[2024-01-25 18:43:35,676] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:43:35,677] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:43:35,677] [INFO] DQC Reference Directory: /var/lib/cwl/stgbdade38a-a285-4b40-84b0-ff53a5ca3894/dqc_reference
[2024-01-25 18:43:36,855] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:43:36,856] [INFO] Task started: Prodigal
[2024-01-25 18:43:36,856] [INFO] Running command: gunzip -c /var/lib/cwl/stg96c1cdda-b0e2-47e7-8617-0a0b7c0e016d/GCF_025770725.1_ASM2577072v1_genomic.fna.gz | prodigal -d GCF_025770725.1_ASM2577072v1_genomic.fna/cds.fna -a GCF_025770725.1_ASM2577072v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:43:42,510] [INFO] Task succeeded: Prodigal
[2024-01-25 18:43:42,510] [INFO] Task started: HMMsearch
[2024-01-25 18:43:42,510] [INFO] Running command: hmmsearch --tblout GCF_025770725.1_ASM2577072v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbdade38a-a285-4b40-84b0-ff53a5ca3894/dqc_reference/reference_markers.hmm GCF_025770725.1_ASM2577072v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:43:42,708] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:43:42,709] [INFO] Found 6/6 markers.
[2024-01-25 18:43:42,732] [INFO] Query marker FASTA was written to GCF_025770725.1_ASM2577072v1_genomic.fna/markers.fasta
[2024-01-25 18:43:42,732] [INFO] Task started: Blastn
[2024-01-25 18:43:42,732] [INFO] Running command: blastn -query GCF_025770725.1_ASM2577072v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbdade38a-a285-4b40-84b0-ff53a5ca3894/dqc_reference/reference_markers.fasta -out GCF_025770725.1_ASM2577072v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:43,281] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:43,284] [INFO] Selected 10 target genomes.
[2024-01-25 18:43:43,284] [INFO] Target genome list was writen to GCF_025770725.1_ASM2577072v1_genomic.fna/target_genomes.txt
[2024-01-25 18:43:43,293] [INFO] Task started: fastANI
[2024-01-25 18:43:43,293] [INFO] Running command: fastANI --query /var/lib/cwl/stg96c1cdda-b0e2-47e7-8617-0a0b7c0e016d/GCF_025770725.1_ASM2577072v1_genomic.fna.gz --refList GCF_025770725.1_ASM2577072v1_genomic.fna/target_genomes.txt --output GCF_025770725.1_ASM2577072v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:43:47,686] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:47,687] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbdade38a-a285-4b40-84b0-ff53a5ca3894/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:43:47,687] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbdade38a-a285-4b40-84b0-ff53a5ca3894/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:43:47,692] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:43:47,692] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:43:47,693] [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 halorespirans	strain=DSM 13726; PCE-M2	GCA_001723605.1	194424	194424	type	True	82.7563	600	872	95	below_threshold
Sulfurospirillum multivorans	strain=DSM 12446	GCA_000568815.1	66821	66821	type	True	82.3462	603	872	95	below_threshold
Sulfurospirillum barnesii	strain=SES-3	GCA_000265295.1	44674	44674	type	True	79.6183	394	872	95	below_threshold
Sulfurospirillum deleyianum	strain=DSM 6946	GCA_000024885.1	65553	65553	type	True	79.4277	362	872	95	below_threshold
Sulfurospirillum arcachonense	strain=DSM 9755	GCA_000597725.1	57666	57666	type	True	77.2011	82	872	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:43:47,694] [INFO] DFAST Taxonomy check result was written to GCF_025770725.1_ASM2577072v1_genomic.fna/tc_result.tsv
[2024-01-25 18:43:47,694] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:43:47,695] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:43:47,695] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbdade38a-a285-4b40-84b0-ff53a5ca3894/dqc_reference/checkm_data
[2024-01-25 18:43:47,695] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:43:47,724] [INFO] Task started: CheckM
[2024-01-25 18:43:47,724] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025770725.1_ASM2577072v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025770725.1_ASM2577072v1_genomic.fna/checkm_input GCF_025770725.1_ASM2577072v1_genomic.fna/checkm_result
[2024-01-25 18:44:09,670] [INFO] Task succeeded: CheckM
[2024-01-25 18:44:09,671] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:44:09,687] [INFO] ===== Completeness check finished =====
[2024-01-25 18:44:09,687] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:44:09,688] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025770725.1_ASM2577072v1_genomic.fna/markers.fasta)
[2024-01-25 18:44:09,688] [INFO] Task started: Blastn
[2024-01-25 18:44:09,688] [INFO] Running command: blastn -query GCF_025770725.1_ASM2577072v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbdade38a-a285-4b40-84b0-ff53a5ca3894/dqc_reference/reference_markers_gtdb.fasta -out GCF_025770725.1_ASM2577072v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:10,460] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:10,462] [INFO] Selected 9 target genomes.
[2024-01-25 18:44:10,462] [INFO] Target genome list was writen to GCF_025770725.1_ASM2577072v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:44:10,468] [INFO] Task started: fastANI
[2024-01-25 18:44:10,468] [INFO] Running command: fastANI --query /var/lib/cwl/stg96c1cdda-b0e2-47e7-8617-0a0b7c0e016d/GCF_025770725.1_ASM2577072v1_genomic.fna.gz --refList GCF_025770725.1_ASM2577072v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025770725.1_ASM2577072v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:44:16,134] [INFO] Task succeeded: fastANI
[2024-01-25 18:44:16,141] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:44:16,141] [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_000813345.1	s__Sulfurospirillum arsenophilum	85.2934	667	872	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurospirillaceae;g__Sulfurospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017860615.1	s__Sulfurospirillum sp017860615	83.6967	644	872	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurospirillaceae;g__Sulfurospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002162315.1	s__Sulfurospirillum sp002162315	83.2579	644	872	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurospirillaceae;g__Sulfurospirillum	95.0	99.96	99.96	1.00	1.00	2	-
GCF_002309535.1	s__Sulfurospirillum sp002309535	83.2057	621	872	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurospirillaceae;g__Sulfurospirillum	95.0	96.54	96.51	0.90	0.89	3	-
GCF_001723605.1	s__Sulfurospirillum halorespirans	82.7307	599	872	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurospirillaceae;g__Sulfurospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000568815.1	s__Sulfurospirillum multivorans	82.3462	603	872	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurospirillaceae;g__Sulfurospirillum	95.0	99.98	99.98	1.00	1.00	2	-
GCF_001548035.1	s__Sulfurospirillum sp001548035	82.0489	586	872	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurospirillaceae;g__Sulfurospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000743525.1	s__Sulfurospirillum sp000743525	81.9815	583	872	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurospirillaceae;g__Sulfurospirillum	95.0	99.99	99.99	0.99	0.99	3	-
GCA_002307095.1	s__Sulfurospirillum sp002307095	81.3461	446	872	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurospirillaceae;g__Sulfurospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:44:16,142] [INFO] GTDB search result was written to GCF_025770725.1_ASM2577072v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:44:16,143] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:44:16,145] [INFO] DFAST_QC result json was written to GCF_025770725.1_ASM2577072v1_genomic.fna/dqc_result.json
[2024-01-25 18:44:16,145] [INFO] DFAST_QC completed!
[2024-01-25 18:44:16,145] [INFO] Total running time: 0h0m40s