[2024-01-24 13:36:45,765] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:45,767] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:45,768] [INFO] DQC Reference Directory: /var/lib/cwl/stgdac42a11-d8eb-4a83-b081-95987cd27dfd/dqc_reference
[2024-01-24 13:36:46,992] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:46,993] [INFO] Task started: Prodigal
[2024-01-24 13:36:46,993] [INFO] Running command: gunzip -c /var/lib/cwl/stg7341ef2f-e549-47bc-be5b-8d48ef4d9199/GCF_000621145.1_ASM62114v1_genomic.fna.gz | prodigal -d GCF_000621145.1_ASM62114v1_genomic.fna/cds.fna -a GCF_000621145.1_ASM62114v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:59,117] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:59,118] [INFO] Task started: HMMsearch
[2024-01-24 13:36:59,118] [INFO] Running command: hmmsearch --tblout GCF_000621145.1_ASM62114v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdac42a11-d8eb-4a83-b081-95987cd27dfd/dqc_reference/reference_markers.hmm GCF_000621145.1_ASM62114v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:59,444] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:59,446] [INFO] Found 6/6 markers.
[2024-01-24 13:36:59,479] [INFO] Query marker FASTA was written to GCF_000621145.1_ASM62114v1_genomic.fna/markers.fasta
[2024-01-24 13:36:59,480] [INFO] Task started: Blastn
[2024-01-24 13:36:59,480] [INFO] Running command: blastn -query GCF_000621145.1_ASM62114v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdac42a11-d8eb-4a83-b081-95987cd27dfd/dqc_reference/reference_markers.fasta -out GCF_000621145.1_ASM62114v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:00,140] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:00,144] [INFO] Selected 14 target genomes.
[2024-01-24 13:37:00,144] [INFO] Target genome list was writen to GCF_000621145.1_ASM62114v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:00,156] [INFO] Task started: fastANI
[2024-01-24 13:37:00,157] [INFO] Running command: fastANI --query /var/lib/cwl/stg7341ef2f-e549-47bc-be5b-8d48ef4d9199/GCF_000621145.1_ASM62114v1_genomic.fna.gz --refList GCF_000621145.1_ASM62114v1_genomic.fna/target_genomes.txt --output GCF_000621145.1_ASM62114v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:10,862] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:10,863] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdac42a11-d8eb-4a83-b081-95987cd27dfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:10,863] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdac42a11-d8eb-4a83-b081-95987cd27dfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:10,872] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:10,872] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:10,872] [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
Desulfobulbus elongatus	strain=DSM 2908	GCA_000621145.1	53332	53332	type	True	100.0	1265	1269	95	conclusive
Desulfobulbus propionicus	strain=DSM 2032	GCA_000186885.1	894	894	type	True	81.2026	629	1269	95	below_threshold
Desulfobulbus oralis	strain=HOT041/ORNL	GCA_002952055.1	1986146	1986146	type	True	77.9559	150	1269	95	below_threshold
Desulfobulbus oligotrophicus	strain=Prop6	GCA_016446285.1	1909699	1909699	type	True	77.8546	181	1269	95	below_threshold
Desulfobulbus alkaliphilus	strain=DSM 24258	GCA_016918545.1	869814	869814	type	True	77.7099	258	1269	95	below_threshold
Desulfogranum mediterraneum	strain=DSM 13871	GCA_000429965.1	160661	160661	type	True	77.6369	266	1269	95	below_threshold
Desulfurivibrio alkaliphilus	strain=AHT 2	GCA_000092205.1	427923	427923	type	True	77.0555	100	1269	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	75.1188	112	1269	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	75.0914	51	1269	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:10,874] [INFO] DFAST Taxonomy check result was written to GCF_000621145.1_ASM62114v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:10,875] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:10,875] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:10,875] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdac42a11-d8eb-4a83-b081-95987cd27dfd/dqc_reference/checkm_data
[2024-01-24 13:37:10,876] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:10,940] [INFO] Task started: CheckM
[2024-01-24 13:37:10,941] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000621145.1_ASM62114v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000621145.1_ASM62114v1_genomic.fna/checkm_input GCF_000621145.1_ASM62114v1_genomic.fna/checkm_result
[2024-01-24 13:37:53,165] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:53,166] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.46%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:53,187] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:53,188] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:53,188] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000621145.1_ASM62114v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:53,188] [INFO] Task started: Blastn
[2024-01-24 13:37:53,189] [INFO] Running command: blastn -query GCF_000621145.1_ASM62114v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdac42a11-d8eb-4a83-b081-95987cd27dfd/dqc_reference/reference_markers_gtdb.fasta -out GCF_000621145.1_ASM62114v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:54,189] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:54,192] [INFO] Selected 9 target genomes.
[2024-01-24 13:37:54,193] [INFO] Target genome list was writen to GCF_000621145.1_ASM62114v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:54,202] [INFO] Task started: fastANI
[2024-01-24 13:37:54,203] [INFO] Running command: fastANI --query /var/lib/cwl/stg7341ef2f-e549-47bc-be5b-8d48ef4d9199/GCF_000621145.1_ASM62114v1_genomic.fna.gz --refList GCF_000621145.1_ASM62114v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000621145.1_ASM62114v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:00,120] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:00,128] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:00,128] [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_000621145.1	s__Desulfobulbus elongatus	100.0	1266	1269	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009782165.1	s__Desulfobulbus sp009782165	84.9305	283	1269	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009778955.1	s__Desulfobulbus sp009778955	83.5752	557	1269	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009778235.1	s__Desulfobulbus sp009778235	82.8885	448	1269	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009780825.1	s__Desulfobulbus sp009780825	82.7376	613	1269	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000186885.1	s__Desulfobulbus propionicus	81.1714	629	1269	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017998195.1	s__Desulfobulbus sp017998195	81.0419	404	1269	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903842475.1	s__Desulfobulbus sp903842475	79.0769	399	1269	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019163135.1	s__Desulfobulbus sp019163135	78.4858	388	1269	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:00,130] [INFO] GTDB search result was written to GCF_000621145.1_ASM62114v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:00,130] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:00,133] [INFO] DFAST_QC result json was written to GCF_000621145.1_ASM62114v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:00,134] [INFO] DFAST_QC completed!
[2024-01-24 13:38:00,134] [INFO] Total running time: 0h1m14s