[2024-01-24 13:40:44,206] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:44,214] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:44,214] [INFO] DQC Reference Directory: /var/lib/cwl/stgc242cf43-40f5-4eab-a72b-85660ebcac12/dqc_reference
[2024-01-24 13:40:45,580] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:45,583] [INFO] Task started: Prodigal
[2024-01-24 13:40:45,587] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb9be39c-ebf2-4134-8d5e-e3236aedc0b8/GCF_000376325.1_ASM37632v1_genomic.fna.gz | prodigal -d GCF_000376325.1_ASM37632v1_genomic.fna/cds.fna -a GCF_000376325.1_ASM37632v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:50,074] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:50,075] [INFO] Task started: HMMsearch
[2024-01-24 13:40:50,075] [INFO] Running command: hmmsearch --tblout GCF_000376325.1_ASM37632v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc242cf43-40f5-4eab-a72b-85660ebcac12/dqc_reference/reference_markers.hmm GCF_000376325.1_ASM37632v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:50,351] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:50,353] [INFO] Found 6/6 markers.
[2024-01-24 13:40:50,376] [INFO] Query marker FASTA was written to GCF_000376325.1_ASM37632v1_genomic.fna/markers.fasta
[2024-01-24 13:40:50,376] [INFO] Task started: Blastn
[2024-01-24 13:40:50,376] [INFO] Running command: blastn -query GCF_000376325.1_ASM37632v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc242cf43-40f5-4eab-a72b-85660ebcac12/dqc_reference/reference_markers.fasta -out GCF_000376325.1_ASM37632v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:50,990] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:50,994] [INFO] Selected 7 target genomes.
[2024-01-24 13:40:50,995] [INFO] Target genome list was writen to GCF_000376325.1_ASM37632v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:51,000] [INFO] Task started: fastANI
[2024-01-24 13:40:51,001] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb9be39c-ebf2-4134-8d5e-e3236aedc0b8/GCF_000376325.1_ASM37632v1_genomic.fna.gz --refList GCF_000376325.1_ASM37632v1_genomic.fna/target_genomes.txt --output GCF_000376325.1_ASM37632v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:54,602] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:54,602] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc242cf43-40f5-4eab-a72b-85660ebcac12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:54,603] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc242cf43-40f5-4eab-a72b-85660ebcac12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:54,610] [INFO] Found 7 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:40:54,610] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:54,611] [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 curvus	strain=DSM 6644	GCA_000376325.1	200	200	suspected-type	True	100.0	648	648	95	conclusive
Campylobacter curvus	strain=FDAARGOS_1547	GCA_020736225.1	200	200	suspected-type	True	99.9999	648	648	95	conclusive
Campylobacter curvus	strain=ATCC 35224	GCA_013372125.1	200	200	suspected-type	True	99.9987	647	648	95	conclusive
Campylobacter curvus	strain=ATCC 35224	GCA_012978875.1	200	200	suspected-type	True	99.9799	637	648	95	conclusive
Campylobacter massiliensis	strain=Marseille-Q3452	GCA_014253065.1	2762557	2762557	type	True	78.5408	244	648	95	below_threshold
Campylobacter showae	strain=ATCC 51146	GCA_004803815.1	204	204	suspected-type	True	78.5273	239	648	95	below_threshold
Campylobacter concisus	strain=ATCC 33237	GCA_001298465.1	199	199	suspected-type	True	78.0329	242	648	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:54,613] [INFO] DFAST Taxonomy check result was written to GCF_000376325.1_ASM37632v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:54,613] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:54,613] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:54,614] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc242cf43-40f5-4eab-a72b-85660ebcac12/dqc_reference/checkm_data
[2024-01-24 13:40:54,615] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:54,646] [INFO] Task started: CheckM
[2024-01-24 13:40:54,646] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000376325.1_ASM37632v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000376325.1_ASM37632v1_genomic.fna/checkm_input GCF_000376325.1_ASM37632v1_genomic.fna/checkm_result
[2024-01-24 13:41:16,309] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:16,310] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:16,329] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:16,329] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:16,330] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000376325.1_ASM37632v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:16,330] [INFO] Task started: Blastn
[2024-01-24 13:41:16,331] [INFO] Running command: blastn -query GCF_000376325.1_ASM37632v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc242cf43-40f5-4eab-a72b-85660ebcac12/dqc_reference/reference_markers_gtdb.fasta -out GCF_000376325.1_ASM37632v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:17,215] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:17,220] [INFO] Selected 19 target genomes.
[2024-01-24 13:41:17,220] [INFO] Target genome list was writen to GCF_000376325.1_ASM37632v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:17,233] [INFO] Task started: fastANI
[2024-01-24 13:41:17,234] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb9be39c-ebf2-4134-8d5e-e3236aedc0b8/GCF_000376325.1_ASM37632v1_genomic.fna.gz --refList GCF_000376325.1_ASM37632v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000376325.1_ASM37632v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:24,510] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:24,533] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:24,534] [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_013372125.1	s__Campylobacter_A curvus	99.9987	647	648	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	96.39	95.49	0.91	0.89	16	conclusive
GCF_902460415.1	s__Campylobacter_A concisus_Y	78.6815	230	648	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	95.32	95.32	0.92	0.92	2	-
GCF_000466685.1	s__Campylobacter_A concisus_A	78.6154	283	648	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_002913225.1	s__Campylobacter_A concisus_J	78.5493	282	648	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_004803815.1	s__Campylobacter_A showae	78.5442	238	648	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_014253065.1	s__Campylobacter_A sp014253065	78.5086	246	648	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900699785.1	s__Campylobacter_A showae_D	78.4778	252	648	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	99.98	99.98	0.99	0.99	3	-
GCF_003048375.1	s__Campylobacter_A concisus_T	78.461	281	648	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_003048405.1	s__Campylobacter_A concisus_Q	78.4154	246	648	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	97.74	96.49	0.97	0.95	3	-
GCF_003048835.2	s__Campylobacter_A concisus_D	78.3638	273	648	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0092	97.26	95.33	0.94	0.89	6	-
GCF_900573985.1	s__Campylobacter_A showae_E	78.3417	249	648	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015230015.1	s__Campylobacter_A concisus_AF	78.3384	282	648	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018375265.1	s__Campylobacter_A concisus_AB	78.2688	178	648	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	78.2625	286	648	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_004803795.1	s__Campylobacter_A rectus	78.1432	224	648	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	97.92	96.44	0.98	0.96	4	-
GCF_002912895.1	s__Campylobacter_A concisus_G	78.1335	236	648	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	95.40	95.36	0.91	0.89	5	-
GCF_000344295.2	s__Campylobacter_A showae_B	78.1326	214	648	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000313615.1	s__Campylobacter_A showae_A	78.1253	239	648	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	96.64	96.14	0.94	0.93	5	-
GCF_018145735.1	s__Campylobacter_A sp018145735	77.6084	149	648	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	99.06	99.05	0.97	0.96	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:24,538] [INFO] GTDB search result was written to GCF_000376325.1_ASM37632v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:24,539] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:24,543] [INFO] DFAST_QC result json was written to GCF_000376325.1_ASM37632v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:24,543] [INFO] DFAST_QC completed!
[2024-01-24 13:41:24,543] [INFO] Total running time: 0h0m40s