[2024-01-24 13:49:54,833] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:54,834] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:54,834] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1e6655c-3b84-48b1-952e-ccfaceb61012/dqc_reference
[2024-01-24 13:49:55,942] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:55,943] [INFO] Task started: Prodigal
[2024-01-24 13:49:55,943] [INFO] Running command: gunzip -c /var/lib/cwl/stgde1bb0a8-8fe4-415d-a350-0e792991bea5/GCF_009017255.1_ASM901725v1_genomic.fna.gz | prodigal -d GCF_009017255.1_ASM901725v1_genomic.fna/cds.fna -a GCF_009017255.1_ASM901725v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:00,943] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:00,943] [INFO] Task started: HMMsearch
[2024-01-24 13:50:00,943] [INFO] Running command: hmmsearch --tblout GCF_009017255.1_ASM901725v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1e6655c-3b84-48b1-952e-ccfaceb61012/dqc_reference/reference_markers.hmm GCF_009017255.1_ASM901725v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:01,155] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:01,156] [INFO] Found 6/6 markers.
[2024-01-24 13:50:01,180] [INFO] Query marker FASTA was written to GCF_009017255.1_ASM901725v1_genomic.fna/markers.fasta
[2024-01-24 13:50:01,180] [INFO] Task started: Blastn
[2024-01-24 13:50:01,181] [INFO] Running command: blastn -query GCF_009017255.1_ASM901725v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1e6655c-3b84-48b1-952e-ccfaceb61012/dqc_reference/reference_markers.fasta -out GCF_009017255.1_ASM901725v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:01,747] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:01,749] [INFO] Selected 15 target genomes.
[2024-01-24 13:50:01,750] [INFO] Target genome list was writen to GCF_009017255.1_ASM901725v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:01,767] [INFO] Task started: fastANI
[2024-01-24 13:50:01,767] [INFO] Running command: fastANI --query /var/lib/cwl/stgde1bb0a8-8fe4-415d-a350-0e792991bea5/GCF_009017255.1_ASM901725v1_genomic.fna.gz --refList GCF_009017255.1_ASM901725v1_genomic.fna/target_genomes.txt --output GCF_009017255.1_ASM901725v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:09,871] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:09,871] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1e6655c-3b84-48b1-952e-ccfaceb61012/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:09,872] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1e6655c-3b84-48b1-952e-ccfaceb61012/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:09,878] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:09,878] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:09,878] [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
Alkaliphilus serpentinus	strain=LacT	GCA_009017255.1	1482731	1482731	type	True	100.0	1044	1052	95	conclusive
Alkaliphilus peptidifermentans	strain=DSM 18978	GCA_900101495.1	426129	426129	type	True	77.2166	158	1052	95	below_threshold
Alkaliphilus hydrothermalis	strain=DSM 25890	GCA_016908555.1	1482730	1482730	type	True	77.0785	95	1052	95	below_threshold
Alkaliphilus transvaalensis	strain=ATCC 700919	GCA_000621485.1	114628	114628	type	True	77.0004	98	1052	95	below_threshold
Natronincola peptidivorans	strain=DSM 18979	GCA_900111615.1	426128	426128	type	True	76.5305	73	1052	95	below_threshold
Clostridium aceticum	strain=DSM 1496	GCA_001042715.1	84022	84022	type	True	76.3754	55	1052	95	below_threshold
Clostridium aceticum	strain=DSM 1496	GCA_000949285.1	84022	84022	type	True	76.1751	52	1052	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:09,879] [INFO] DFAST Taxonomy check result was written to GCF_009017255.1_ASM901725v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:09,879] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:09,880] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:09,880] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1e6655c-3b84-48b1-952e-ccfaceb61012/dqc_reference/checkm_data
[2024-01-24 13:50:09,880] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:09,912] [INFO] Task started: CheckM
[2024-01-24 13:50:09,912] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009017255.1_ASM901725v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009017255.1_ASM901725v1_genomic.fna/checkm_input GCF_009017255.1_ASM901725v1_genomic.fna/checkm_result
[2024-01-24 13:50:29,934] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:29,935] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:29,950] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:29,950] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:29,951] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009017255.1_ASM901725v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:29,951] [INFO] Task started: Blastn
[2024-01-24 13:50:29,951] [INFO] Running command: blastn -query GCF_009017255.1_ASM901725v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1e6655c-3b84-48b1-952e-ccfaceb61012/dqc_reference/reference_markers_gtdb.fasta -out GCF_009017255.1_ASM901725v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:30,830] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:30,833] [INFO] Selected 21 target genomes.
[2024-01-24 13:50:30,834] [INFO] Target genome list was writen to GCF_009017255.1_ASM901725v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:30,845] [INFO] Task started: fastANI
[2024-01-24 13:50:30,845] [INFO] Running command: fastANI --query /var/lib/cwl/stgde1bb0a8-8fe4-415d-a350-0e792991bea5/GCF_009017255.1_ASM901725v1_genomic.fna.gz --refList GCF_009017255.1_ASM901725v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009017255.1_ASM901725v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:41,273] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:41,278] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:41,278] [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_009017255.1	s__LacT sp009017255	100.0	1044	1052	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__LacT	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900101495.1	s__Alkaliphilus_C peptidifermentans	77.2289	158	1052	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__Alkaliphilus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908555.1	s__Alkaliphilus hydrothermalis	77.1096	96	1052	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__Alkaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000621485.1	s__Alkaliphilus transvaalensis	77.0004	98	1052	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__Alkaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111615.1	s__Natronincola_A peptidivorans	76.5305	73	1052	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__Natronincola_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001042715.1	s__Clostridium_W aceticum	76.3754	55	1052	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__Clostridium_W	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:41,280] [INFO] GTDB search result was written to GCF_009017255.1_ASM901725v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:41,280] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:41,282] [INFO] DFAST_QC result json was written to GCF_009017255.1_ASM901725v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:41,282] [INFO] DFAST_QC completed!
[2024-01-24 13:50:41,282] [INFO] Total running time: 0h0m46s