[2024-01-24 13:58:25,379] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:25,382] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:25,382] [INFO] DQC Reference Directory: /var/lib/cwl/stg640397cd-3f0d-4778-b4fb-f65b8cf51ab1/dqc_reference
[2024-01-24 13:58:26,721] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:26,722] [INFO] Task started: Prodigal
[2024-01-24 13:58:26,723] [INFO] Running command: gunzip -c /var/lib/cwl/stgfd2004e2-a9f3-4438-a0de-2ab9a15ca5d1/GCF_001672295.1_ASM167229v1_genomic.fna.gz | prodigal -d GCF_001672295.1_ASM167229v1_genomic.fna/cds.fna -a GCF_001672295.1_ASM167229v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:36,836] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:36,836] [INFO] Task started: HMMsearch
[2024-01-24 13:58:36,837] [INFO] Running command: hmmsearch --tblout GCF_001672295.1_ASM167229v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg640397cd-3f0d-4778-b4fb-f65b8cf51ab1/dqc_reference/reference_markers.hmm GCF_001672295.1_ASM167229v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:37,116] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:37,118] [INFO] Found 6/6 markers.
[2024-01-24 13:58:37,153] [INFO] Query marker FASTA was written to GCF_001672295.1_ASM167229v1_genomic.fna/markers.fasta
[2024-01-24 13:58:37,153] [INFO] Task started: Blastn
[2024-01-24 13:58:37,153] [INFO] Running command: blastn -query GCF_001672295.1_ASM167229v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg640397cd-3f0d-4778-b4fb-f65b8cf51ab1/dqc_reference/reference_markers.fasta -out GCF_001672295.1_ASM167229v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:37,743] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:37,747] [INFO] Selected 15 target genomes.
[2024-01-24 13:58:37,747] [INFO] Target genome list was writen to GCF_001672295.1_ASM167229v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:37,754] [INFO] Task started: fastANI
[2024-01-24 13:58:37,754] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd2004e2-a9f3-4438-a0de-2ab9a15ca5d1/GCF_001672295.1_ASM167229v1_genomic.fna.gz --refList GCF_001672295.1_ASM167229v1_genomic.fna/target_genomes.txt --output GCF_001672295.1_ASM167229v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:47,803] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:47,804] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg640397cd-3f0d-4778-b4fb-f65b8cf51ab1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:47,805] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg640397cd-3f0d-4778-b4fb-f65b8cf51ab1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:47,814] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:47,815] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:47,815] [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
Halodesulfovibrio spirochaetisodalis	strain=JC271	GCA_001672295.1	1560234	1560234	type	True	100.0	1169	1172	95	conclusive
Halodesulfovibrio aestuarii	strain=DSM 17919	GCA_900142115.1	126333	126333	type	True	82.359	649	1172	95	below_threshold
Maridesulfovibrio salexigens	strain=DSM 2638	GCA_000023445.1	880	880	type	True	77.7764	63	1172	95	below_threshold
Oleidesulfovibrio alaskensis	strain=DSM 16109	GCA_000482745.1	58180	58180	type	True	76.1771	52	1172	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:47,817] [INFO] DFAST Taxonomy check result was written to GCF_001672295.1_ASM167229v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:47,817] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:47,817] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:47,818] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg640397cd-3f0d-4778-b4fb-f65b8cf51ab1/dqc_reference/checkm_data
[2024-01-24 13:58:47,819] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:47,859] [INFO] Task started: CheckM
[2024-01-24 13:58:47,859] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001672295.1_ASM167229v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001672295.1_ASM167229v1_genomic.fna/checkm_input GCF_001672295.1_ASM167229v1_genomic.fna/checkm_result
[2024-01-24 13:59:20,930] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:20,932] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:20,949] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:20,949] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:20,950] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001672295.1_ASM167229v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:20,950] [INFO] Task started: Blastn
[2024-01-24 13:59:20,950] [INFO] Running command: blastn -query GCF_001672295.1_ASM167229v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg640397cd-3f0d-4778-b4fb-f65b8cf51ab1/dqc_reference/reference_markers_gtdb.fasta -out GCF_001672295.1_ASM167229v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:21,726] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:21,730] [INFO] Selected 6 target genomes.
[2024-01-24 13:59:21,730] [INFO] Target genome list was writen to GCF_001672295.1_ASM167229v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:21,744] [INFO] Task started: fastANI
[2024-01-24 13:59:21,745] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd2004e2-a9f3-4438-a0de-2ab9a15ca5d1/GCF_001672295.1_ASM167229v1_genomic.fna.gz --refList GCF_001672295.1_ASM167229v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001672295.1_ASM167229v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:26,632] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:26,644] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:26,644] [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_001672295.1	s__Halodesulfovibrio spirochaetisodalis	100.0	1169	1172	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Halodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015482765.1	s__Halodesulfovibrio sp015482765	82.6808	638	1172	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Halodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009914765.1	s__Halodesulfovibrio sp009914765	82.5682	669	1172	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Halodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129975.1	s__Halodesulfovibrio marinisediminis	82.4828	682	1172	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Halodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000384815.1	s__Halodesulfovibrio aestuarii	82.3193	649	1172	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Halodesulfovibrio	95.0	99.51	99.03	0.97	0.95	3	-
GCF_000023445.1	s__Maridesulfovibrio salexigens	77.7766	63	1172	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Maridesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:26,645] [INFO] GTDB search result was written to GCF_001672295.1_ASM167229v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:26,645] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:26,648] [INFO] DFAST_QC result json was written to GCF_001672295.1_ASM167229v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:26,648] [INFO] DFAST_QC completed!
[2024-01-24 13:59:26,648] [INFO] Total running time: 0h1m1s