[2024-01-25 17:44:35,581] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:44:35,582] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:44:35,582] [INFO] DQC Reference Directory: /var/lib/cwl/stg5988998d-0e94-4126-966e-7061b321c0fb/dqc_reference
[2024-01-25 17:44:36,687] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:44:36,688] [INFO] Task started: Prodigal
[2024-01-25 17:44:36,688] [INFO] Running command: gunzip -c /var/lib/cwl/stgfc5387a4-1ebe-4625-93db-bdc92192164f/GCF_025950235.1_ASM2595023v1_genomic.fna.gz | prodigal -d GCF_025950235.1_ASM2595023v1_genomic.fna/cds.fna -a GCF_025950235.1_ASM2595023v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:45:18,005] [INFO] Task succeeded: Prodigal
[2024-01-25 17:45:18,005] [INFO] Task started: HMMsearch
[2024-01-25 17:45:18,005] [INFO] Running command: hmmsearch --tblout GCF_025950235.1_ASM2595023v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5988998d-0e94-4126-966e-7061b321c0fb/dqc_reference/reference_markers.hmm GCF_025950235.1_ASM2595023v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:45:18,303] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:45:18,304] [INFO] Found 6/6 markers.
[2024-01-25 17:45:18,370] [INFO] Query marker FASTA was written to GCF_025950235.1_ASM2595023v1_genomic.fna/markers.fasta
[2024-01-25 17:45:18,370] [INFO] Task started: Blastn
[2024-01-25 17:45:18,370] [INFO] Running command: blastn -query GCF_025950235.1_ASM2595023v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5988998d-0e94-4126-966e-7061b321c0fb/dqc_reference/reference_markers.fasta -out GCF_025950235.1_ASM2595023v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:45:18,934] [INFO] Task succeeded: Blastn
[2024-01-25 17:45:18,937] [INFO] Selected 17 target genomes.
[2024-01-25 17:45:18,937] [INFO] Target genome list was writen to GCF_025950235.1_ASM2595023v1_genomic.fna/target_genomes.txt
[2024-01-25 17:45:18,945] [INFO] Task started: fastANI
[2024-01-25 17:45:18,945] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc5387a4-1ebe-4625-93db-bdc92192164f/GCF_025950235.1_ASM2595023v1_genomic.fna.gz --refList GCF_025950235.1_ASM2595023v1_genomic.fna/target_genomes.txt --output GCF_025950235.1_ASM2595023v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:45:35,647] [INFO] Task succeeded: fastANI
[2024-01-25 17:45:35,647] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5988998d-0e94-4126-966e-7061b321c0fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:45:35,648] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5988998d-0e94-4126-966e-7061b321c0fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:45:35,657] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:45:35,657] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:45:35,657] [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
Luteolibacter luteus	strain=G-1-1-1	GCA_012913485.1	2728835	2728835	type	True	79.4536	808	2476	95	below_threshold
Luteolibacter ambystomatis	strain=32A	GCA_018137965.1	2824561	2824561	type	True	78.4979	460	2476	95	below_threshold
Haloferula rosea	strain=KCTC 22201	GCA_016595525.1	490093	490093	type	True	77.57	265	2476	95	below_threshold
Luteolibacter yonseiensis	strain=JCM 18052	GCA_016595465.1	1144680	1144680	type	True	77.5047	339	2476	95	below_threshold
Haloferula luteola	strain=YC6886	GCA_014201715.1	595692	595692	type	True	76.88	174	2476	95	below_threshold
Verrucomicrobium spinosum	strain=DSM 4136	GCA_000172155.1	2736	2736	type	True	76.2573	117	2476	95	below_threshold
Chthoniobacter flavus	strain=Ellin428	GCA_000173075.1	191863	191863	type	True	76.1434	115	2476	95	below_threshold
Chthoniobacter flavus	strain=DSM 22515	GCA_004341915.1	191863	191863	type	True	76.1361	112	2476	95	below_threshold
Prosthecobacter vanneervenii	strain=DSM 12252	GCA_014203095.1	48466	48466	type	True	76.1264	146	2476	95	below_threshold
Roseimicrobium gellanilyticum	strain=DSM 25532	GCA_003315205.1	748857	748857	type	True	76.0154	124	2476	95	below_threshold
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	75.54	54	2476	95	below_threshold
Chromobacterium vaccinii	strain=MWU205	GCA_000971335.1	1108595	1108595	type	True	75.2061	74	2476	95	below_threshold
Sulfidibacter corallicola	strain=M133	GCA_017498545.1	2818388	2818388	type	True	74.8379	59	2476	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:45:35,658] [INFO] DFAST Taxonomy check result was written to GCF_025950235.1_ASM2595023v1_genomic.fna/tc_result.tsv
[2024-01-25 17:45:35,659] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:45:35,659] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:45:35,659] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5988998d-0e94-4126-966e-7061b321c0fb/dqc_reference/checkm_data
[2024-01-25 17:45:35,660] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:45:35,729] [INFO] Task started: CheckM
[2024-01-25 17:45:35,729] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025950235.1_ASM2595023v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025950235.1_ASM2595023v1_genomic.fna/checkm_input GCF_025950235.1_ASM2595023v1_genomic.fna/checkm_result
[2024-01-25 17:47:26,729] [INFO] Task succeeded: CheckM
[2024-01-25 17:47:26,730] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:47:26,752] [INFO] ===== Completeness check finished =====
[2024-01-25 17:47:26,752] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:47:26,753] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025950235.1_ASM2595023v1_genomic.fna/markers.fasta)
[2024-01-25 17:47:26,754] [INFO] Task started: Blastn
[2024-01-25 17:47:26,754] [INFO] Running command: blastn -query GCF_025950235.1_ASM2595023v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5988998d-0e94-4126-966e-7061b321c0fb/dqc_reference/reference_markers_gtdb.fasta -out GCF_025950235.1_ASM2595023v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:47:27,661] [INFO] Task succeeded: Blastn
[2024-01-25 17:47:27,664] [INFO] Selected 11 target genomes.
[2024-01-25 17:47:27,664] [INFO] Target genome list was writen to GCF_025950235.1_ASM2595023v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:47:27,676] [INFO] Task started: fastANI
[2024-01-25 17:47:27,676] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc5387a4-1ebe-4625-93db-bdc92192164f/GCF_025950235.1_ASM2595023v1_genomic.fna.gz --refList GCF_025950235.1_ASM2595023v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025950235.1_ASM2595023v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:47:37,794] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:37,802] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:47:37,802] [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_002304315.1	s__Haloferula sp002304315	80.2348	628	2476	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012913485.1	s__Haloferula lutea	79.4581	808	2476	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904755.1	s__Haloferula sp014904755	79.4475	826	2476	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000739615.1	s__Haloferula sp000739615	79.3631	956	2476	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004293445.1	s__Haloferula sp004293445	78.9465	421	2476	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	99.99	99.98	0.97	0.96	4	-
GCF_018137965.1	s__Luteolibacter sp018137965	78.4896	461	2476	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003820635.1	s__Luteolibacter sp003820635	77.8884	243	2476	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871685.1	s__Luteolibacter sp016871685	77.1996	128	2476	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007126655.1	s__Luteolibacter sp007126655	76.8089	208	2476	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	99.62	99.62	0.82	0.82	2	-
GCF_011601295.1	s__Chromobacterium vaccinii_A	75.4534	57	2476	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	95.84	95.77	0.89	0.88	3	-
GCF_015831345.1	s__Ramlibacter sp015831345	75.2111	69	2476	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:47:37,804] [INFO] GTDB search result was written to GCF_025950235.1_ASM2595023v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:47:37,804] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:47:37,807] [INFO] DFAST_QC result json was written to GCF_025950235.1_ASM2595023v1_genomic.fna/dqc_result.json
[2024-01-25 17:47:37,807] [INFO] DFAST_QC completed!
[2024-01-25 17:47:37,807] [INFO] Total running time: 0h3m2s