[2023-06-08 02:08:40,697] [INFO] DFAST_QC pipeline started.
[2023-06-08 02:08:40,701] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 02:08:40,701] [INFO] DQC Reference Directory: /var/lib/cwl/stg01bc40bd-4c02-45de-810f-4bfad027ed87/dqc_reference
[2023-06-08 02:08:42,426] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 02:08:42,427] [INFO] Task started: Prodigal
[2023-06-08 02:08:42,428] [INFO] Running command: gunzip -c /var/lib/cwl/stgdaf31298-1eb5-4604-a252-fa4095b2deb3/GCA_945923685.1_SRR11489748_bin.72_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945923685.1_SRR11489748_bin.72_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945923685.1_SRR11489748_bin.72_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 02:08:44,301] [INFO] Task succeeded: Prodigal
[2023-06-08 02:08:44,301] [INFO] Task started: HMMsearch
[2023-06-08 02:08:44,301] [INFO] Running command: hmmsearch --tblout GCA_945923685.1_SRR11489748_bin.72_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg01bc40bd-4c02-45de-810f-4bfad027ed87/dqc_reference/reference_markers.hmm GCA_945923685.1_SRR11489748_bin.72_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 02:08:44,514] [INFO] Task succeeded: HMMsearch
[2023-06-08 02:08:44,516] [INFO] Found 6/6 markers.
[2023-06-08 02:08:44,537] [INFO] Query marker FASTA was written to GCA_945923685.1_SRR11489748_bin.72_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 02:08:44,537] [INFO] Task started: Blastn
[2023-06-08 02:08:44,537] [INFO] Running command: blastn -query GCA_945923685.1_SRR11489748_bin.72_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg01bc40bd-4c02-45de-810f-4bfad027ed87/dqc_reference/reference_markers.fasta -out GCA_945923685.1_SRR11489748_bin.72_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 02:08:45,147] [INFO] Task succeeded: Blastn
[2023-06-08 02:08:45,151] [INFO] Selected 10 target genomes.
[2023-06-08 02:08:45,152] [INFO] Target genome list was writen to GCA_945923685.1_SRR11489748_bin.72_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 02:08:45,153] [INFO] Task started: fastANI
[2023-06-08 02:08:45,153] [INFO] Running command: fastANI --query /var/lib/cwl/stgdaf31298-1eb5-4604-a252-fa4095b2deb3/GCA_945923685.1_SRR11489748_bin.72_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945923685.1_SRR11489748_bin.72_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945923685.1_SRR11489748_bin.72_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 02:08:47,896] [INFO] Task succeeded: fastANI
[2023-06-08 02:08:47,897] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg01bc40bd-4c02-45de-810f-4bfad027ed87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 02:08:47,897] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg01bc40bd-4c02-45de-810f-4bfad027ed87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 02:08:47,906] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2023-06-08 02:08:47,907] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-08 02:08:47,907] [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 lanienae	strain=NCTC 13004	GCA_002139935.1	75658	75658	type	True	95.8386	269	295	95	conclusive
Campylobacter hyointestinalis subsp. lawsonii	strain=CHY5	GCA_003289475.1	91353	198	type	True	82.0272	119	295	95	below_threshold
Campylobacter hyointestinalis subsp. lawsonii	strain=CCUG 34538	GCA_008802075.1	91353	198	type	True	81.9198	122	295	95	below_threshold
Campylobacter hyointestinalis subsp. lawsonii	strain=CHY5	GCA_013372165.1	91353	198	type	True	81.8002	125	295	95	below_threshold
Campylobacter hyointestinalis subsp. hyointestinalis	strain=DSM 19053	GCA_000705275.1	91352	198	type	True	78.3674	93	295	95	below_threshold
Campylobacter iguaniorum	strain=1485E	GCA_000736415.1	1244531	1244531	type	True	77.7731	87	295	95	below_threshold
Campylobacter fetus subsp. venerealis	strain=NCTC 10354	GCA_008271385.1	32020	196	type	True	77.7391	73	295	95	below_threshold
Campylobacter fetus subsp. fetus	strain=NCTC10842	GCA_900475935.1	32019	196	type	True	77.6983	75	295	95	below_threshold
Campylobacter fetus subsp. fetus	strain=CCUG 6823 AT	GCA_008693125.1	32019	196	type	True	77.6041	76	295	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 02:08:47,909] [INFO] DFAST Taxonomy check result was written to GCA_945923685.1_SRR11489748_bin.72_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 02:08:47,909] [INFO] ===== Taxonomy check completed =====
[2023-06-08 02:08:47,909] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 02:08:47,910] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg01bc40bd-4c02-45de-810f-4bfad027ed87/dqc_reference/checkm_data
[2023-06-08 02:08:47,911] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 02:08:47,925] [INFO] Task started: CheckM
[2023-06-08 02:08:47,925] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945923685.1_SRR11489748_bin.72_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945923685.1_SRR11489748_bin.72_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945923685.1_SRR11489748_bin.72_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 02:09:03,310] [INFO] Task succeeded: CheckM
[2023-06-08 02:09:03,312] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.62%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-08 02:09:03,336] [INFO] ===== Completeness check finished =====
[2023-06-08 02:09:03,337] [INFO] ===== Start GTDB Search =====
[2023-06-08 02:09:03,337] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945923685.1_SRR11489748_bin.72_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 02:09:03,338] [INFO] Task started: Blastn
[2023-06-08 02:09:03,338] [INFO] Running command: blastn -query GCA_945923685.1_SRR11489748_bin.72_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg01bc40bd-4c02-45de-810f-4bfad027ed87/dqc_reference/reference_markers_gtdb.fasta -out GCA_945923685.1_SRR11489748_bin.72_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 02:09:04,138] [INFO] Task succeeded: Blastn
[2023-06-08 02:09:04,143] [INFO] Selected 7 target genomes.
[2023-06-08 02:09:04,143] [INFO] Target genome list was writen to GCA_945923685.1_SRR11489748_bin.72_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 02:09:04,147] [INFO] Task started: fastANI
[2023-06-08 02:09:04,147] [INFO] Running command: fastANI --query /var/lib/cwl/stgdaf31298-1eb5-4604-a252-fa4095b2deb3/GCA_945923685.1_SRR11489748_bin.72_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945923685.1_SRR11489748_bin.72_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945923685.1_SRR11489748_bin.72_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 02:09:06,468] [INFO] Task succeeded: fastANI
[2023-06-08 02:09:06,483] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 02:09:06,483] [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_002139935.1	s__Campylobacter lanienae	95.8386	269	295	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	97.68	97.32	0.93	0.87	30	conclusive
GCF_002139915.1	s__Campylobacter sp002139915	88.9218	248	295	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	97.90	97.72	0.92	0.90	37	-
GCF_002139855.1	s__Campylobacter sp002139855	86.2312	260	295	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	98.28	98.16	0.95	0.94	4	-
GCF_002139875.1	s__Campylobacter sp002139875	82.7099	235	295	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	97.96	97.26	0.92	0.83	16	-
GCA_017506845.1	s__Campylobacter sp017506845	81.8256	178	295	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	97.29	97.15	0.81	0.79	3	-
GCF_013372165.1	s__Campylobacter lawsonii	81.8002	125	295	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	98.50	98.05	0.94	0.87	13	-
GCA_017646085.1	s__Campylobacter sp017646085	81.1314	198	295	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 02:09:06,485] [INFO] GTDB search result was written to GCA_945923685.1_SRR11489748_bin.72_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 02:09:06,486] [INFO] ===== GTDB Search completed =====
[2023-06-08 02:09:06,490] [INFO] DFAST_QC result json was written to GCA_945923685.1_SRR11489748_bin.72_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 02:09:06,491] [INFO] DFAST_QC completed!
[2023-06-08 02:09:06,491] [INFO] Total running time: 0h0m26s