[2023-06-29 17:08:57,577] [INFO] DFAST_QC pipeline started.
[2023-06-29 17:08:57,579] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 17:08:57,579] [INFO] DQC Reference Directory: /var/lib/cwl/stg39e77a3d-b5ca-4896-97a7-97bb0238f640/dqc_reference
[2023-06-29 17:08:58,740] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 17:08:58,741] [INFO] Task started: Prodigal
[2023-06-29 17:08:58,741] [INFO] Running command: gunzip -c /var/lib/cwl/stg22e0822f-27fe-431b-a617-c222f380dc0b/GCA_021821995.1_ASM2182199v1_genomic.fna.gz | prodigal -d GCA_021821995.1_ASM2182199v1_genomic.fna/cds.fna -a GCA_021821995.1_ASM2182199v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 17:09:02,088] [INFO] Task succeeded: Prodigal
[2023-06-29 17:09:02,088] [INFO] Task started: HMMsearch
[2023-06-29 17:09:02,088] [INFO] Running command: hmmsearch --tblout GCA_021821995.1_ASM2182199v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg39e77a3d-b5ca-4896-97a7-97bb0238f640/dqc_reference/reference_markers.hmm GCA_021821995.1_ASM2182199v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 17:09:02,236] [INFO] Task succeeded: HMMsearch
[2023-06-29 17:09:02,237] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg22e0822f-27fe-431b-a617-c222f380dc0b/GCA_021821995.1_ASM2182199v1_genomic.fna.gz]
[2023-06-29 17:09:02,255] [INFO] Query marker FASTA was written to GCA_021821995.1_ASM2182199v1_genomic.fna/markers.fasta
[2023-06-29 17:09:02,255] [INFO] Task started: Blastn
[2023-06-29 17:09:02,255] [INFO] Running command: blastn -query GCA_021821995.1_ASM2182199v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39e77a3d-b5ca-4896-97a7-97bb0238f640/dqc_reference/reference_markers.fasta -out GCA_021821995.1_ASM2182199v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 17:09:02,812] [INFO] Task succeeded: Blastn
[2023-06-29 17:09:02,816] [INFO] Selected 10 target genomes.
[2023-06-29 17:09:02,816] [INFO] Target genome list was writen to GCA_021821995.1_ASM2182199v1_genomic.fna/target_genomes.txt
[2023-06-29 17:09:02,818] [INFO] Task started: fastANI
[2023-06-29 17:09:02,818] [INFO] Running command: fastANI --query /var/lib/cwl/stg22e0822f-27fe-431b-a617-c222f380dc0b/GCA_021821995.1_ASM2182199v1_genomic.fna.gz --refList GCA_021821995.1_ASM2182199v1_genomic.fna/target_genomes.txt --output GCA_021821995.1_ASM2182199v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 17:09:07,864] [INFO] Task succeeded: fastANI
[2023-06-29 17:09:07,864] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg39e77a3d-b5ca-4896-97a7-97bb0238f640/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 17:09:07,865] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg39e77a3d-b5ca-4896-97a7-97bb0238f640/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 17:09:07,871] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2023-06-29 17:09:07,872] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-29 17:09:07,872] [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
Desulforamulus profundi	strain=Bs107	GCA_002607855.1	1383067	1383067	type	True	97.636	378	393	95	conclusive
Desulforamulus putei	strain=DSM 12395	GCA_900129195.1	74701	74701	type	True	85.4824	344	393	95	below_threshold
Desulforamulus hydrothermalis	strain=Lam5	GCA_000315365.1	412895	412895	type	True	78.9595	211	393	95	below_threshold
Desulforamulus hydrothermalis	strain=DSM 18033	GCA_900129895.1	412895	412895	type	True	78.883	213	393	95	below_threshold
Desulfotomaculum nigrificans	strain=DSM 574	GCA_000189755.3	1565	1565	type	True	78.2524	120	393	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 17:09:07,873] [INFO] DFAST Taxonomy check result was written to GCA_021821995.1_ASM2182199v1_genomic.fna/tc_result.tsv
[2023-06-29 17:09:07,874] [INFO] ===== Taxonomy check completed =====
[2023-06-29 17:09:07,874] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 17:09:07,874] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg39e77a3d-b5ca-4896-97a7-97bb0238f640/dqc_reference/checkm_data
[2023-06-29 17:09:07,875] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 17:09:07,893] [INFO] Task started: CheckM
[2023-06-29 17:09:07,893] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021821995.1_ASM2182199v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021821995.1_ASM2182199v1_genomic.fna/checkm_input GCA_021821995.1_ASM2182199v1_genomic.fna/checkm_result
[2023-06-29 17:09:24,331] [INFO] Task succeeded: CheckM
[2023-06-29 17:09:24,333] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.40%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 17:09:24,349] [INFO] ===== Completeness check finished =====
[2023-06-29 17:09:24,349] [INFO] ===== Start GTDB Search =====
[2023-06-29 17:09:24,350] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021821995.1_ASM2182199v1_genomic.fna/markers.fasta)
[2023-06-29 17:09:24,350] [INFO] Task started: Blastn
[2023-06-29 17:09:24,350] [INFO] Running command: blastn -query GCA_021821995.1_ASM2182199v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39e77a3d-b5ca-4896-97a7-97bb0238f640/dqc_reference/reference_markers_gtdb.fasta -out GCA_021821995.1_ASM2182199v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 17:09:25,089] [INFO] Task succeeded: Blastn
[2023-06-29 17:09:25,093] [INFO] Selected 12 target genomes.
[2023-06-29 17:09:25,093] [INFO] Target genome list was writen to GCA_021821995.1_ASM2182199v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 17:09:25,099] [INFO] Task started: fastANI
[2023-06-29 17:09:25,099] [INFO] Running command: fastANI --query /var/lib/cwl/stg22e0822f-27fe-431b-a617-c222f380dc0b/GCA_021821995.1_ASM2182199v1_genomic.fna.gz --refList GCA_021821995.1_ASM2182199v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021821995.1_ASM2182199v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 17:09:31,833] [INFO] Task succeeded: fastANI
[2023-06-29 17:09:31,840] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 17:09:31,841] [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_002607855.1	s__Desulfotomaculum profundi	97.6234	379	393	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfotomaculaceae;g__Desulfotomaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900129195.1	s__Desulfotomaculum putei	85.4825	344	393	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfotomaculaceae;g__Desulfotomaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315365.1	s__Desulfotomaculum hydrothermale	78.9804	210	393	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfotomaculaceae;g__Desulfotomaculum	95.0	99.95	99.95	1.00	1.00	2	-
GCF_000189755.2	s__Desulfotomaculum nigrificans	78.2509	120	393	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfotomaculaceae;g__Desulfotomaculum	95.0	98.87	98.87	0.87	0.87	2	-
GCF_002005145.1	s__Desulfotomaculum ferrireducens	77.7568	123	393	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfotomaculaceae;g__Desulfotomaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004143605.1	s__Desulfotomaculum aquiferis	77.5655	64	393	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfotomaculaceae;g__Desulfotomaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000215085.1	s__Desulfotomaculum ruminis	77.5631	128	393	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfotomaculaceae;g__Desulfotomaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 17:09:31,842] [INFO] GTDB search result was written to GCA_021821995.1_ASM2182199v1_genomic.fna/result_gtdb.tsv
[2023-06-29 17:09:31,843] [INFO] ===== GTDB Search completed =====
[2023-06-29 17:09:31,846] [INFO] DFAST_QC result json was written to GCA_021821995.1_ASM2182199v1_genomic.fna/dqc_result.json
[2023-06-29 17:09:31,846] [INFO] DFAST_QC completed!
[2023-06-29 17:09:31,846] [INFO] Total running time: 0h0m34s