[2024-01-24 13:40:34,842] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:34,853] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:34,854] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf930525-cdd2-4001-9705-62ff459684ce/dqc_reference
[2024-01-24 13:40:36,410] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:36,411] [INFO] Task started: Prodigal
[2024-01-24 13:40:36,412] [INFO] Running command: gunzip -c /var/lib/cwl/stgffa6acda-b280-438e-9231-bb1828338c01/GCF_013177655.1_ASM1317765v1_genomic.fna.gz | prodigal -d GCF_013177655.1_ASM1317765v1_genomic.fna/cds.fna -a GCF_013177655.1_ASM1317765v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:39,622] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:39,623] [INFO] Task started: HMMsearch
[2024-01-24 13:40:39,623] [INFO] Running command: hmmsearch --tblout GCF_013177655.1_ASM1317765v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf930525-cdd2-4001-9705-62ff459684ce/dqc_reference/reference_markers.hmm GCF_013177655.1_ASM1317765v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:39,922] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:39,923] [INFO] Found 6/6 markers.
[2024-01-24 13:40:39,943] [INFO] Query marker FASTA was written to GCF_013177655.1_ASM1317765v1_genomic.fna/markers.fasta
[2024-01-24 13:40:39,944] [INFO] Task started: Blastn
[2024-01-24 13:40:39,944] [INFO] Running command: blastn -query GCF_013177655.1_ASM1317765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf930525-cdd2-4001-9705-62ff459684ce/dqc_reference/reference_markers.fasta -out GCF_013177655.1_ASM1317765v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:40,567] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:40,571] [INFO] Selected 19 target genomes.
[2024-01-24 13:40:40,571] [INFO] Target genome list was writen to GCF_013177655.1_ASM1317765v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:40,582] [INFO] Task started: fastANI
[2024-01-24 13:40:40,582] [INFO] Running command: fastANI --query /var/lib/cwl/stgffa6acda-b280-438e-9231-bb1828338c01/GCF_013177655.1_ASM1317765v1_genomic.fna.gz --refList GCF_013177655.1_ASM1317765v1_genomic.fna/target_genomes.txt --output GCF_013177655.1_ASM1317765v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:46,397] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:46,397] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf930525-cdd2-4001-9705-62ff459684ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:46,397] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf930525-cdd2-4001-9705-62ff459684ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:46,415] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:40:46,415] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:46,415] [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 canadensis	strain=LMG 24001	GCA_013177655.1	449520	449520	type	True	100.0	638	641	95	conclusive
Campylobacter jejuni subsp. jejuni	strain=ATCC 33560	GCA_000254515.2	32022	197	type	True	79.3969	105	641	95	below_threshold
Campylobacter jejuni subsp. jejuni	strain=CCUG 11284	GCA_008802045.1	32022	197	type	True	79.1699	116	641	95	below_threshold
Campylobacter lari subsp. concheus	strain=LMG 21009	GCA_008245025.1	488545	201	type	True	77.8556	101	641	95	below_threshold
Campylobacter armoricus	strain=CCUG 73571	GCA_013372105.1	2505970	2505970	type	True	77.8541	127	641	95	below_threshold
Campylobacter hepaticus	strain=HV10	GCA_001687475.2	1813019	1813019	type	True	77.7446	117	641	95	below_threshold
Campylobacter subantarcticus	strain=LMG 24377	GCA_000816305.1	497724	497724	type	True	77.6785	103	641	95	below_threshold
Campylobacter volucris	strain=LMG 24380	GCA_008245045.1	1031542	1031542	type	True	77.671	131	641	95	below_threshold
Campylobacter peloridis	strain=LMG 23910	GCA_000816785.1	488546	488546	type	True	77.6036	130	641	95	below_threshold
Campylobacter armoricus	strain=CA656	GCA_006176165.1	2505970	2505970	type	True	77.5286	114	641	95	below_threshold
Campylobacter corcagiensis	strain=LMG 27932	GCA_013201645.1	1448857	1448857	type	True	77.4774	52	641	95	below_threshold
Campylobacter lari subsp. concheus	strain=CCUG 55786	GCA_008802005.1	488545	201	type	True	77.3595	97	641	95	below_threshold
Campylobacter volucris	strain=CCUG 57498	GCA_008801985.1	1031542	1031542	type	True	77.1184	129	641	95	below_threshold
Campylobacter aviculae	strain=MIT17-670	GCA_005406215.1	2510190	2510190	type	True	77.0117	92	641	95	below_threshold
Campylobacter taeniopygiae	strain=MIT10-5678	GCA_005406225.1	2510188	2510188	type	True	76.9181	97	641	95	below_threshold
Campylobacter novaezeelandiae	strain=B423b	GCA_004323845.1	2267891	2267891	type	True	76.7812	116	641	95	below_threshold
Arcobacter vandammei	strain=R-73987	GCA_016106035.1	2782243	2782243	type	True	76.0087	59	641	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:46,418] [INFO] DFAST Taxonomy check result was written to GCF_013177655.1_ASM1317765v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:46,419] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:46,420] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:46,420] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf930525-cdd2-4001-9705-62ff459684ce/dqc_reference/checkm_data
[2024-01-24 13:40:46,421] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:46,459] [INFO] Task started: CheckM
[2024-01-24 13:40:46,459] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013177655.1_ASM1317765v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013177655.1_ASM1317765v1_genomic.fna/checkm_input GCF_013177655.1_ASM1317765v1_genomic.fna/checkm_result
[2024-01-24 13:41:03,913] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:03,914] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:03,934] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:03,934] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:03,935] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013177655.1_ASM1317765v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:03,935] [INFO] Task started: Blastn
[2024-01-24 13:41:03,935] [INFO] Running command: blastn -query GCF_013177655.1_ASM1317765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf930525-cdd2-4001-9705-62ff459684ce/dqc_reference/reference_markers_gtdb.fasta -out GCF_013177655.1_ASM1317765v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:04,786] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:04,790] [INFO] Selected 19 target genomes.
[2024-01-24 13:41:04,790] [INFO] Target genome list was writen to GCF_013177655.1_ASM1317765v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:04,809] [INFO] Task started: fastANI
[2024-01-24 13:41:04,809] [INFO] Running command: fastANI --query /var/lib/cwl/stgffa6acda-b280-438e-9231-bb1828338c01/GCF_013177655.1_ASM1317765v1_genomic.fna.gz --refList GCF_013177655.1_ASM1317765v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013177655.1_ASM1317765v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:11,174] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:11,185] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:11,185] [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_013177655.1	s__Campylobacter_E canadensis	100.0	638	641	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018501205.1	s__Campylobacter_E sp018501205	79.3712	288	641	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_E	95.0	98.57	98.53	0.90	0.87	4	-
GCF_001457695.1	s__Campylobacter_D jejuni	79.3047	126	641	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	97.50	95.69	0.92	0.84	1918	-
GCF_001687475.2	s__Campylobacter_D hepaticus	77.9422	118	641	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.94	99.56	0.99	0.97	33	-
GCF_013372105.1	s__Campylobacter_D armoricus	77.9079	127	641	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_000816785.1	s__Campylobacter_D peloridis	77.6404	129	641	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_000816245.1	s__Campylobacter_D sp000816245	77.6163	117	641	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000163995.1	s__Campylobacter_D jejuni_A	77.5602	113	641	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_008245045.1	s__Campylobacter_D volucris	77.4931	131	641	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	98.63	97.46	0.95	0.86	15	-
GCF_013201645.1	s__Campylobacter_B corcagiensis	77.486	50	641	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B	95.0	99.99	99.99	1.00	1.00	3	-
GCF_002179635.1	s__Campylobacter_D jejuni_C	77.3568	105	641	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_016598935.1	s__Campylobacter_D sp016598935	76.9215	115	641	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_008633915.1	s__Campylobacter_D sp008633915	76.5166	86	641	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.75	99.64	0.99	0.99	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:11,187] [INFO] GTDB search result was written to GCF_013177655.1_ASM1317765v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:11,187] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:11,194] [INFO] DFAST_QC result json was written to GCF_013177655.1_ASM1317765v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:11,195] [INFO] DFAST_QC completed!
[2024-01-24 13:41:11,195] [INFO] Total running time: 0h0m36s