[2024-01-24 13:51:12,005] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:51:12,007] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:51:12,007] [INFO] DQC Reference Directory: /var/lib/cwl/stg051cf0fc-cb3e-4698-84ca-fa9f60154b77/dqc_reference
[2024-01-24 13:51:13,311] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:51:13,312] [INFO] Task started: Prodigal
[2024-01-24 13:51:13,312] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ea56ad3-c3fe-4ff7-9d86-31044836648d/GCF_004323845.1_ASM432384v1_genomic.fna.gz | prodigal -d GCF_004323845.1_ASM432384v1_genomic.fna/cds.fna -a GCF_004323845.1_ASM432384v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:51:15,680] [INFO] Task succeeded: Prodigal
[2024-01-24 13:51:15,681] [INFO] Task started: HMMsearch
[2024-01-24 13:51:15,681] [INFO] Running command: hmmsearch --tblout GCF_004323845.1_ASM432384v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg051cf0fc-cb3e-4698-84ca-fa9f60154b77/dqc_reference/reference_markers.hmm GCF_004323845.1_ASM432384v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:51:15,935] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:51:15,937] [INFO] Found 6/6 markers.
[2024-01-24 13:51:15,963] [INFO] Query marker FASTA was written to GCF_004323845.1_ASM432384v1_genomic.fna/markers.fasta
[2024-01-24 13:51:15,964] [INFO] Task started: Blastn
[2024-01-24 13:51:15,964] [INFO] Running command: blastn -query GCF_004323845.1_ASM432384v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg051cf0fc-cb3e-4698-84ca-fa9f60154b77/dqc_reference/reference_markers.fasta -out GCF_004323845.1_ASM432384v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:16,582] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:16,586] [INFO] Selected 19 target genomes.
[2024-01-24 13:51:16,587] [INFO] Target genome list was writen to GCF_004323845.1_ASM432384v1_genomic.fna/target_genomes.txt
[2024-01-24 13:51:16,597] [INFO] Task started: fastANI
[2024-01-24 13:51:16,597] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ea56ad3-c3fe-4ff7-9d86-31044836648d/GCF_004323845.1_ASM432384v1_genomic.fna.gz --refList GCF_004323845.1_ASM432384v1_genomic.fna/target_genomes.txt --output GCF_004323845.1_ASM432384v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:51:22,076] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:22,076] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg051cf0fc-cb3e-4698-84ca-fa9f60154b77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:51:22,077] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg051cf0fc-cb3e-4698-84ca-fa9f60154b77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:51:22,092] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:51:22,092] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:51:22,092] [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 novaezeelandiae	strain=B423b	GCA_004323845.1	2267891	2267891	type	True	100.0	501	504	95	conclusive
Campylobacter coli	strain=LMG6440	GCA_003590975.1	195	195	type	True	80.232	305	504	95	below_threshold
Campylobacter coli	strain=CCUG 11283	GCA_008802085.1	195	195	type	True	80.107	317	504	95	below_threshold
Campylobacter jejuni subsp. jejuni	strain=ATCC 33560	GCA_000254515.2	32022	197	type	True	79.952	278	504	95	below_threshold
Campylobacter jejuni	strain=NCTC11351	GCA_001457695.1	197	197	type	True	79.9142	303	504	95	below_threshold
Campylobacter jejuni subsp. jejuni	strain=type strain: CCUG11284	GCA_905410075.1	32022	197	type	True	79.9035	298	504	95	below_threshold
Campylobacter jejuni subsp. jejuni	strain=CCUG 11284	GCA_008802045.1	32022	197	type	True	79.8881	301	504	95	below_threshold
Campylobacter coli	strain=LMG 9860	GCA_000254135.2	195	195	type	True	79.7614	284	504	95	below_threshold
Campylobacter hepaticus	strain=HV10	GCA_001687475.2	1813019	1813019	type	True	79.5051	287	504	95	below_threshold
Campylobacter aviculae	strain=MIT17-670	GCA_005406215.1	2510190	2510190	type	True	79.4752	286	504	95	below_threshold
Campylobacter bilis	strain=VicNov18	GCA_016806695.1	2691918	2691918	type	True	78.9366	243	504	95	below_threshold
Campylobacter ornithocola	strain=WBE38	GCA_001705345.1	1848766	1848766	type	True	78.6868	201	504	95	below_threshold
Campylobacter lari	strain=FDAARGOS_1101	GCA_016726265.1	201	201	type	True	78.6626	210	504	95	below_threshold
Campylobacter ornithocola	strain=LMG 29815	GCA_013201605.1	1848766	1848766	type	True	78.6478	209	504	95	below_threshold
Campylobacter lari subsp. lari	strain=LMG 8846	GCA_013372185.1	650054	201	type	True	78.6417	209	504	95	below_threshold
Campylobacter lari	strain=NCTC11352	GCA_900446615.1	201	201	type	True	78.601	210	504	95	below_threshold
Campylobacter volucris	strain=CCUG 57498	GCA_008801985.1	1031542	1031542	type	True	78.4679	230	504	95	below_threshold
Campylobacter lari subsp. lari	strain=ATCC 35221	GCA_900111465.1	650054	201	type	True	78.4656	199	504	95	below_threshold
Campylobacter volucris	strain=LMG 24380	GCA_008245045.1	1031542	1031542	type	True	78.4604	229	504	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:51:22,094] [INFO] DFAST Taxonomy check result was written to GCF_004323845.1_ASM432384v1_genomic.fna/tc_result.tsv
[2024-01-24 13:51:22,095] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:51:22,095] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:51:22,095] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg051cf0fc-cb3e-4698-84ca-fa9f60154b77/dqc_reference/checkm_data
[2024-01-24 13:51:22,096] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:51:22,114] [INFO] Task started: CheckM
[2024-01-24 13:51:22,115] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004323845.1_ASM432384v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004323845.1_ASM432384v1_genomic.fna/checkm_input GCF_004323845.1_ASM432384v1_genomic.fna/checkm_result
[2024-01-24 13:51:37,947] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:37,949] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:37,969] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:37,969] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:37,970] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004323845.1_ASM432384v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:37,970] [INFO] Task started: Blastn
[2024-01-24 13:51:37,970] [INFO] Running command: blastn -query GCF_004323845.1_ASM432384v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg051cf0fc-cb3e-4698-84ca-fa9f60154b77/dqc_reference/reference_markers_gtdb.fasta -out GCF_004323845.1_ASM432384v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:38,946] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:38,951] [INFO] Selected 16 target genomes.
[2024-01-24 13:51:38,951] [INFO] Target genome list was writen to GCF_004323845.1_ASM432384v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:38,966] [INFO] Task started: fastANI
[2024-01-24 13:51:38,966] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ea56ad3-c3fe-4ff7-9d86-31044836648d/GCF_004323845.1_ASM432384v1_genomic.fna.gz --refList GCF_004323845.1_ASM432384v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004323845.1_ASM432384v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:44,721] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:44,741] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:44,741] [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_004323845.1	s__Campylobacter_D novaezeelandiae	100.0	501	504	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	98.63	98.04	0.93	0.83	5	conclusive
GCF_016599045.1	s__Campylobacter_D sp016599045	90.1168	444	504	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.00	98.98	0.95	0.93	3	-
GCF_001457695.1	s__Campylobacter_D jejuni	79.8943	305	504	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	97.50	95.69	0.92	0.84	1918	-
GCA_000163995.1	s__Campylobacter_D jejuni_A	79.8777	289	504	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_000254135.1	s__Campylobacter_D coli	79.8001	282	504	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	98.69	96.32	0.91	0.84	983	-
GCF_016598935.1	s__Campylobacter_D sp016598935	79.6143	286	504	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_014305285.1	s__Campylobacter_D jejuni_D	79.5868	285	504	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001687475.2	s__Campylobacter_D hepaticus	79.5051	287	504	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_005406215.1	s__Campylobacter_D aviculae	79.4752	286	504	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_001492295.1	s__Campylobacter_D coli_B	79.35	286	504	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	98.63	98.33	0.93	0.85	59	-
GCF_009362725.1	s__Campylobacter_D hepaticus_A	78.9659	241	504	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	100.00	100.00	0.99	0.99	2	-
GCF_004378855.1	s__Campylobacter_D sp004378855	78.9386	247	504	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	78.7075	206	504	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_013372185.1	s__Campylobacter_D lari	78.6417	209	504	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_008245045.1	s__Campylobacter_D volucris	78.4845	227	504	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_004357905.1	s__Campylobacter_D lari_D	78.4826	206	504	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:44,743] [INFO] GTDB search result was written to GCF_004323845.1_ASM432384v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:44,743] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:44,747] [INFO] DFAST_QC result json was written to GCF_004323845.1_ASM432384v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:44,747] [INFO] DFAST_QC completed!
[2024-01-24 13:51:44,747] [INFO] Total running time: 0h0m33s