[2024-01-24 12:29:37,802] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:37,804] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:37,804] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4f22a1b-fca9-4368-81e4-08eef4f94841/dqc_reference
[2024-01-24 12:29:39,126] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:39,127] [INFO] Task started: Prodigal
[2024-01-24 12:29:39,127] [INFO] Running command: gunzip -c /var/lib/cwl/stg8470d619-fc08-4dd3-9d1d-66f4844b5666/GCF_025950085.1_ASM2595008v1_genomic.fna.gz | prodigal -d GCF_025950085.1_ASM2595008v1_genomic.fna/cds.fna -a GCF_025950085.1_ASM2595008v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:17,080] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:17,081] [INFO] Task started: HMMsearch
[2024-01-24 12:30:17,081] [INFO] Running command: hmmsearch --tblout GCF_025950085.1_ASM2595008v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4f22a1b-fca9-4368-81e4-08eef4f94841/dqc_reference/reference_markers.hmm GCF_025950085.1_ASM2595008v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:17,444] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:17,447] [INFO] Found 6/6 markers.
[2024-01-24 12:30:17,504] [INFO] Query marker FASTA was written to GCF_025950085.1_ASM2595008v1_genomic.fna/markers.fasta
[2024-01-24 12:30:17,504] [INFO] Task started: Blastn
[2024-01-24 12:30:17,504] [INFO] Running command: blastn -query GCF_025950085.1_ASM2595008v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4f22a1b-fca9-4368-81e4-08eef4f94841/dqc_reference/reference_markers.fasta -out GCF_025950085.1_ASM2595008v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:18,126] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:18,130] [INFO] Selected 18 target genomes.
[2024-01-24 12:30:18,130] [INFO] Target genome list was writen to GCF_025950085.1_ASM2595008v1_genomic.fna/target_genomes.txt
[2024-01-24 12:30:18,147] [INFO] Task started: fastANI
[2024-01-24 12:30:18,147] [INFO] Running command: fastANI --query /var/lib/cwl/stg8470d619-fc08-4dd3-9d1d-66f4844b5666/GCF_025950085.1_ASM2595008v1_genomic.fna.gz --refList GCF_025950085.1_ASM2595008v1_genomic.fna/target_genomes.txt --output GCF_025950085.1_ASM2595008v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:33,155] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:33,156] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4f22a1b-fca9-4368-81e4-08eef4f94841/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:33,156] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4f22a1b-fca9-4368-81e4-08eef4f94841/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:33,170] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:30:33,170] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:30:33,171] [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	79.5645	792	1936	95	below_threshold
Luteolibacter ambystomatis	strain=32A	GCA_018137965.1	2824561	2824561	type	True	78.5671	469	1936	95	below_threshold
Luteolibacter yonseiensis	strain=JCM 18052	GCA_016595465.1	1144680	1144680	type	True	77.6301	357	1936	95	below_threshold
Haloferula rosea	strain=KCTC 22201	GCA_016595525.1	490093	490093	type	True	77.3533	265	1936	95	below_threshold
Haloferula luteola	strain=YC6886	GCA_014201715.1	595692	595692	type	True	77.2874	158	1936	95	below_threshold
Verrucomicrobium spinosum	strain=JCM 18804	GCA_001313125.1	2736	2736	type	True	76.4523	103	1936	95	below_threshold
Verrucomicrobium spinosum	strain=DSM 4136	GCA_000172155.1	2736	2736	type	True	76.4477	110	1936	95	below_threshold
Sulfuriroseicoccus oceanibius	strain=T37	GCA_010681825.2	2707525	2707525	type	True	76.3511	80	1936	95	below_threshold
Roseimicrobium gellanilyticum	strain=DSM 25532	GCA_003315205.1	748857	748857	type	True	76.2975	135	1936	95	below_threshold
Chthoniobacter flavus	strain=DSM 22515	GCA_004341915.1	191863	191863	type	True	76.1991	122	1936	95	below_threshold
Akkermansia glycaniphila	strain=Pyt	GCA_001683795.1	1679444	1679444	type	True	75.8736	76	1936	95	below_threshold
Ramlibacter algicola	strain=CrO1	GCA_016641735.1	2795217	2795217	type	True	75.0617	67	1936	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:33,172] [INFO] DFAST Taxonomy check result was written to GCF_025950085.1_ASM2595008v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:33,173] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:33,173] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:33,174] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4f22a1b-fca9-4368-81e4-08eef4f94841/dqc_reference/checkm_data
[2024-01-24 12:30:33,175] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:33,231] [INFO] Task started: CheckM
[2024-01-24 12:30:33,231] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025950085.1_ASM2595008v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025950085.1_ASM2595008v1_genomic.fna/checkm_input GCF_025950085.1_ASM2595008v1_genomic.fna/checkm_result
[2024-01-24 12:32:18,874] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:18,876] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:18,904] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:18,904] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:18,905] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025950085.1_ASM2595008v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:18,905] [INFO] Task started: Blastn
[2024-01-24 12:32:18,905] [INFO] Running command: blastn -query GCF_025950085.1_ASM2595008v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4f22a1b-fca9-4368-81e4-08eef4f94841/dqc_reference/reference_markers_gtdb.fasta -out GCF_025950085.1_ASM2595008v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:19,753] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:19,757] [INFO] Selected 9 target genomes.
[2024-01-24 12:32:19,757] [INFO] Target genome list was writen to GCF_025950085.1_ASM2595008v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:19,764] [INFO] Task started: fastANI
[2024-01-24 12:32:19,764] [INFO] Running command: fastANI --query /var/lib/cwl/stg8470d619-fc08-4dd3-9d1d-66f4844b5666/GCF_025950085.1_ASM2595008v1_genomic.fna.gz --refList GCF_025950085.1_ASM2595008v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025950085.1_ASM2595008v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:28,030] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:28,041] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:32:28,041] [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_000739615.1	s__Haloferula sp000739615	79.6565	818	1936	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	79.5339	796	1936	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002304315.1	s__Haloferula sp002304315	79.4488	539	1936	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	79.1938	745	1936	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018137965.1	s__Luteolibacter sp018137965	78.5754	468	1936	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004293445.1	s__Haloferula sp004293445	78.5591	405	1936	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	99.99	99.98	0.97	0.96	4	-
GCA_003820635.1	s__Luteolibacter sp003820635	77.9286	247	1936	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	77.433	196	1936	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	99.62	99.62	0.82	0.82	2	-
GCF_016595525.1	s__Haloferula rosea	77.342	266	1936	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:28,043] [INFO] GTDB search result was written to GCF_025950085.1_ASM2595008v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:28,043] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:28,047] [INFO] DFAST_QC result json was written to GCF_025950085.1_ASM2595008v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:28,047] [INFO] DFAST_QC completed!
[2024-01-24 12:32:28,047] [INFO] Total running time: 0h2m50s