[2024-01-24 13:31:30,018] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:30,020] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:30,021] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0efdf44-4233-4bb6-a268-b6f5374c825e/dqc_reference
[2024-01-24 13:31:31,252] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:31,253] [INFO] Task started: Prodigal
[2024-01-24 13:31:31,253] [INFO] Running command: gunzip -c /var/lib/cwl/stgc9263b5f-6b31-482a-9e3a-edccdf4a6d21/GCF_014253065.1_ASM1425306v1_genomic.fna.gz | prodigal -d GCF_014253065.1_ASM1425306v1_genomic.fna/cds.fna -a GCF_014253065.1_ASM1425306v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:36,075] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:36,076] [INFO] Task started: HMMsearch
[2024-01-24 13:31:36,076] [INFO] Running command: hmmsearch --tblout GCF_014253065.1_ASM1425306v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0efdf44-4233-4bb6-a268-b6f5374c825e/dqc_reference/reference_markers.hmm GCF_014253065.1_ASM1425306v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:36,319] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:36,321] [INFO] Found 6/6 markers.
[2024-01-24 13:31:36,347] [INFO] Query marker FASTA was written to GCF_014253065.1_ASM1425306v1_genomic.fna/markers.fasta
[2024-01-24 13:31:36,348] [INFO] Task started: Blastn
[2024-01-24 13:31:36,348] [INFO] Running command: blastn -query GCF_014253065.1_ASM1425306v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0efdf44-4233-4bb6-a268-b6f5374c825e/dqc_reference/reference_markers.fasta -out GCF_014253065.1_ASM1425306v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:36,961] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:36,965] [INFO] Selected 6 target genomes.
[2024-01-24 13:31:36,966] [INFO] Target genome list was writen to GCF_014253065.1_ASM1425306v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:36,975] [INFO] Task started: fastANI
[2024-01-24 13:31:36,975] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9263b5f-6b31-482a-9e3a-edccdf4a6d21/GCF_014253065.1_ASM1425306v1_genomic.fna.gz --refList GCF_014253065.1_ASM1425306v1_genomic.fna/target_genomes.txt --output GCF_014253065.1_ASM1425306v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:31:40,319] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:40,319] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0efdf44-4233-4bb6-a268-b6f5374c825e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:31:40,320] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0efdf44-4233-4bb6-a268-b6f5374c825e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:31:40,326] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:31:40,326] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:31:40,326] [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 massiliensis	strain=Marseille-Q3452	GCA_014253065.1	2762557	2762557	type	True	100.0	747	749	95	conclusive
Campylobacter showae	strain=ATCC 51146	GCA_004803815.1	204	204	suspected-type	True	92.4533	604	749	95	below_threshold
Campylobacter rectus	strain=ATCC 33238	GCA_004803795.1	203	203	type	True	90.3765	606	749	95	below_threshold
Campylobacter rectus	strain=FDAARGOS_1549	GCA_020736205.1	203	203	type	True	90.2672	613	749	95	below_threshold
Campylobacter gracilis	strain=NCTC12738	GCA_900446335.1	824	824	type	True	80.6283	180	749	95	below_threshold
Campylobacter curvus	strain=DSM 6644	GCA_000376325.1	200	200	suspected-type	True	78.397	246	749	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:31:40,328] [INFO] DFAST Taxonomy check result was written to GCF_014253065.1_ASM1425306v1_genomic.fna/tc_result.tsv
[2024-01-24 13:31:40,328] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:31:40,328] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:31:40,329] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0efdf44-4233-4bb6-a268-b6f5374c825e/dqc_reference/checkm_data
[2024-01-24 13:31:40,329] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:31:40,354] [INFO] Task started: CheckM
[2024-01-24 13:31:40,354] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014253065.1_ASM1425306v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014253065.1_ASM1425306v1_genomic.fna/checkm_input GCF_014253065.1_ASM1425306v1_genomic.fna/checkm_result
[2024-01-24 13:32:01,595] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:01,596] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:01,617] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:01,617] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:01,618] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014253065.1_ASM1425306v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:01,618] [INFO] Task started: Blastn
[2024-01-24 13:32:01,618] [INFO] Running command: blastn -query GCF_014253065.1_ASM1425306v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0efdf44-4233-4bb6-a268-b6f5374c825e/dqc_reference/reference_markers_gtdb.fasta -out GCF_014253065.1_ASM1425306v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:02,470] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:02,473] [INFO] Selected 8 target genomes.
[2024-01-24 13:32:02,474] [INFO] Target genome list was writen to GCF_014253065.1_ASM1425306v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:02,480] [INFO] Task started: fastANI
[2024-01-24 13:32:02,480] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9263b5f-6b31-482a-9e3a-edccdf4a6d21/GCF_014253065.1_ASM1425306v1_genomic.fna.gz --refList GCF_014253065.1_ASM1425306v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014253065.1_ASM1425306v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:07,567] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:07,582] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:07,582] [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_014253065.1	s__Campylobacter_A sp014253065	100.0	748	749	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900699785.1	s__Campylobacter_A showae_D	93.958	634	749	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	99.98	99.98	0.99	0.99	3	-
GCF_900573985.1	s__Campylobacter_A showae_E	92.6554	638	749	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000344295.2	s__Campylobacter_A showae_B	92.625	517	749	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004803815.1	s__Campylobacter_A showae	92.4525	604	749	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000313615.1	s__Campylobacter_A showae_A	91.5216	587	749	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	96.64	96.14	0.94	0.93	5	-
GCA_905372745.1	s__Campylobacter_A sp905372745	91.1924	560	749	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004803795.1	s__Campylobacter_A rectus	90.376	606	749	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	97.92	96.44	0.98	0.96	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:07,584] [INFO] GTDB search result was written to GCF_014253065.1_ASM1425306v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:07,585] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:07,588] [INFO] DFAST_QC result json was written to GCF_014253065.1_ASM1425306v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:07,588] [INFO] DFAST_QC completed!
[2024-01-24 13:32:07,588] [INFO] Total running time: 0h0m38s