[2024-01-24 13:41:18,681] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:18,683] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:18,684] [INFO] DQC Reference Directory: /var/lib/cwl/stg34be5cbe-4ec0-4bdd-a65c-41ebb73cb950/dqc_reference
[2024-01-24 13:41:20,014] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:20,015] [INFO] Task started: Prodigal
[2024-01-24 13:41:20,016] [INFO] Running command: gunzip -c /var/lib/cwl/stg23003673-87e9-41dc-98c1-a0262790cc5a/GCF_000265075.1_ASM26507v1_genomic.fna.gz | prodigal -d GCF_000265075.1_ASM26507v1_genomic.fna/cds.fna -a GCF_000265075.1_ASM26507v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:36,576] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:36,576] [INFO] Task started: HMMsearch
[2024-01-24 13:41:36,576] [INFO] Running command: hmmsearch --tblout GCF_000265075.1_ASM26507v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34be5cbe-4ec0-4bdd-a65c-41ebb73cb950/dqc_reference/reference_markers.hmm GCF_000265075.1_ASM26507v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:36,837] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:36,838] [INFO] Found 6/6 markers.
[2024-01-24 13:41:36,873] [INFO] Query marker FASTA was written to GCF_000265075.1_ASM26507v1_genomic.fna/markers.fasta
[2024-01-24 13:41:36,874] [INFO] Task started: Blastn
[2024-01-24 13:41:36,874] [INFO] Running command: blastn -query GCF_000265075.1_ASM26507v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34be5cbe-4ec0-4bdd-a65c-41ebb73cb950/dqc_reference/reference_markers.fasta -out GCF_000265075.1_ASM26507v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:37,509] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:37,513] [INFO] Selected 20 target genomes.
[2024-01-24 13:41:37,513] [INFO] Target genome list was writen to GCF_000265075.1_ASM26507v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:37,523] [INFO] Task started: fastANI
[2024-01-24 13:41:37,523] [INFO] Running command: fastANI --query /var/lib/cwl/stg23003673-87e9-41dc-98c1-a0262790cc5a/GCF_000265075.1_ASM26507v1_genomic.fna.gz --refList GCF_000265075.1_ASM26507v1_genomic.fna/target_genomes.txt --output GCF_000265075.1_ASM26507v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:52,809] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:52,810] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34be5cbe-4ec0-4bdd-a65c-41ebb73cb950/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:52,810] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34be5cbe-4ec0-4bdd-a65c-41ebb73cb950/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:52,818] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:52,818] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:52,818] [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
Nitritalea halalkaliphila	strain=LW7	GCA_000265075.1	590849	590849	type	True	100.0	1133	1141	95	conclusive
Mongoliitalea lutea	strain=KCTC 23224	GCA_014652135.1	849756	849756	type	True	78.6322	76	1141	95	below_threshold
Cecembia rubra	strain=DSM 28057	GCA_003014575.1	1485585	1485585	type	True	77.9491	66	1141	95	below_threshold
Belliella buryatensis	strain=5C	GCA_900188245.1	1500549	1500549	type	True	77.6017	69	1141	95	below_threshold
Echinicola vietnamensis	strain=DSM 17526	GCA_000325705.1	390884	390884	type	True	76.9731	51	1141	95	below_threshold
Algoriphagus faecimaris	strain=JCM 16561	GCA_002150585.1	686796	686796	type	True	76.8791	54	1141	95	below_threshold
Algoriphagus vanfongensis	strain=DSM 17529	GCA_000429465.1	426371	426371	type	True	76.528	50	1141	95	below_threshold
Algoriphagus faecimaris	strain=DSM 23095	GCA_900101705.1	686796	686796	type	True	76.2851	53	1141	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:52,820] [INFO] DFAST Taxonomy check result was written to GCF_000265075.1_ASM26507v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:52,821] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:52,821] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:52,821] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34be5cbe-4ec0-4bdd-a65c-41ebb73cb950/dqc_reference/checkm_data
[2024-01-24 13:41:52,822] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:52,862] [INFO] Task started: CheckM
[2024-01-24 13:41:52,862] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000265075.1_ASM26507v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000265075.1_ASM26507v1_genomic.fna/checkm_input GCF_000265075.1_ASM26507v1_genomic.fna/checkm_result
[2024-01-24 13:42:40,086] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:40,087] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:40,109] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:40,110] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:40,110] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000265075.1_ASM26507v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:40,111] [INFO] Task started: Blastn
[2024-01-24 13:42:40,111] [INFO] Running command: blastn -query GCF_000265075.1_ASM26507v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34be5cbe-4ec0-4bdd-a65c-41ebb73cb950/dqc_reference/reference_markers_gtdb.fasta -out GCF_000265075.1_ASM26507v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:40,906] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:40,911] [INFO] Selected 22 target genomes.
[2024-01-24 13:42:40,911] [INFO] Target genome list was writen to GCF_000265075.1_ASM26507v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:40,928] [INFO] Task started: fastANI
[2024-01-24 13:42:40,928] [INFO] Running command: fastANI --query /var/lib/cwl/stg23003673-87e9-41dc-98c1-a0262790cc5a/GCF_000265075.1_ASM26507v1_genomic.fna.gz --refList GCF_000265075.1_ASM26507v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000265075.1_ASM26507v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:55,383] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:55,394] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:55,395] [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_000265075.1	s__Nitritalea halalkaliphila	100.0	1133	1141	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Nitritalea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014652135.1	s__Mongoliitalea lutea	78.6322	76	1141	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188245.1	s__Belliella buryatensis	77.6017	69	1141	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000295935.2	s__Indibacter alkaliphilus	76.9892	61	1141	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Indibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000325705.1	s__Echinicola vietnamensis	76.923	53	1141	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101705.1	s__Algoriphagus faecimaris	76.2935	54	1141	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.99	99.99	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:55,397] [INFO] GTDB search result was written to GCF_000265075.1_ASM26507v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:55,397] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:55,401] [INFO] DFAST_QC result json was written to GCF_000265075.1_ASM26507v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:55,401] [INFO] DFAST_QC completed!
[2024-01-24 13:42:55,401] [INFO] Total running time: 0h1m37s