[2024-01-24 12:06:24,098] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:24,100] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:24,100] [INFO] DQC Reference Directory: /var/lib/cwl/stg67b2cf97-5c8f-47e4-a343-ce25ce40b050/dqc_reference
[2024-01-24 12:06:25,404] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:25,405] [INFO] Task started: Prodigal
[2024-01-24 12:06:25,405] [INFO] Running command: gunzip -c /var/lib/cwl/stg419fa886-8ef7-4e39-b50f-21d556aac38b/GCF_004345905.1_ASM434590v1_genomic.fna.gz | prodigal -d GCF_004345905.1_ASM434590v1_genomic.fna/cds.fna -a GCF_004345905.1_ASM434590v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:30,062] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:30,063] [INFO] Task started: HMMsearch
[2024-01-24 12:06:30,063] [INFO] Running command: hmmsearch --tblout GCF_004345905.1_ASM434590v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67b2cf97-5c8f-47e4-a343-ce25ce40b050/dqc_reference/reference_markers.hmm GCF_004345905.1_ASM434590v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:30,318] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:30,320] [INFO] Found 6/6 markers.
[2024-01-24 12:06:30,346] [INFO] Query marker FASTA was written to GCF_004345905.1_ASM434590v1_genomic.fna/markers.fasta
[2024-01-24 12:06:30,347] [INFO] Task started: Blastn
[2024-01-24 12:06:30,347] [INFO] Running command: blastn -query GCF_004345905.1_ASM434590v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67b2cf97-5c8f-47e4-a343-ce25ce40b050/dqc_reference/reference_markers.fasta -out GCF_004345905.1_ASM434590v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:30,953] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:30,957] [INFO] Selected 17 target genomes.
[2024-01-24 12:06:30,958] [INFO] Target genome list was writen to GCF_004345905.1_ASM434590v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:30,968] [INFO] Task started: fastANI
[2024-01-24 12:06:30,968] [INFO] Running command: fastANI --query /var/lib/cwl/stg419fa886-8ef7-4e39-b50f-21d556aac38b/GCF_004345905.1_ASM434590v1_genomic.fna.gz --refList GCF_004345905.1_ASM434590v1_genomic.fna/target_genomes.txt --output GCF_004345905.1_ASM434590v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:40,433] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:40,433] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67b2cf97-5c8f-47e4-a343-ce25ce40b050/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:40,433] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67b2cf97-5c8f-47e4-a343-ce25ce40b050/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:40,440] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:06:40,441] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:40,441] [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=DSM 100013	GCA_004345905.1	1734049	1734049	type	True	100.0	942	952	95	conclusive
Serpentinicella alkaliphila	strain=3B	GCA_018141405.1	1734049	1734049	type	True	99.9944	951	952	95	conclusive
Natronincola peptidivorans	strain=DSM 18979	GCA_900111615.1	426128	426128	type	True	76.9276	76	952	95	below_threshold
Alkaliphilus pronyensis	strain=LacV	GCA_009017275.1	1482732	1482732	type	True	76.5465	61	952	95	below_threshold
Alkaliphilus flagellatus	strain=MSJ-5	GCA_018919215.1	2841507	2841507	type	True	75.9146	80	952	95	below_threshold
Romboutsia timonensis	strain=Marseille-P326	GCA_900106845.1	1776391	1776391	type	True	75.8077	50	952	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:40,446] [INFO] DFAST Taxonomy check result was written to GCF_004345905.1_ASM434590v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:40,447] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:40,447] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:40,448] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67b2cf97-5c8f-47e4-a343-ce25ce40b050/dqc_reference/checkm_data
[2024-01-24 12:06:40,449] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:40,482] [INFO] Task started: CheckM
[2024-01-24 12:06:40,482] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004345905.1_ASM434590v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004345905.1_ASM434590v1_genomic.fna/checkm_input GCF_004345905.1_ASM434590v1_genomic.fna/checkm_result
[2024-01-24 12:07:00,360] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:00,362] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:00,378] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:00,378] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:00,378] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004345905.1_ASM434590v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:00,378] [INFO] Task started: Blastn
[2024-01-24 12:07:00,378] [INFO] Running command: blastn -query GCF_004345905.1_ASM434590v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67b2cf97-5c8f-47e4-a343-ce25ce40b050/dqc_reference/reference_markers_gtdb.fasta -out GCF_004345905.1_ASM434590v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:01,175] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:01,179] [INFO] Selected 19 target genomes.
[2024-01-24 12:07:01,180] [INFO] Target genome list was writen to GCF_004345905.1_ASM434590v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:01,216] [INFO] Task started: fastANI
[2024-01-24 12:07:01,216] [INFO] Running command: fastANI --query /var/lib/cwl/stg419fa886-8ef7-4e39-b50f-21d556aac38b/GCF_004345905.1_ASM434590v1_genomic.fna.gz --refList GCF_004345905.1_ASM434590v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004345905.1_ASM434590v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:09,882] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:09,888] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:09,888] [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	99.9944	951	952	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_900111615.1	s__Natronincola_A peptidivorans	76.8641	78	952	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	76.7302	57	952	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_009017275.1	s__Alkaliphilus_C pronyensis	76.5465	61	952	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	75.9146	80	952	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	75.8077	50	952	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia	95.0	98.20	98.12	0.88	0.86	5	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:09,890] [INFO] GTDB search result was written to GCF_004345905.1_ASM434590v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:09,891] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:09,896] [INFO] DFAST_QC result json was written to GCF_004345905.1_ASM434590v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:09,896] [INFO] DFAST_QC completed!
[2024-01-24 12:07:09,896] [INFO] Total running time: 0h0m46s