTDB search result was written to GCF_006176165.1_ASM617616v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:20:32,361] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:20:32,363] [INFO] DFAST_QC result json was written to GCF_006176165.1_ASM617616v1_genomic.fna/dqc_result.json
[2024-01-24 11:20:32,363] [INFO] DFAST_QC completed!
[2024-01-24 11:20:32,363] [INFO] Total running time: 0h0m29s