[2024-01-25 17:43:35,396] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:43:35,400] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:43:35,400] [INFO] DQC Reference Directory: /var/lib/cwl/stg7275d27e-6b49-44c0-94b7-d9dc99281e04/dqc_reference
[2024-01-25 17:43:36,510] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:43:36,515] [INFO] Task started: Prodigal
[2024-01-25 17:43:36,515] [INFO] Running command: gunzip -c /var/lib/cwl/stge782197c-4f26-40bf-a27f-683b95ee258c/GCF_013372205.1_ASM1337220v1_genomic.fna.gz | prodigal -d GCF_013372205.1_ASM1337220v1_genomic.fna/cds.fna -a GCF_013372205.1_ASM1337220v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:43:39,623] [INFO] Task succeeded: Prodigal
[2024-01-25 17:43:39,623] [INFO] Task started: HMMsearch
[2024-01-25 17:43:39,623] [INFO] Running command: hmmsearch --tblout GCF_013372205.1_ASM1337220v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7275d27e-6b49-44c0-94b7-d9dc99281e04/dqc_reference/reference_markers.hmm GCF_013372205.1_ASM1337220v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:43:39,791] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:43:39,792] [INFO] Found 6/6 markers.
[2024-01-25 17:43:39,810] [INFO] Query marker FASTA was written to GCF_013372205.1_ASM1337220v1_genomic.fna/markers.fasta
[2024-01-25 17:43:39,811] [INFO] Task started: Blastn
[2024-01-25 17:43:39,811] [INFO] Running command: blastn -query GCF_013372205.1_ASM1337220v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7275d27e-6b49-44c0-94b7-d9dc99281e04/dqc_reference/reference_markers.fasta -out GCF_013372205.1_ASM1337220v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:40,359] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:40,362] [INFO] Selected 14 target genomes.
[2024-01-25 17:43:40,363] [INFO] Target genome list was writen to GCF_013372205.1_ASM1337220v1_genomic.fna/target_genomes.txt
[2024-01-25 17:43:40,383] [INFO] Task started: fastANI
[2024-01-25 17:43:40,383] [INFO] Running command: fastANI --query /var/lib/cwl/stge782197c-4f26-40bf-a27f-683b95ee258c/GCF_013372205.1_ASM1337220v1_genomic.fna.gz --refList GCF_013372205.1_ASM1337220v1_genomic.fna/target_genomes.txt --output GCF_013372205.1_ASM1337220v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:43:45,101] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:45,101] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7275d27e-6b49-44c0-94b7-d9dc99281e04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:43:45,101] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7275d27e-6b49-44c0-94b7-d9dc99281e04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:43:45,108] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:43:45,109] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:43:45,109] [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_013372205.1	202	202	type	True	100.0	590	591	95	conclusive
Campylobacter mucosalis	strain=ATCC 43264	GCA_012978755.1	202	202	type	True	96.9718	498	591	95	conclusive
Campylobacter anatolicus	strain=faydin-G140	GCA_018145655.1	2829105	2829105	type	True	78.1524	183	591	95	below_threshold
Campylobacter curvus	strain=FDAARGOS_1547	GCA_020736225.1	200	200	suspected-type	True	77.8264	118	591	95	below_threshold
Campylobacter rectus	strain=FDAARGOS_1549	GCA_020736205.1	203	203	type	True	77.7907	72	591	95	below_threshold
Campylobacter concisus	strain=ATCC 33237	GCA_001298465.1	199	199	suspected-type	True	77.7215	178	591	95	below_threshold
Campylobacter curvus	strain=DSM 6644	GCA_000376325.1	200	200	suspected-type	True	77.7086	120	591	95	below_threshold
Campylobacter hyointestinalis subsp. lawsonii	strain=CHY5	GCA_013372165.1	91353	198	type	True	77.1762	73	591	95	below_threshold
Campylobacter hyointestinalis subsp. lawsonii	strain=CCUG 34538	GCA_008802075.1	91353	198	type	True	76.5022	69	591	95	below_threshold
Campylobacter hyointestinalis subsp. lawsonii	strain=CHY5	GCA_003289475.1	91353	198	type	True	76.4107	66	591	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:43:45,110] [INFO] DFAST Taxonomy check result was written to GCF_013372205.1_ASM1337220v1_genomic.fna/tc_result.tsv
[2024-01-25 17:43:45,111] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:43:45,111] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:43:45,111] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7275d27e-6b49-44c0-94b7-d9dc99281e04/dqc_reference/checkm_data
[2024-01-25 17:43:45,112] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:43:45,132] [INFO] Task started: CheckM
[2024-01-25 17:43:45,132] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013372205.1_ASM1337220v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013372205.1_ASM1337220v1_genomic.fna/checkm_input GCF_013372205.1_ASM1337220v1_genomic.fna/checkm_result
[2024-01-25 17:44:00,487] [INFO] Task succeeded: CheckM
[2024-01-25 17:44:00,487] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:44:00,507] [INFO] ===== Completeness check finished =====
[2024-01-25 17:44:00,507] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:44:00,508] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013372205.1_ASM1337220v1_genomic.fna/markers.fasta)
[2024-01-25 17:44:00,508] [INFO] Task started: Blastn
[2024-01-25 17:44:00,508] [INFO] Running command: blastn -query GCF_013372205.1_ASM1337220v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7275d27e-6b49-44c0-94b7-d9dc99281e04/dqc_reference/reference_markers_gtdb.fasta -out GCF_013372205.1_ASM1337220v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:01,308] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:01,311] [INFO] Selected 21 target genomes.
[2024-01-25 17:44:01,311] [INFO] Target genome list was writen to GCF_013372205.1_ASM1337220v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:44:01,328] [INFO] Task started: fastANI
[2024-01-25 17:44:01,328] [INFO] Running command: fastANI --query /var/lib/cwl/stge782197c-4f26-40bf-a27f-683b95ee258c/GCF_013372205.1_ASM1337220v1_genomic.fna.gz --refList GCF_013372205.1_ASM1337220v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013372205.1_ASM1337220v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:44:09,177] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:09,198] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:44:09,198] [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	100.0	590	591	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_002139855.1	s__Campylobacter sp002139855	78.6627	59	591	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	98.28	98.16	0.95	0.94	4	-
GCF_004803835.1	s__Campylobacter_A sp004803835	78.2586	184	591	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_018145735.1	s__Campylobacter_A sp018145735	77.9688	185	591	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	99.06	99.05	0.97	0.96	3	-
GCF_002021925.1	s__Campylobacter_A pinnipediorum	77.9632	116	591	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_013372125.1	s__Campylobacter_A curvus	77.9183	124	591	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	96.39	95.49	0.91	0.89	16	-
GCF_003048675.2	s__Campylobacter_A concisus_F	77.8942	180	591	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0092	95.49	95.08	0.92	0.88	22	-
GCF_000466685.1	s__Campylobacter_A concisus_A	77.8226	164	591	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_015679985.1	s__Campylobacter_A concisus_AC	77.7608	186	591	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_001891085.1	s__Campylobacter_A concisus_O	77.708	180	591	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_002022005.1	s__Campylobacter_A caledonicus	77.6474	125	591	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_003049085.1	s__Campylobacter_A concisus_H	77.6382	183	591	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_902460845.1	s__Campylobacter_A concisus_X	77.5875	182	591	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_002092835.1	s__Campylobacter_A concisus_K	77.5871	175	591	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_002913745.1	s__Campylobacter_A concisus_R	77.5639	169	591	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	95.56	95.41	0.90	0.84	18	-
GCA_018375265.1	s__Campylobacter_A concisus_AB	77.5023	112	591	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_013372165.1	s__Campylobacter lawsonii	77.4205	75	591	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	98.50	98.05	0.94	0.87	13	-
--------------------------------------------------------------------------------
[2024-01-25 17:44:09,199] [INFO] GTDB search result was written to GCF_013372205.1_ASM1337220v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:44:09,200] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:44:09,203] [INFO] DFAST_QC result json was written to GCF_013372205.1_ASM1337220v1_genomic.fna/dqc_result.json
[2024-01-25 17:44:09,203] [INFO] DFAST_QC completed!
[2024-01-25 17:44:09,203] [INFO] Total running time: 0h0m34s