[2024-01-24 14:19:45,521] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:45,539] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:45,539] [INFO] DQC Reference Directory: /var/lib/cwl/stgb7ba8f8e-248d-43fb-9a97-e3b7c3378b7a/dqc_reference
[2024-01-24 14:19:46,803] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:46,804] [INFO] Task started: Prodigal
[2024-01-24 14:19:46,804] [INFO] Running command: gunzip -c /var/lib/cwl/stge8270223-5d1d-445c-8a23-60e8c4a4e19e/GCF_008245045.1_ASM824504v1_genomic.fna.gz | prodigal -d GCF_008245045.1_ASM824504v1_genomic.fna/cds.fna -a GCF_008245045.1_ASM824504v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:49,585] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:49,585] [INFO] Task started: HMMsearch
[2024-01-24 14:19:49,585] [INFO] Running command: hmmsearch --tblout GCF_008245045.1_ASM824504v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb7ba8f8e-248d-43fb-9a97-e3b7c3378b7a/dqc_reference/reference_markers.hmm GCF_008245045.1_ASM824504v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:49,795] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:49,796] [INFO] Found 6/6 markers.
[2024-01-24 14:19:49,814] [INFO] Query marker FASTA was written to GCF_008245045.1_ASM824504v1_genomic.fna/markers.fasta
[2024-01-24 14:19:49,814] [INFO] Task started: Blastn
[2024-01-24 14:19:49,814] [INFO] Running command: blastn -query GCF_008245045.1_ASM824504v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7ba8f8e-248d-43fb-9a97-e3b7c3378b7a/dqc_reference/reference_markers.fasta -out GCF_008245045.1_ASM824504v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:50,442] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:50,445] [INFO] Selected 10 target genomes.
[2024-01-24 14:19:50,445] [INFO] Target genome list was writen to GCF_008245045.1_ASM824504v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:50,452] [INFO] Task started: fastANI
[2024-01-24 14:19:50,452] [INFO] Running command: fastANI --query /var/lib/cwl/stge8270223-5d1d-445c-8a23-60e8c4a4e19e/GCF_008245045.1_ASM824504v1_genomic.fna.gz --refList GCF_008245045.1_ASM824504v1_genomic.fna/target_genomes.txt --output GCF_008245045.1_ASM824504v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:54,281] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:54,282] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb7ba8f8e-248d-43fb-9a97-e3b7c3378b7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:54,282] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb7ba8f8e-248d-43fb-9a97-e3b7c3378b7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:54,293] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:19:54,294] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:54,294] [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 volucris	strain=LMG 24380	GCA_008245045.1	1031542	1031542	type	True	100.0	509	510	95	conclusive
Campylobacter volucris	strain=CCUG 57498	GCA_008801985.1	1031542	1031542	type	True	99.9647	492	510	95	conclusive
Campylobacter lari	strain=FDAARGOS_1101	GCA_016726265.1	201	201	type	True	84.7197	425	510	95	below_threshold
Campylobacter lari	strain=NCTC11352	GCA_900446615.1	201	201	type	True	84.625	434	510	95	below_threshold
Campylobacter lari subsp. lari	strain=ATCC 35221	GCA_900111465.1	650054	201	type	True	84.5935	421	510	95	below_threshold
Campylobacter peloridis	strain=LMG 23910	GCA_000816785.1	488546	488546	type	True	84.0143	416	510	95	below_threshold
Campylobacter lari subsp. concheus	strain=LMG 21009	GCA_008245025.1	488545	201	type	True	83.7078	421	510	95	below_threshold
Campylobacter lari subsp. concheus	strain=CCUG 55786	GCA_008802005.1	488545	201	type	True	83.699	409	510	95	below_threshold
Campylobacter insulaenigrae	strain=NCTC 12927	GCA_000816185.1	260714	260714	type	True	83.5405	413	510	95	below_threshold
Campylobacter insulaenigrae	strain=NCTC12927	GCA_900637885.1	260714	260714	type	True	83.4763	417	510	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:54,296] [INFO] DFAST Taxonomy check result was written to GCF_008245045.1_ASM824504v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:54,296] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:54,296] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:54,297] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb7ba8f8e-248d-43fb-9a97-e3b7c3378b7a/dqc_reference/checkm_data
[2024-01-24 14:19:54,298] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:54,317] [INFO] Task started: CheckM
[2024-01-24 14:19:54,318] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008245045.1_ASM824504v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008245045.1_ASM824504v1_genomic.fna/checkm_input GCF_008245045.1_ASM824504v1_genomic.fna/checkm_result
[2024-01-24 14:20:11,863] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:11,864] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:11,883] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:11,884] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:11,884] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008245045.1_ASM824504v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:11,885] [INFO] Task started: Blastn
[2024-01-24 14:20:11,885] [INFO] Running command: blastn -query GCF_008245045.1_ASM824504v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7ba8f8e-248d-43fb-9a97-e3b7c3378b7a/dqc_reference/reference_markers_gtdb.fasta -out GCF_008245045.1_ASM824504v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:12,789] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:12,793] [INFO] Selected 10 target genomes.
[2024-01-24 14:20:12,793] [INFO] Target genome list was writen to GCF_008245045.1_ASM824504v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:12,824] [INFO] Task started: fastANI
[2024-01-24 14:20:12,824] [INFO] Running command: fastANI --query /var/lib/cwl/stge8270223-5d1d-445c-8a23-60e8c4a4e19e/GCF_008245045.1_ASM824504v1_genomic.fna.gz --refList GCF_008245045.1_ASM824504v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008245045.1_ASM824504v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:16,995] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:17,006] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:17,006] [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_008245045.1	s__Campylobacter_D volucris	100.0	509	510	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	98.63	97.46	0.95	0.86	15	conclusive
GCF_008011665.1	s__Campylobacter_D volucris_A	94.354	437	510	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_013372105.1	s__Campylobacter_D armoricus	84.8128	424	510	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.30	98.87	0.93	0.88	11	-
GCF_013372185.1	s__Campylobacter_D lari	84.642	438	510	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_000816785.1	s__Campylobacter_D peloridis	84.0681	416	510	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	98.24	96.49	0.94	0.89	3	-
GCF_001017575.1	s__Campylobacter_D lari_C	83.8688	418	510	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	83.8497	414	510	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	83.6866	420	510	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_002179635.1	s__Campylobacter_D jejuni_C	83.6327	397	510	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_000816185.1	s__Campylobacter_D insulaenigrae	83.5345	414	510	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.29	98.72	0.96	0.93	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:17,009] [INFO] GTDB search result was written to GCF_008245045.1_ASM824504v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:17,011] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:17,017] [INFO] DFAST_QC result json was written to GCF_008245045.1_ASM824504v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:17,017] [INFO] DFAST_QC completed!
[2024-01-24 14:20:17,018] [INFO] Total running time: 0h0m31s