[2024-01-24 13:01:18,810] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:18,813] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:18,813] [INFO] DQC Reference Directory: /var/lib/cwl/stg78b0aa9c-814f-42c4-9d09-902714ccf5bb/dqc_reference
[2024-01-24 13:01:20,073] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:20,074] [INFO] Task started: Prodigal
[2024-01-24 13:01:20,074] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b43b228-0d97-4b5f-be96-8165fc4f8572/GCF_000024885.1_ASM2488v1_genomic.fna.gz | prodigal -d GCF_000024885.1_ASM2488v1_genomic.fna/cds.fna -a GCF_000024885.1_ASM2488v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:25,902] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:25,902] [INFO] Task started: HMMsearch
[2024-01-24 13:01:25,902] [INFO] Running command: hmmsearch --tblout GCF_000024885.1_ASM2488v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78b0aa9c-814f-42c4-9d09-902714ccf5bb/dqc_reference/reference_markers.hmm GCF_000024885.1_ASM2488v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:26,165] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:26,167] [INFO] Found 6/6 markers.
[2024-01-24 13:01:26,192] [INFO] Query marker FASTA was written to GCF_000024885.1_ASM2488v1_genomic.fna/markers.fasta
[2024-01-24 13:01:26,192] [INFO] Task started: Blastn
[2024-01-24 13:01:26,192] [INFO] Running command: blastn -query GCF_000024885.1_ASM2488v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78b0aa9c-814f-42c4-9d09-902714ccf5bb/dqc_reference/reference_markers.fasta -out GCF_000024885.1_ASM2488v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:26,808] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:26,812] [INFO] Selected 12 target genomes.
[2024-01-24 13:01:26,813] [INFO] Target genome list was writen to GCF_000024885.1_ASM2488v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:26,821] [INFO] Task started: fastANI
[2024-01-24 13:01:26,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b43b228-0d97-4b5f-be96-8165fc4f8572/GCF_000024885.1_ASM2488v1_genomic.fna.gz --refList GCF_000024885.1_ASM2488v1_genomic.fna/target_genomes.txt --output GCF_000024885.1_ASM2488v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:33,001] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:33,001] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78b0aa9c-814f-42c4-9d09-902714ccf5bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:33,001] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78b0aa9c-814f-42c4-9d09-902714ccf5bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:33,007] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:01:33,007] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:33,007] [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
Sulfurospirillum deleyianum	strain=DSM 6946	GCA_000024885.1	65553	65553	type	True	100.0	767	768	95	conclusive
Sulfurospirillum barnesii	strain=SES-3	GCA_000265295.1	44674	44674	type	True	83.0115	542	768	95	below_threshold
Sulfurospirillum multivorans	strain=DSM 12446	GCA_000568815.1	66821	66821	type	True	79.8542	377	768	95	below_threshold
Sulfurospirillum halorespirans	strain=DSM 13726; PCE-M2	GCA_001723605.1	194424	194424	type	True	79.6136	368	768	95	below_threshold
Sulfurospirillum arcachonense	strain=DSM 9755	GCA_000597725.1	57666	57666	type	True	77.2195	68	768	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:33,009] [INFO] DFAST Taxonomy check result was written to GCF_000024885.1_ASM2488v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:33,010] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:33,010] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:33,010] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78b0aa9c-814f-42c4-9d09-902714ccf5bb/dqc_reference/checkm_data
[2024-01-24 13:01:33,011] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:33,039] [INFO] Task started: CheckM
[2024-01-24 13:01:33,040] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000024885.1_ASM2488v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000024885.1_ASM2488v1_genomic.fna/checkm_input GCF_000024885.1_ASM2488v1_genomic.fna/checkm_result
[2024-01-24 13:01:56,484] [INFO] Task succeeded: CheckM
[2024-01-24 13:01:56,486] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:01:56,508] [INFO] ===== Completeness check finished =====
[2024-01-24 13:01:56,508] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:01:56,509] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000024885.1_ASM2488v1_genomic.fna/markers.fasta)
[2024-01-24 13:01:56,509] [INFO] Task started: Blastn
[2024-01-24 13:01:56,509] [INFO] Running command: blastn -query GCF_000024885.1_ASM2488v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78b0aa9c-814f-42c4-9d09-902714ccf5bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_000024885.1_ASM2488v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:57,291] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:57,294] [INFO] Selected 8 target genomes.
[2024-01-24 13:01:57,295] [INFO] Target genome list was writen to GCF_000024885.1_ASM2488v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:01:57,301] [INFO] Task started: fastANI
[2024-01-24 13:01:57,302] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b43b228-0d97-4b5f-be96-8165fc4f8572/GCF_000024885.1_ASM2488v1_genomic.fna.gz --refList GCF_000024885.1_ASM2488v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000024885.1_ASM2488v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:01,851] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:01,862] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:01,862] [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_000024885.1	s__Sulfurospirillum deleyianum	100.0	768	768	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurospirillaceae;g__Sulfurospirillum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016930915.1	s__Sulfurospirillum sp016930915	85.9128	580	768	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurospirillaceae;g__Sulfurospirillum	95.0	99.92	99.92	0.95	0.95	2	-
GCA_009930355.1	s__Sulfurospirillum sp009930355	85.3477	399	768	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurospirillaceae;g__Sulfurospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265295.1	s__Sulfurospirillum barnesii	82.996	543	768	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurospirillaceae;g__Sulfurospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813345.1	s__Sulfurospirillum arsenophilum	79.8059	356	768	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurospirillaceae;g__Sulfurospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002309535.1	s__Sulfurospirillum sp002309535	79.6394	356	768	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurospirillaceae;g__Sulfurospirillum	95.0	96.54	96.51	0.90	0.89	3	-
GCF_001548035.1	s__Sulfurospirillum sp001548035	79.5965	355	768	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurospirillaceae;g__Sulfurospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002307095.1	s__Sulfurospirillum sp002307095	78.1435	282	768	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurospirillaceae;g__Sulfurospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:01,863] [INFO] GTDB search result was written to GCF_000024885.1_ASM2488v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:01,865] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:01,868] [INFO] DFAST_QC result json was written to GCF_000024885.1_ASM2488v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:01,868] [INFO] DFAST_QC completed!
[2024-01-24 13:02:01,868] [INFO] Total running time: 0h0m43s