[2024-01-24 12:25:20,201] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:25:20,204] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:25:20,204] [INFO] DQC Reference Directory: /var/lib/cwl/stg446e2d46-53b4-4a9f-97ee-403f6910ce34/dqc_reference
[2024-01-24 12:25:21,417] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:25:21,418] [INFO] Task started: Prodigal
[2024-01-24 12:25:21,419] [INFO] Running command: gunzip -c /var/lib/cwl/stg0a329d92-adda-4366-923b-2fe633d6c41a/GCF_012978755.1_ASM1297875v1_genomic.fna.gz | prodigal -d GCF_012978755.1_ASM1297875v1_genomic.fna/cds.fna -a GCF_012978755.1_ASM1297875v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:25:24,575] [INFO] Task succeeded: Prodigal
[2024-01-24 12:25:24,575] [INFO] Task started: HMMsearch
[2024-01-24 12:25:24,575] [INFO] Running command: hmmsearch --tblout GCF_012978755.1_ASM1297875v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg446e2d46-53b4-4a9f-97ee-403f6910ce34/dqc_reference/reference_markers.hmm GCF_012978755.1_ASM1297875v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:25:24,788] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:25:24,790] [INFO] Found 6/6 markers.
[2024-01-24 12:25:24,808] [INFO] Query marker FASTA was written to GCF_012978755.1_ASM1297875v1_genomic.fna/markers.fasta
[2024-01-24 12:25:24,808] [INFO] Task started: Blastn
[2024-01-24 12:25:24,809] [INFO] Running command: blastn -query GCF_012978755.1_ASM1297875v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg446e2d46-53b4-4a9f-97ee-403f6910ce34/dqc_reference/reference_markers.fasta -out GCF_012978755.1_ASM1297875v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:25,386] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:25,390] [INFO] Selected 15 target genomes.
[2024-01-24 12:25:25,391] [INFO] Target genome list was writen to GCF_012978755.1_ASM1297875v1_genomic.fna/target_genomes.txt
[2024-01-24 12:25:25,397] [INFO] Task started: fastANI
[2024-01-24 12:25:25,397] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a329d92-adda-4366-923b-2fe633d6c41a/GCF_012978755.1_ASM1297875v1_genomic.fna.gz --refList GCF_012978755.1_ASM1297875v1_genomic.fna/target_genomes.txt --output GCF_012978755.1_ASM1297875v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:25:29,886] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:29,887] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg446e2d46-53b4-4a9f-97ee-403f6910ce34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:25:29,887] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg446e2d46-53b4-4a9f-97ee-403f6910ce34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:25:29,900] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:25:29,900] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:25:29,900] [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 mucosalis	strain=ATCC 43264	GCA_012978755.1	202	202	type	True	100.0	530	531	95	conclusive
Campylobacter mucosalis	strain=ATCC 43264	GCA_013372205.1	202	202	type	True	97.0889	491	531	95	conclusive
Campylobacter anatolicus	strain=faydin-G140	GCA_018145655.1	2829105	2829105	type	True	77.8535	174	531	95	below_threshold
Campylobacter concisus	strain=ATCC 33237	GCA_001298465.1	199	199	suspected-type	True	77.4649	184	531	95	below_threshold
Campylobacter curvus	strain=DSM 6644	GCA_000376325.1	200	200	suspected-type	True	77.3751	121	531	95	below_threshold
Campylobacter curvus	strain=FDAARGOS_1547	GCA_020736225.1	200	200	suspected-type	True	77.3674	120	531	95	below_threshold
Campylobacter curvus	strain=ATCC 35224	GCA_013372125.1	200	200	suspected-type	True	77.3533	123	531	95	below_threshold
Campylobacter iguaniorum	strain=1485E	GCA_000736415.1	1244531	1244531	type	True	76.9507	75	531	95	below_threshold
Campylobacter rectus	strain=FDAARGOS_1549	GCA_020736205.1	203	203	type	True	76.7039	68	531	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:25:29,902] [INFO] DFAST Taxonomy check result was written to GCF_012978755.1_ASM1297875v1_genomic.fna/tc_result.tsv
[2024-01-24 12:25:29,903] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:25:29,903] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:25:29,903] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg446e2d46-53b4-4a9f-97ee-403f6910ce34/dqc_reference/checkm_data
[2024-01-24 12:25:29,904] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:25:29,927] [INFO] Task started: CheckM
[2024-01-24 12:25:29,927] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012978755.1_ASM1297875v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012978755.1_ASM1297875v1_genomic.fna/checkm_input GCF_012978755.1_ASM1297875v1_genomic.fna/checkm_result
[2024-01-24 12:25:46,752] [INFO] Task succeeded: CheckM
[2024-01-24 12:25:46,753] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:25:46,775] [INFO] ===== Completeness check finished =====
[2024-01-24 12:25:46,776] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:25:46,777] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012978755.1_ASM1297875v1_genomic.fna/markers.fasta)
[2024-01-24 12:25:46,777] [INFO] Task started: Blastn
[2024-01-24 12:25:46,777] [INFO] Running command: blastn -query GCF_012978755.1_ASM1297875v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg446e2d46-53b4-4a9f-97ee-403f6910ce34/dqc_reference/reference_markers_gtdb.fasta -out GCF_012978755.1_ASM1297875v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:47,644] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:47,648] [INFO] Selected 22 target genomes.
[2024-01-24 12:25:47,649] [INFO] Target genome list was writen to GCF_012978755.1_ASM1297875v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:25:47,667] [INFO] Task started: fastANI
[2024-01-24 12:25:47,668] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a329d92-adda-4366-923b-2fe633d6c41a/GCF_012978755.1_ASM1297875v1_genomic.fna.gz --refList GCF_012978755.1_ASM1297875v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012978755.1_ASM1297875v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:54,575] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:54,602] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:25:54,603] [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_013372205.1	s__Campylobacter_A mucosalis	97.0889	491	531	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	98.18	96.99	0.95	0.92	7	conclusive
GCF_003048375.1	s__Campylobacter_A concisus_T	77.837	155	531	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	95.30	95.13	0.90	0.85	33	-
GCF_004803835.1	s__Campylobacter_A sp004803835	77.7187	175	531	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	99.48	98.76	0.97	0.94	10	-
GCF_902460845.1	s__Campylobacter_A concisus_X	77.6981	168	531	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	99.79	99.67	0.94	0.93	3	-
GCA_018375265.1	s__Campylobacter_A concisus_AB	77.6939	104	531	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	95.35	95.14	0.82	0.77	23	-
GCF_003048675.2	s__Campylobacter_A concisus_F	77.679	166	531	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0092	95.49	95.08	0.92	0.88	22	-
GCA_002092835.1	s__Campylobacter_A concisus_K	77.6291	170	531	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_000466685.1	s__Campylobacter_A concisus_A	77.6193	165	531	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	95.29	95.22	0.88	0.86	5	-
GCF_002165775.1	s__Campylobacter_A concisus_E	77.5832	169	531	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002913745.1	s__Campylobacter_A concisus_R	77.575	165	531	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	95.56	95.41	0.90	0.84	18	-
GCF_003049085.1	s__Campylobacter_A concisus_H	77.558	177	531	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.031	N/A	N/A	N/A	N/A	1	-
GCF_002913945.1	s__Campylobacter_A concisus_P	77.5438	174	531	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_015679985.1	s__Campylobacter_A concisus_AC	77.5287	168	531	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0251	96.37	95.15	0.93	0.89	5	-
GCF_002022005.1	s__Campylobacter_A caledonicus	77.5067	115	531	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	99.31	99.26	0.98	0.97	3	-
GCF_002913225.1	s__Campylobacter_A concisus_J	77.4905	172	531	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	95.08	95.08	0.89	0.89	2	-
GCF_002139855.1	s__Campylobacter sp002139855	77.4874	55	531	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	98.28	98.16	0.95	0.94	4	-
GCF_001891085.1	s__Campylobacter_A concisus_O	77.4818	170	531	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	95.13	95.13	0.93	0.93	2	-
GCF_002021925.1	s__Campylobacter_A pinnipediorum	77.3948	112	531	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	98.45	97.81	0.98	0.95	8	-
GCF_000736415.1	s__Campylobacter iguaniorum	76.9507	75	531	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	98.53	97.69	0.92	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:25:54,605] [INFO] GTDB search result was written to GCF_012978755.1_ASM1297875v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:54,605] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:54,609] [INFO] DFAST_QC result json was written to GCF_012978755.1_ASM1297875v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:54,609] [INFO] DFAST_QC completed!
[2024-01-24 12:25:54,609] [INFO] Total running time: 0h0m34s