[2024-01-24 12:30:18,565] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:18,567] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:18,568] [INFO] DQC Reference Directory: /var/lib/cwl/stg770efbe0-6110-4f6c-8176-a98a763560be/dqc_reference
[2024-01-24 12:30:19,944] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:19,945] [INFO] Task started: Prodigal
[2024-01-24 12:30:19,945] [INFO] Running command: gunzip -c /var/lib/cwl/stgc546941b-4afe-43e6-82fd-b7fbdaa3c730/GCF_018141405.1_ASM1814140v1_genomic.fna.gz | prodigal -d GCF_018141405.1_ASM1814140v1_genomic.fna/cds.fna -a GCF_018141405.1_ASM1814140v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:25,580] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:25,580] [INFO] Task started: HMMsearch
[2024-01-24 12:30:25,580] [INFO] Running command: hmmsearch --tblout GCF_018141405.1_ASM1814140v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg770efbe0-6110-4f6c-8176-a98a763560be/dqc_reference/reference_markers.hmm GCF_018141405.1_ASM1814140v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:25,873] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:25,875] [INFO] Found 6/6 markers.
[2024-01-24 12:30:25,906] [INFO] Query marker FASTA was written to GCF_018141405.1_ASM1814140v1_genomic.fna/markers.fasta
[2024-01-24 12:30:25,907] [INFO] Task started: Blastn
[2024-01-24 12:30:25,907] [INFO] Running command: blastn -query GCF_018141405.1_ASM1814140v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg770efbe0-6110-4f6c-8176-a98a763560be/dqc_reference/reference_markers.fasta -out GCF_018141405.1_ASM1814140v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:26,520] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:26,524] [INFO] Selected 17 target genomes.
[2024-01-24 12:30:26,525] [INFO] Target genome list was writen to GCF_018141405.1_ASM1814140v1_genomic.fna/target_genomes.txt
[2024-01-24 12:30:26,532] [INFO] Task started: fastANI
[2024-01-24 12:30:26,532] [INFO] Running command: fastANI --query /var/lib/cwl/stgc546941b-4afe-43e6-82fd-b7fbdaa3c730/GCF_018141405.1_ASM1814140v1_genomic.fna.gz --refList GCF_018141405.1_ASM1814140v1_genomic.fna/target_genomes.txt --output GCF_018141405.1_ASM1814140v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:38,163] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:38,164] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg770efbe0-6110-4f6c-8176-a98a763560be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:38,164] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg770efbe0-6110-4f6c-8176-a98a763560be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:38,179] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:30:38,179] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:38,179] [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
Serpentinicella alkaliphila	strain=3B	GCA_018141405.1	1734049	1734049	type	True	100.0	1085	1085	95	conclusive
Serpentinicella alkaliphila	strain=DSM 100013	GCA_004345905.1	1734049	1734049	type	True	99.9018	946	1085	95	conclusive
Romboutsia hominis	strain=FRIFI	GCA_900002575.1	1507512	1507512	type	True	79.0425	58	1085	95	below_threshold
Romboutsia ilealis	strain=CRIB	GCA_900015215.1	1115758	1115758	type	True	78.3676	58	1085	95	below_threshold
Natronincola peptidivorans	strain=DSM 18979	GCA_900111615.1	426128	426128	type	True	77.5163	81	1085	95	below_threshold
Clostridium carboxidivorans	strain=P7	GCA_001038625.1	217159	217159	type	True	77.4481	61	1085	95	below_threshold
Clostridium scatologenes	strain=ATCC 25775	GCA_000968375.1	1548	1548	type	True	77.1431	73	1085	95	below_threshold
Alkaliphilus pronyensis	strain=LacV	GCA_009017275.1	1482732	1482732	type	True	76.7119	64	1085	95	below_threshold
Romboutsia timonensis	strain=Marseille-P326	GCA_900106845.1	1776391	1776391	type	True	76.631	54	1085	95	below_threshold
Alkaliphilus flagellatus	strain=MSJ-5	GCA_018919215.1	2841507	2841507	type	True	76.5944	86	1085	95	below_threshold
Gottschalkia purinilytica	strain=DSM 1384	GCA_001190785.1	1503	1503	type	True	75.5751	57	1085	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:38,183] [INFO] DFAST Taxonomy check result was written to GCF_018141405.1_ASM1814140v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:38,186] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:38,186] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:38,186] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg770efbe0-6110-4f6c-8176-a98a763560be/dqc_reference/checkm_data
[2024-01-24 12:30:38,188] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:38,223] [INFO] Task started: CheckM
[2024-01-24 12:30:38,223] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018141405.1_ASM1814140v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018141405.1_ASM1814140v1_genomic.fna/checkm_input GCF_018141405.1_ASM1814140v1_genomic.fna/checkm_result
[2024-01-24 12:31:02,506] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:02,507] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:02,528] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:02,529] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:02,529] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018141405.1_ASM1814140v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:02,530] [INFO] Task started: Blastn
[2024-01-24 12:31:02,530] [INFO] Running command: blastn -query GCF_018141405.1_ASM1814140v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg770efbe0-6110-4f6c-8176-a98a763560be/dqc_reference/reference_markers_gtdb.fasta -out GCF_018141405.1_ASM1814140v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:03,346] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:03,351] [INFO] Selected 19 target genomes.
[2024-01-24 12:31:03,352] [INFO] Target genome list was writen to GCF_018141405.1_ASM1814140v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:03,373] [INFO] Task started: fastANI
[2024-01-24 12:31:03,373] [INFO] Running command: fastANI --query /var/lib/cwl/stgc546941b-4afe-43e6-82fd-b7fbdaa3c730/GCF_018141405.1_ASM1814140v1_genomic.fna.gz --refList GCF_018141405.1_ASM1814140v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018141405.1_ASM1814140v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:13,418] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:13,427] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:13,427] [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_018141405.1	s__Serpentinicella alkaliphila	100.0	1085	1085	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__Serpentinicella	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_900002575.1	s__Romboutsia_C hominis	79.0448	58	1085	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia_C	95.0	98.29	95.25	0.93	0.90	6	-
GCF_900015215.1	s__Romboutsia ilealis	78.7435	60	1085	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia	95.0	98.59	98.59	0.90	0.90	2	-
GCF_001038625.1	s__Clostridium_AM carboxidivorans	77.5915	62	1085	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	95.0	99.97	99.96	1.00	0.99	3	-
GCF_900111615.1	s__Natronincola_A peptidivorans	77.5528	80	1085	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_016908555.1	s__Alkaliphilus hydrothermalis	77.1589	61	1085	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_000968375.1	s__Clostridium_AM scatologenes	76.9872	71	1085	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	96.092	N/A	N/A	N/A	N/A	1	-
GCF_009017275.1	s__Alkaliphilus_C pronyensis	76.7148	64	1085	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_018919215.1	s__Alkaliphilus_B sp018919215	76.5951	85	1085	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_900106845.1	s__Romboutsia timonensis	76.4567	53	1085	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia	95.0	98.20	98.12	0.88	0.86	5	-
GCF_001190785.1	s__Gottschalkia_A purinilytica	75.5921	56	1085	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Gottschalkiaceae;g__Gottschalkia_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:13,429] [INFO] GTDB search result was written to GCF_018141405.1_ASM1814140v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:13,430] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:13,434] [INFO] DFAST_QC result json was written to GCF_018141405.1_ASM1814140v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:13,434] [INFO] DFAST_QC completed!
[2024-01-24 12:31:13,434] [INFO] Total running time: 0h0m55s