[2024-01-24 12:21:43,713] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:43,717] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:43,717] [INFO] DQC Reference Directory: /var/lib/cwl/stg24a48d46-1469-4810-8feb-b7f14ba7ef1b/dqc_reference
[2024-01-24 12:21:45,260] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:45,262] [INFO] Task started: Prodigal
[2024-01-24 12:21:45,262] [INFO] Running command: gunzip -c /var/lib/cwl/stgf4e7e8a5-39e9-4a63-a8bb-5a6be00488f5/GCF_008245025.1_ASM824502v1_genomic.fna.gz | prodigal -d GCF_008245025.1_ASM824502v1_genomic.fna/cds.fna -a GCF_008245025.1_ASM824502v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:21:47,973] [INFO] Task succeeded: Prodigal
[2024-01-24 12:21:47,973] [INFO] Task started: HMMsearch
[2024-01-24 12:21:47,973] [INFO] Running command: hmmsearch --tblout GCF_008245025.1_ASM824502v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24a48d46-1469-4810-8feb-b7f14ba7ef1b/dqc_reference/reference_markers.hmm GCF_008245025.1_ASM824502v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:21:48,218] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:21:48,220] [INFO] Found 6/6 markers.
[2024-01-24 12:21:48,241] [INFO] Query marker FASTA was written to GCF_008245025.1_ASM824502v1_genomic.fna/markers.fasta
[2024-01-24 12:21:48,241] [INFO] Task started: Blastn
[2024-01-24 12:21:48,241] [INFO] Running command: blastn -query GCF_008245025.1_ASM824502v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24a48d46-1469-4810-8feb-b7f14ba7ef1b/dqc_reference/reference_markers.fasta -out GCF_008245025.1_ASM824502v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:21:50,140] [INFO] Task succeeded: Blastn
[2024-01-24 12:21:50,144] [INFO] Selected 8 target genomes.
[2024-01-24 12:21:50,144] [INFO] Target genome list was writen to GCF_008245025.1_ASM824502v1_genomic.fna/target_genomes.txt
[2024-01-24 12:21:50,215] [INFO] Task started: fastANI
[2024-01-24 12:21:50,215] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4e7e8a5-39e9-4a63-a8bb-5a6be00488f5/GCF_008245025.1_ASM824502v1_genomic.fna.gz --refList GCF_008245025.1_ASM824502v1_genomic.fna/target_genomes.txt --output GCF_008245025.1_ASM824502v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:21:53,462] [INFO] Task succeeded: fastANI
[2024-01-24 12:21:53,463] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24a48d46-1469-4810-8feb-b7f14ba7ef1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:21:53,463] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24a48d46-1469-4810-8feb-b7f14ba7ef1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:21:53,470] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:21:53,471] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:21:53,471] [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 lari subsp. concheus	strain=LMG 21009	GCA_008245025.1	488545	201	type	True	100.0	495	496	95	conclusive
Campylobacter lari subsp. concheus	strain=CCUG 55786	GCA_008802005.1	488545	201	type	True	99.9759	472	496	95	conclusive
Campylobacter lari subsp. lari	strain=ATCC 35221	GCA_900111465.1	650054	201	type	True	93.3959	432	496	95	below_threshold
Campylobacter lari	strain=FDAARGOS_1101	GCA_016726265.1	201	201	type	True	93.3698	450	496	95	below_threshold
Campylobacter lari	strain=NCTC11352	GCA_900446615.1	201	201	type	True	93.3275	451	496	95	below_threshold
Campylobacter ornithocola	strain=WBE38	GCA_001705345.1	1848766	1848766	type	True	90.9616	417	496	95	below_threshold
Campylobacter ornithocola	strain=LMG 29815	GCA_013201605.1	1848766	1848766	type	True	90.8807	442	496	95	below_threshold
Campylobacter subantarcticus	strain=LMG 24377	GCA_000816305.1	497724	497724	type	True	89.9567	448	496	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:21:53,474] [INFO] DFAST Taxonomy check result was written to GCF_008245025.1_ASM824502v1_genomic.fna/tc_result.tsv
[2024-01-24 12:21:53,474] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:21:53,474] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:21:53,474] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24a48d46-1469-4810-8feb-b7f14ba7ef1b/dqc_reference/checkm_data
[2024-01-24 12:21:53,475] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:21:53,496] [INFO] Task started: CheckM
[2024-01-24 12:21:53,497] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008245025.1_ASM824502v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008245025.1_ASM824502v1_genomic.fna/checkm_input GCF_008245025.1_ASM824502v1_genomic.fna/checkm_result
[2024-01-24 12:22:11,070] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:11,071] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:11,104] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:11,105] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:11,105] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008245025.1_ASM824502v1_genomic.fna/markers.fasta)
[2024-01-24 12:22:11,106] [INFO] Task started: Blastn
[2024-01-24 12:22:11,106] [INFO] Running command: blastn -query GCF_008245025.1_ASM824502v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24a48d46-1469-4810-8feb-b7f14ba7ef1b/dqc_reference/reference_markers_gtdb.fasta -out GCF_008245025.1_ASM824502v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:11,989] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:11,993] [INFO] Selected 7 target genomes.
[2024-01-24 12:22:11,994] [INFO] Target genome list was writen to GCF_008245025.1_ASM824502v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:12,000] [INFO] Task started: fastANI
[2024-01-24 12:22:12,000] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4e7e8a5-39e9-4a63-a8bb-5a6be00488f5/GCF_008245025.1_ASM824502v1_genomic.fna.gz --refList GCF_008245025.1_ASM824502v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008245025.1_ASM824502v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:22:15,023] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:15,030] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:22:15,030] [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_008245025.1	s__Campylobacter_D concheus	100.0	495	496	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.27	98.88	0.96	0.94	4	conclusive
GCF_001017575.1	s__Campylobacter_D lari_C	93.9902	447	496	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	93.6678	424	496	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_013372185.1	s__Campylobacter_D lari	93.4018	445	496	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_004357905.1	s__Campylobacter_D lari_D	92.6339	441	496	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	90.8253	444	496	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_014931215.1	s__Campylobacter_D sp003627915	87.6252	438	496	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	98.78	98.78	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:22:15,032] [INFO] GTDB search result was written to GCF_008245025.1_ASM824502v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:22:15,033] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:22:15,036] [INFO] DFAST_QC result json was written to GCF_008245025.1_ASM824502v1_genomic.fna/dqc_result.json
[2024-01-24 12:22:15,036] [INFO] DFAST_QC completed!
[2024-01-24 12:22:15,036] [INFO] Total running time: 0h0m31s