[2024-01-24 11:18:17,697] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:18:17,699] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:18:17,699] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f3b5738-8662-4ff1-8f13-234fc3df4bd7/dqc_reference
[2024-01-24 11:18:19,086] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:18:19,087] [INFO] Task started: Prodigal
[2024-01-24 11:18:19,087] [INFO] Running command: gunzip -c /var/lib/cwl/stg7baefd45-d775-423d-9bda-54a04ec79f58/GCF_024267655.1_ASM2426765v1_genomic.fna.gz | prodigal -d GCF_024267655.1_ASM2426765v1_genomic.fna/cds.fna -a GCF_024267655.1_ASM2426765v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:18:23,957] [INFO] Task succeeded: Prodigal
[2024-01-24 11:18:23,958] [INFO] Task started: HMMsearch
[2024-01-24 11:18:23,958] [INFO] Running command: hmmsearch --tblout GCF_024267655.1_ASM2426765v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f3b5738-8662-4ff1-8f13-234fc3df4bd7/dqc_reference/reference_markers.hmm GCF_024267655.1_ASM2426765v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:18:24,223] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:18:24,225] [INFO] Found 6/6 markers.
[2024-01-24 11:18:24,256] [INFO] Query marker FASTA was written to GCF_024267655.1_ASM2426765v1_genomic.fna/markers.fasta
[2024-01-24 11:18:24,256] [INFO] Task started: Blastn
[2024-01-24 11:18:24,256] [INFO] Running command: blastn -query GCF_024267655.1_ASM2426765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f3b5738-8662-4ff1-8f13-234fc3df4bd7/dqc_reference/reference_markers.fasta -out GCF_024267655.1_ASM2426765v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:18:24,841] [INFO] Task succeeded: Blastn
[2024-01-24 11:18:24,845] [INFO] Selected 14 target genomes.
[2024-01-24 11:18:24,846] [INFO] Target genome list was writen to GCF_024267655.1_ASM2426765v1_genomic.fna/target_genomes.txt
[2024-01-24 11:18:25,755] [INFO] Task started: fastANI
[2024-01-24 11:18:25,755] [INFO] Running command: fastANI --query /var/lib/cwl/stg7baefd45-d775-423d-9bda-54a04ec79f58/GCF_024267655.1_ASM2426765v1_genomic.fna.gz --refList GCF_024267655.1_ASM2426765v1_genomic.fna/target_genomes.txt --output GCF_024267655.1_ASM2426765v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:18:34,144] [INFO] Task succeeded: fastANI
[2024-01-24 11:18:34,144] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f3b5738-8662-4ff1-8f13-234fc3df4bd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:18:34,144] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f3b5738-8662-4ff1-8f13-234fc3df4bd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:18:34,156] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:18:34,156] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:18:34,156] [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
Poseidonibacter lekithochrous	strain=DSM 100870	GCA_013283835.1	1904463	1904463	type	True	81.7511	641	1051	95	below_threshold
Poseidonibacter lekithochrous	strain=LFT 1.7	GCA_001878855.1	1904463	1904463	type	True	81.4902	634	1051	95	below_threshold
Malaciobacter pacificus	strain=LMG 26638	GCA_004214795.1	1080223	1080223	type	True	81.0834	495	1051	95	below_threshold
Malaciobacter pacificus	strain=CGMCC 1.11011	GCA_014636355.1	1080223	1080223	type	True	80.9368	475	1051	95	below_threshold
Arcobacter ellisii	strain=LMG 26155	GCA_003544915.1	913109	913109	type	True	80.2379	469	1051	95	below_threshold
Arcobacter venerupis	strain=LMG 26156	GCA_013201665.1	1054033	1054033	type	True	80.1286	479	1051	95	below_threshold
Arcobacter acticola	strain=KCTC 52212	GCA_013177675.1	1849015	1849015	type	True	80.0884	486	1051	95	below_threshold
Halarcobacter bivalviorum	strain=LMG 26154	GCA_003346815.1	663364	663364	type	True	79.9894	446	1051	95	below_threshold
Malaciobacter mytili	strain=LMG 24559	GCA_003346775.1	603050	603050	type	True	79.8501	444	1051	95	below_threshold
Arcobacter cloacae	strain=LMG 26153	GCA_013201935.1	1054034	1054034	type	True	79.8178	483	1051	95	below_threshold
Arcobacter cloacae	strain=CECT 7834	GCA_004115805.1	1054034	1054034	type	True	79.5643	460	1051	95	below_threshold
Malaciobacter mytili	strain=CECT 7386	GCA_004116555.1	603050	603050	type	True	79.4686	435	1051	95	below_threshold
Malaciobacter molluscorum	strain=CECT 7696	GCA_003544935.1	1032072	1032072	type	True	79.1539	409	1051	95	below_threshold
Malaciobacter molluscorum	strain=F98-3	GCA_002701265.1	1032072	1032072	type	True	78.8734	396	1051	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:18:34,157] [INFO] DFAST Taxonomy check result was written to GCF_024267655.1_ASM2426765v1_genomic.fna/tc_result.tsv
[2024-01-24 11:18:34,158] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:18:34,158] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:18:34,158] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f3b5738-8662-4ff1-8f13-234fc3df4bd7/dqc_reference/checkm_data
[2024-01-24 11:18:34,159] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:18:34,191] [INFO] Task started: CheckM
[2024-01-24 11:18:34,191] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024267655.1_ASM2426765v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024267655.1_ASM2426765v1_genomic.fna/checkm_input GCF_024267655.1_ASM2426765v1_genomic.fna/checkm_result
[2024-01-24 11:18:56,091] [INFO] Task succeeded: CheckM
[2024-01-24 11:18:56,092] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:18:56,114] [INFO] ===== Completeness check finished =====
[2024-01-24 11:18:56,114] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:18:56,114] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024267655.1_ASM2426765v1_genomic.fna/markers.fasta)
[2024-01-24 11:18:56,115] [INFO] Task started: Blastn
[2024-01-24 11:18:56,115] [INFO] Running command: blastn -query GCF_024267655.1_ASM2426765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f3b5738-8662-4ff1-8f13-234fc3df4bd7/dqc_reference/reference_markers_gtdb.fasta -out GCF_024267655.1_ASM2426765v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:18:56,868] [INFO] Task succeeded: Blastn
[2024-01-24 11:18:56,873] [INFO] Selected 19 target genomes.
[2024-01-24 11:18:56,873] [INFO] Target genome list was writen to GCF_024267655.1_ASM2426765v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:18:57,634] [INFO] Task started: fastANI
[2024-01-24 11:18:57,634] [INFO] Running command: fastANI --query /var/lib/cwl/stg7baefd45-d775-423d-9bda-54a04ec79f58/GCF_024267655.1_ASM2426765v1_genomic.fna.gz --refList GCF_024267655.1_ASM2426765v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024267655.1_ASM2426765v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:19:09,298] [INFO] Task succeeded: fastANI
[2024-01-24 11:19:09,318] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:19:09,318] [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
GCA_002470185.1	s__Poseidonibacter sp002470185	82.0349	446	1051	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013283835.1	s__Poseidonibacter lekithochrous	81.8227	637	1051	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	99.16	98.33	0.97	0.93	3	-
GCF_004214795.1	s__Aliarcobacter pacificus	81.0756	499	1051	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009208075.1	s__Poseidonibacter sp009208075	80.5415	503	1051	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	99.63	99.63	0.93	0.93	3	-
GCF_001956695.1	s__Poseidonibacter parvus	80.5167	527	1051	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	98.33	98.33	0.91	0.91	2	-
GCF_003667345.1	s__Poseidonibacter antarcticus	80.3542	477	1051	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004116455.1	s__Halarcobacter sp004116455	80.3373	434	1051	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	96.86	96.86	0.84	0.84	2	-
GCA_905479135.1	s__Poseidonibacter sp905479135	80.2381	308	1051	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013201665.1	s__Aliarcobacter venerupis	80.1596	481	1051	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	100.00	100.00	0.99	0.99	2	-
GCA_018816105.1	s__Aliarcobacter sp018816105	80.0917	426	1051	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013177675.1	s__Aliarcobacter acticola	80.0284	485	1051	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004118855.1	s__Halarcobacter sp004118855	79.9033	455	1051	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001895145.1	s__Halarcobacter sp001895145	79.833	453	1051	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003346775.1	s__Malaciobacter mytili	79.8198	442	1051	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	99.45	98.91	0.96	0.92	3	-
GCF_013201935.1	s__Aliarcobacter cloacae	79.7986	481	1051	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.96	95.91	0.93	0.87	3	-
GCA_002685075.1	s__Poseidonibacter sp002685075	79.5798	430	1051	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003544935.1	s__Malaciobacter molluscorum	79.1379	405	1051	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	99.44	98.88	0.96	0.91	3	-
GCA_013215915.1	s__NORP36 sp013215915	78.8059	282	1051	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__NORP36	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004116495.1	s__Malaciobacter sp004116495	78.7671	387	1051	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:19:09,320] [INFO] GTDB search result was written to GCF_024267655.1_ASM2426765v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:19:09,321] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:19:09,324] [INFO] DFAST_QC result json was written to GCF_024267655.1_ASM2426765v1_genomic.fna/dqc_result.json
[2024-01-24 11:19:09,325] [INFO] DFAST_QC completed!
[2024-01-24 11:19:09,325] [INFO] Total running time: 0h0m52s