[2024-01-24 13:42:57,488] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:42:57,490] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:42:57,490] [INFO] DQC Reference Directory: /var/lib/cwl/stg797a1e4c-7384-4996-9240-28e5d5c31ee2/dqc_reference
[2024-01-24 13:42:58,736] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:42:58,736] [INFO] Task started: Prodigal
[2024-01-24 13:42:58,737] [INFO] Running command: gunzip -c /var/lib/cwl/stg5fe57d22-ccc6-4819-b3c4-26ecc2f07319/GCF_018919215.1_ASM1891921v1_genomic.fna.gz | prodigal -d GCF_018919215.1_ASM1891921v1_genomic.fna/cds.fna -a GCF_018919215.1_ASM1891921v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:43:04,526] [INFO] Task succeeded: Prodigal
[2024-01-24 13:43:04,526] [INFO] Task started: HMMsearch
[2024-01-24 13:43:04,527] [INFO] Running command: hmmsearch --tblout GCF_018919215.1_ASM1891921v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg797a1e4c-7384-4996-9240-28e5d5c31ee2/dqc_reference/reference_markers.hmm GCF_018919215.1_ASM1891921v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:43:04,799] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:43:04,801] [INFO] Found 6/6 markers.
[2024-01-24 13:43:04,833] [INFO] Query marker FASTA was written to GCF_018919215.1_ASM1891921v1_genomic.fna/markers.fasta
[2024-01-24 13:43:04,833] [INFO] Task started: Blastn
[2024-01-24 13:43:04,834] [INFO] Running command: blastn -query GCF_018919215.1_ASM1891921v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg797a1e4c-7384-4996-9240-28e5d5c31ee2/dqc_reference/reference_markers.fasta -out GCF_018919215.1_ASM1891921v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:05,428] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:05,433] [INFO] Selected 17 target genomes.
[2024-01-24 13:43:05,433] [INFO] Target genome list was writen to GCF_018919215.1_ASM1891921v1_genomic.fna/target_genomes.txt
[2024-01-24 13:43:05,463] [INFO] Task started: fastANI
[2024-01-24 13:43:05,463] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fe57d22-ccc6-4819-b3c4-26ecc2f07319/GCF_018919215.1_ASM1891921v1_genomic.fna.gz --refList GCF_018919215.1_ASM1891921v1_genomic.fna/target_genomes.txt --output GCF_018919215.1_ASM1891921v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:43:15,085] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:15,086] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg797a1e4c-7384-4996-9240-28e5d5c31ee2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:43:15,087] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg797a1e4c-7384-4996-9240-28e5d5c31ee2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:43:15,109] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:43:15,109] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:43:15,109] [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 flagellatus	strain=MSJ-5	GCA_018919215.1	2841507	2841507	type	True	100.0	1188	1188	95	conclusive
Tissierella simiarum	strain=MSJ-40	GCA_018917865.1	2841534	2841534	type	True	78.9608	139	1188	95	below_threshold
Alkaliphilus oremlandii	strain=OhILAs	GCA_000018325.1	461876	461876	type	True	78.6896	304	1188	95	below_threshold
Clostridium formicaceticum	strain=ATCC 27076	GCA_001854185.1	1497	1497	type	True	77.1491	97	1188	95	below_threshold
Clostridium formicaceticum	strain=DSM 92	GCA_002080475.1	1497	1497	type	True	77.0464	96	1188	95	below_threshold
Alkaliphilus metalliredigens	strain=QYMF	GCA_000016985.1	208226	208226	type	True	76.8161	96	1188	95	below_threshold
Anaerovirgula multivorans	strain=SCA	GCA_900188145.1	312168	312168	type	True	76.6838	115	1188	95	below_threshold
Clostridium aceticum	strain=DSM 1496	GCA_000949285.1	84022	84022	type	True	76.5814	90	1188	95	below_threshold
Alkaliphilus peptidifermentans	strain=DSM 18978	GCA_900101495.1	426129	426129	type	True	76.3951	101	1188	95	below_threshold
Serpentinicella alkaliphila	strain=DSM 100013	GCA_004345905.1	1734049	1734049	type	True	75.9839	83	1188	95	below_threshold
Proteiniborus ethanoligenes	strain=DSM 21650	GCA_900107485.1	415015	415015	type	True	75.7602	52	1188	95	below_threshold
Tepidibacter formicigenes	strain=DSM 15518	GCA_900142235.1	227138	227138	type	True	75.4953	80	1188	95	below_threshold
Paeniclostridium sordellii	strain=ATCC9714	GCA_000953675.1	1505	1505	type	True	75.2227	65	1188	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:43:15,111] [INFO] DFAST Taxonomy check result was written to GCF_018919215.1_ASM1891921v1_genomic.fna/tc_result.tsv
[2024-01-24 13:43:15,112] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:43:15,112] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:43:15,112] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg797a1e4c-7384-4996-9240-28e5d5c31ee2/dqc_reference/checkm_data
[2024-01-24 13:43:15,114] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:43:15,151] [INFO] Task started: CheckM
[2024-01-24 13:43:15,152] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018919215.1_ASM1891921v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018919215.1_ASM1891921v1_genomic.fna/checkm_input GCF_018919215.1_ASM1891921v1_genomic.fna/checkm_result
[2024-01-24 13:43:39,128] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:39,130] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:39,151] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:39,152] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:39,152] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018919215.1_ASM1891921v1_genomic.fna/markers.fasta)
[2024-01-24 13:43:39,153] [INFO] Task started: Blastn
[2024-01-24 13:43:39,153] [INFO] Running command: blastn -query GCF_018919215.1_ASM1891921v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg797a1e4c-7384-4996-9240-28e5d5c31ee2/dqc_reference/reference_markers_gtdb.fasta -out GCF_018919215.1_ASM1891921v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:39,924] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:39,927] [INFO] Selected 10 target genomes.
[2024-01-24 13:43:39,927] [INFO] Target genome list was writen to GCF_018919215.1_ASM1891921v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:39,940] [INFO] Task started: fastANI
[2024-01-24 13:43:39,940] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fe57d22-ccc6-4819-b3c4-26ecc2f07319/GCF_018919215.1_ASM1891921v1_genomic.fna.gz --refList GCF_018919215.1_ASM1891921v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018919215.1_ASM1891921v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:46,337] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:46,350] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:46,350] [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_018919215.1	s__Alkaliphilus_B sp018919215	100.0	1188	1188	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__Alkaliphilus_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018141165.1	s__Alkaliphilus_B sp018141165	94.7599	933	1188	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__Alkaliphilus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015978205.1	s__Alkaliphilus_B sp015978205	79.7954	420	1188	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__Alkaliphilus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908435.1	s__Alkaliphilus_B halophilus	79.5221	419	1188	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__Alkaliphilus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018917865.1	s__MSJ-40 sp018917865	78.9621	139	1188	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tissierellaceae;g__MSJ-40	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000018325.1	s__Alkaliphilus_B oremlandii	78.6771	305	1188	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__Alkaliphilus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101495.1	s__Alkaliphilus_C peptidifermentans	76.3875	99	1188	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_900107485.1	s__Proteiniborus ethanoligenes	75.7602	52	1188	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Proteiniboraceae;g__Proteiniborus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000953675.1	s__Paraclostridium sordellii	75.2227	65	1188	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	95.0	98.12	96.78	0.93	0.89	59	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:46,351] [INFO] GTDB search result was written to GCF_018919215.1_ASM1891921v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:46,352] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:46,355] [INFO] DFAST_QC result json was written to GCF_018919215.1_ASM1891921v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:46,355] [INFO] DFAST_QC completed!
[2024-01-24 13:43:46,355] [INFO] Total running time: 0h0m49s