[2024-01-24 12:36:24,810] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:24,814] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:24,814] [INFO] DQC Reference Directory: /var/lib/cwl/stg26f49ee3-d57c-406b-b638-701792d4ddd3/dqc_reference
[2024-01-24 12:36:26,122] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:26,123] [INFO] Task started: Prodigal
[2024-01-24 12:36:26,123] [INFO] Running command: gunzip -c /var/lib/cwl/stgaae08842-69da-4e47-86ce-89f633ecf9ca/GCF_002021925.1_ASM202192v1_genomic.fna.gz | prodigal -d GCF_002021925.1_ASM202192v1_genomic.fna/cds.fna -a GCF_002021925.1_ASM202192v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:29,352] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:29,352] [INFO] Task started: HMMsearch
[2024-01-24 12:36:29,352] [INFO] Running command: hmmsearch --tblout GCF_002021925.1_ASM202192v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg26f49ee3-d57c-406b-b638-701792d4ddd3/dqc_reference/reference_markers.hmm GCF_002021925.1_ASM202192v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:29,603] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:29,605] [INFO] Found 6/6 markers.
[2024-01-24 12:36:29,625] [INFO] Query marker FASTA was written to GCF_002021925.1_ASM202192v1_genomic.fna/markers.fasta
[2024-01-24 12:36:29,625] [INFO] Task started: Blastn
[2024-01-24 12:36:29,625] [INFO] Running command: blastn -query GCF_002021925.1_ASM202192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26f49ee3-d57c-406b-b638-701792d4ddd3/dqc_reference/reference_markers.fasta -out GCF_002021925.1_ASM202192v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:30,224] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:30,228] [INFO] Selected 22 target genomes.
[2024-01-24 12:36:30,229] [INFO] Target genome list was writen to GCF_002021925.1_ASM202192v1_genomic.fna/target_genomes.txt
[2024-01-24 12:36:30,291] [INFO] Task started: fastANI
[2024-01-24 12:36:30,291] [INFO] Running command: fastANI --query /var/lib/cwl/stgaae08842-69da-4e47-86ce-89f633ecf9ca/GCF_002021925.1_ASM202192v1_genomic.fna.gz --refList GCF_002021925.1_ASM202192v1_genomic.fna/target_genomes.txt --output GCF_002021925.1_ASM202192v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:36:36,386] [INFO] Task succeeded: fastANI
[2024-01-24 12:36:36,387] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg26f49ee3-d57c-406b-b638-701792d4ddd3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:36:36,388] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg26f49ee3-d57c-406b-b638-701792d4ddd3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:36:36,415] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:36:36,415] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:36:36,416] [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 blaseri	strain=LMG 30333	GCA_013201895.1	2042961	2042961	type	True	78.6657	140	594	95	below_threshold
Campylobacter blaseri	strain=17S00004-5	GCA_003015205.1	2042961	2042961	type	True	78.4368	137	594	95	below_threshold
Campylobacter mucosalis	strain=ATCC 43264	GCA_013372205.1	202	202	type	True	78.0754	123	594	95	below_threshold
Campylobacter lari	strain=NCTC11352	GCA_900446615.1	201	201	type	True	77.9914	68	594	95	below_threshold
Campylobacter concisus	strain=ATCC 33237	GCA_001298465.1	199	199	suspected-type	True	77.8516	97	594	95	below_threshold
Campylobacter lari subsp. lari	strain=LMG 8846	GCA_013372185.1	650054	201	type	True	77.7615	68	594	95	below_threshold
Campylobacter lari	strain=FDAARGOS_1101	GCA_016726265.1	201	201	type	True	77.5742	69	594	95	below_threshold
Campylobacter mucosalis	strain=ATCC 43264	GCA_012978755.1	202	202	type	True	77.5428	117	594	95	below_threshold
Campylobacter anatolicus	strain=faydin-G140	GCA_018145655.1	2829105	2829105	type	True	77.4598	117	594	95	below_threshold
Campylobacter peloridis	strain=LMG 23910	GCA_000816785.1	488546	488546	type	True	77.3124	81	594	95	below_threshold
Campylobacter hyointestinalis subsp. lawsonii	strain=CHY5	GCA_013372165.1	91353	198	type	True	77.269	93	594	95	below_threshold
Campylobacter hyointestinalis subsp. hyointestinalis	strain=CCUG 14169	GCA_013372145.1	91352	198	type	True	77.231	78	594	95	below_threshold
Campylobacter hyointestinalis	strain=NCTC11608	GCA_900460765.1	198	198	type	True	77.1953	79	594	95	below_threshold
Campylobacter avium	strain=LMG 24591	GCA_002238335.1	522485	522485	type	True	76.9364	62	594	95	below_threshold
Campylobacter hyointestinalis subsp. hyointestinalis	strain=DSM 19053	GCA_000705275.1	91352	198	type	True	76.6039	74	594	95	below_threshold
Campylobacter lari subsp. lari	strain=ATCC 35221	GCA_900111465.1	650054	201	type	True	76.5026	63	594	95	below_threshold
Campylobacter hyointestinalis	strain=ATCC 35217	GCA_900116585.1	198	198	type	True	76.4041	78	594	95	below_threshold
Campylobacter hyointestinalis subsp. lawsonii	strain=CCUG 34538	GCA_008802075.1	91353	198	type	True	76.3495	89	594	95	below_threshold
Campylobacter hyointestinalis subsp. lawsonii	strain=CHY5	GCA_003289475.1	91353	198	type	True	76.1734	84	594	95	below_threshold
Halarcobacter ebronensis	strain=LMG 27922	GCA_013201825.1	1462615	1462615	type	True	75.859	68	594	95	below_threshold
Halarcobacter ebronensis	strain=CECT 8441	GCA_004116565.1	1462615	1462615	type	True	75.0698	61	594	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:36:36,420] [INFO] DFAST Taxonomy check result was written to GCF_002021925.1_ASM202192v1_genomic.fna/tc_result.tsv
[2024-01-24 12:36:36,421] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:36:36,421] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:36:36,422] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg26f49ee3-d57c-406b-b638-701792d4ddd3/dqc_reference/checkm_data
[2024-01-24 12:36:36,423] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:36:36,446] [INFO] Task started: CheckM
[2024-01-24 12:36:36,446] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002021925.1_ASM202192v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002021925.1_ASM202192v1_genomic.fna/checkm_input GCF_002021925.1_ASM202192v1_genomic.fna/checkm_result
[2024-01-24 12:36:53,759] [INFO] Task succeeded: CheckM
[2024-01-24 12:36:53,761] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:36:53,784] [INFO] ===== Completeness check finished =====
[2024-01-24 12:36:53,785] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:36:53,785] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002021925.1_ASM202192v1_genomic.fna/markers.fasta)
[2024-01-24 12:36:53,786] [INFO] Task started: Blastn
[2024-01-24 12:36:53,786] [INFO] Running command: blastn -query GCF_002021925.1_ASM202192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26f49ee3-d57c-406b-b638-701792d4ddd3/dqc_reference/reference_markers_gtdb.fasta -out GCF_002021925.1_ASM202192v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:54,551] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:54,555] [INFO] Selected 19 target genomes.
[2024-01-24 12:36:54,555] [INFO] Target genome list was writen to GCF_002021925.1_ASM202192v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:36:54,581] [INFO] Task started: fastANI
[2024-01-24 12:36:54,582] [INFO] Running command: fastANI --query /var/lib/cwl/stgaae08842-69da-4e47-86ce-89f633ecf9ca/GCF_002021925.1_ASM202192v1_genomic.fna.gz --refList GCF_002021925.1_ASM202192v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002021925.1_ASM202192v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:37:00,494] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:00,508] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:37:00,508] [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_002021925.1	s__Campylobacter_A pinnipediorum	100.0	593	594	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	98.45	97.81	0.98	0.95	8	conclusive
GCF_002022005.1	s__Campylobacter_A caledonicus	94.704	536	594	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_013201895.1	s__Campylobacter_B blaseri	78.6839	140	594	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003048775.2	s__Campylobacter_A concisus_I	77.976	95	594	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.031	96.12	95.05	0.94	0.90	9	-
GCF_013372205.1	s__Campylobacter_A mucosalis	77.9651	122	594	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	98.18	96.99	0.95	0.92	7	-
GCF_004803835.1	s__Campylobacter_A sp004803835	77.8242	134	594	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_015679985.1	s__Campylobacter_A concisus_AC	77.6832	97	594	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0251	96.37	95.15	0.93	0.89	5	-
GCA_002092835.1	s__Campylobacter_A concisus_K	77.6075	92	594	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_013201975.1	s__Campylobacter_A sp013201975	77.5203	83	594	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	96.07	96.03	0.84	0.80	3	-
GCF_013372185.1	s__Campylobacter_D lari	77.4822	66	594	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_000816785.1	s__Campylobacter_D peloridis	77.4614	81	594	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_018145735.1	s__Campylobacter_A sp018145735	77.4392	114	594	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_000466745.1	s__Campylobacter_A concisus_B	77.3638	94	594	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0271	95.14	95.05	0.90	0.88	19	-
GCF_902460845.1	s__Campylobacter_A concisus_X	77.3271	93	594	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	99.79	99.67	0.94	0.93	3	-
GCF_013372145.1	s__Campylobacter hyointestinalis	77.3069	78	594	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	98.64	97.83	0.93	0.88	41	-
GCF_013372165.1	s__Campylobacter lawsonii	77.04	93	594	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	98.50	98.05	0.94	0.87	13	-
GCF_004357905.1	s__Campylobacter_D lari_D	76.9725	57	594	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 12:37:00,510] [INFO] GTDB search result was written to GCF_002021925.1_ASM202192v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:37:00,510] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:37:00,515] [INFO] DFAST_QC result json was written to GCF_002021925.1_ASM202192v1_genomic.fna/dqc_result.json
[2024-01-24 12:37:00,515] [INFO] DFAST_QC completed!
[2024-01-24 12:37:00,515] [INFO] Total running time: 0h0m36s