[2024-01-24 13:47:11,904] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:47:11,907] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:47:11,907] [INFO] DQC Reference Directory: /var/lib/cwl/stg23a01c66-9361-497e-a1f8-4d3945b7a5ae/dqc_reference
[2024-01-24 13:47:13,323] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:47:13,324] [INFO] Task started: Prodigal
[2024-01-24 13:47:13,325] [INFO] Running command: gunzip -c /var/lib/cwl/stgc26020de-94d2-4ea1-907e-47f6397cde3a/GCF_000155475.1_ASM15547v1_genomic.fna.gz | prodigal -d GCF_000155475.1_ASM15547v1_genomic.fna/cds.fna -a GCF_000155475.1_ASM15547v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:47:18,683] [INFO] Task succeeded: Prodigal
[2024-01-24 13:47:18,683] [INFO] Task started: HMMsearch
[2024-01-24 13:47:18,683] [INFO] Running command: hmmsearch --tblout GCF_000155475.1_ASM15547v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg23a01c66-9361-497e-a1f8-4d3945b7a5ae/dqc_reference/reference_markers.hmm GCF_000155475.1_ASM15547v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:47:18,917] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:47:18,919] [INFO] Found 6/6 markers.
[2024-01-24 13:47:18,945] [INFO] Query marker FASTA was written to GCF_000155475.1_ASM15547v1_genomic.fna/markers.fasta
[2024-01-24 13:47:18,946] [INFO] Task started: Blastn
[2024-01-24 13:47:18,946] [INFO] Running command: blastn -query GCF_000155475.1_ASM15547v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg23a01c66-9361-497e-a1f8-4d3945b7a5ae/dqc_reference/reference_markers.fasta -out GCF_000155475.1_ASM15547v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:19,555] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:19,558] [INFO] Selected 5 target genomes.
[2024-01-24 13:47:19,559] [INFO] Target genome list was writen to GCF_000155475.1_ASM15547v1_genomic.fna/target_genomes.txt
[2024-01-24 13:47:19,563] [INFO] Task started: fastANI
[2024-01-24 13:47:19,563] [INFO] Running command: fastANI --query /var/lib/cwl/stgc26020de-94d2-4ea1-907e-47f6397cde3a/GCF_000155475.1_ASM15547v1_genomic.fna.gz --refList GCF_000155475.1_ASM15547v1_genomic.fna/target_genomes.txt --output GCF_000155475.1_ASM15547v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:22,315] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:22,316] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg23a01c66-9361-497e-a1f8-4d3945b7a5ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:22,316] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg23a01c66-9361-497e-a1f8-4d3945b7a5ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:22,326] [INFO] Found 5 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:47:22,327] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:22,327] [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
Helicobacter cinaedi	strain=CCUG 18818	GCA_000155475.1	213	213	type	True	99.9999	716	719	95	conclusive
Helicobacter cinaedi	strain=DSM 5359	GCA_017979495.1	213	213	type	True	99.9241	687	719	95	conclusive
Helicobacter cinaedi	strain=CCUG 18818	GCA_003215615.1	213	213	type	True	99.8703	638	719	95	conclusive
Helicobacter cinaedi	strain=ATCC BAA-847	GCA_000349975.1	213	213	type	True	99.8485	715	719	95	conclusive
Helicobacter labetoulli	strain=48519	GCA_003670275.1	2315333	2315333	type	True	90.3063	581	719	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:22,329] [INFO] DFAST Taxonomy check result was written to GCF_000155475.1_ASM15547v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:22,329] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:22,330] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:22,330] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg23a01c66-9361-497e-a1f8-4d3945b7a5ae/dqc_reference/checkm_data
[2024-01-24 13:47:22,332] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:22,357] [INFO] Task started: CheckM
[2024-01-24 13:47:22,357] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000155475.1_ASM15547v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000155475.1_ASM15547v1_genomic.fna/checkm_input GCF_000155475.1_ASM15547v1_genomic.fna/checkm_result
[2024-01-24 13:47:44,106] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:44,108] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:44,126] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:44,127] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:44,127] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000155475.1_ASM15547v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:44,127] [INFO] Task started: Blastn
[2024-01-24 13:47:44,128] [INFO] Running command: blastn -query GCF_000155475.1_ASM15547v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg23a01c66-9361-497e-a1f8-4d3945b7a5ae/dqc_reference/reference_markers_gtdb.fasta -out GCF_000155475.1_ASM15547v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:44,897] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:44,900] [INFO] Selected 9 target genomes.
[2024-01-24 13:47:44,901] [INFO] Target genome list was writen to GCF_000155475.1_ASM15547v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:44,911] [INFO] Task started: fastANI
[2024-01-24 13:47:44,911] [INFO] Running command: fastANI --query /var/lib/cwl/stgc26020de-94d2-4ea1-907e-47f6397cde3a/GCF_000155475.1_ASM15547v1_genomic.fna.gz --refList GCF_000155475.1_ASM15547v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000155475.1_ASM15547v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:48,984] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:48,999] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:48,999] [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_000155475.1	s__Helicobacter_C cinaedi	99.9999	716	719	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_C	95.0	99.33	98.84	0.97	0.91	38	conclusive
GCF_000765825.2	s__Helicobacter_C magdeburgensis	94.6913	584	719	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_C	95.0	96.93	95.65	0.89	0.84	5	-
GCF_003670275.1	s__Helicobacter_C labetoulli	90.3336	580	719	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000762845.2	s__Helicobacter_C japonicus	78.5538	297	719	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_C	95.0	99.98	99.98	0.99	0.99	2	-
GCA_910577135.1	s__Helicobacter_C sp910577135	78.5506	302	719	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000007905.1	s__Helicobacter_C hepaticus	78.517	282	719	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_C	95.0	98.74	98.74	0.96	0.95	3	-
GCF_000763135.2	s__Helicobacter_C jaachi	78.1362	284	719	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003364255.1	s__Helicobacter_C marmotae	77.9763	254	719	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_C	95.0	99.98	99.98	0.98	0.98	2	-
GCF_000765695.2	s__Helicobacter_D sp000765695	77.1732	53	719	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:49,001] [INFO] GTDB search result was written to GCF_000155475.1_ASM15547v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:49,002] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:49,009] [INFO] DFAST_QC result json was written to GCF_000155475.1_ASM15547v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:49,009] [INFO] DFAST_QC completed!
[2024-01-24 13:47:49,009] [INFO] Total running time: 0h0m37s