[2024-01-25 18:51:05,545] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:51:05,547] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:51:05,547] [INFO] DQC Reference Directory: /var/lib/cwl/stg90f9afde-34f4-49ed-bf37-dcdbb51ab918/dqc_reference
[2024-01-25 18:51:06,657] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:51:06,658] [INFO] Task started: Prodigal
[2024-01-25 18:51:06,658] [INFO] Running command: gunzip -c /var/lib/cwl/stgeac9e2b7-b0a3-4b56-b558-ccd2ade3e357/GCF_015352425.1_ASM1535242v1_genomic.fna.gz | prodigal -d GCF_015352425.1_ASM1535242v1_genomic.fna/cds.fna -a GCF_015352425.1_ASM1535242v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:51:17,044] [INFO] Task succeeded: Prodigal
[2024-01-25 18:51:17,044] [INFO] Task started: HMMsearch
[2024-01-25 18:51:17,044] [INFO] Running command: hmmsearch --tblout GCF_015352425.1_ASM1535242v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90f9afde-34f4-49ed-bf37-dcdbb51ab918/dqc_reference/reference_markers.hmm GCF_015352425.1_ASM1535242v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:51:17,319] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:51:17,320] [INFO] Found 6/6 markers.
[2024-01-25 18:51:17,363] [INFO] Query marker FASTA was written to GCF_015352425.1_ASM1535242v1_genomic.fna/markers.fasta
[2024-01-25 18:51:17,363] [INFO] Task started: Blastn
[2024-01-25 18:51:17,363] [INFO] Running command: blastn -query GCF_015352425.1_ASM1535242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90f9afde-34f4-49ed-bf37-dcdbb51ab918/dqc_reference/reference_markers.fasta -out GCF_015352425.1_ASM1535242v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:17,929] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:17,931] [INFO] Selected 15 target genomes.
[2024-01-25 18:51:17,932] [INFO] Target genome list was writen to GCF_015352425.1_ASM1535242v1_genomic.fna/target_genomes.txt
[2024-01-25 18:51:17,945] [INFO] Task started: fastANI
[2024-01-25 18:51:17,945] [INFO] Running command: fastANI --query /var/lib/cwl/stgeac9e2b7-b0a3-4b56-b558-ccd2ade3e357/GCF_015352425.1_ASM1535242v1_genomic.fna.gz --refList GCF_015352425.1_ASM1535242v1_genomic.fna/target_genomes.txt --output GCF_015352425.1_ASM1535242v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:51:26,057] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:26,058] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90f9afde-34f4-49ed-bf37-dcdbb51ab918/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:51:26,058] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90f9afde-34f4-49ed-bf37-dcdbb51ab918/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:51:26,064] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:51:26,064] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:51:26,064] [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
Fusibacter ferrireducens	strain=Q10-2	GCA_015352425.1	2785058	2785058	type	True	100.0	1730	1734	95	conclusive
Fusibacter tunisiensis	strain=DSM 24436	GCA_016908355.1	1008308	1008308	type	True	77.6149	84	1734	95	below_threshold
Fusibacter paucivorans	strain=DSM 12116	GCA_018390735.1	76009	76009	type	True	76.8087	88	1734	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:51:26,065] [INFO] DFAST Taxonomy check result was written to GCF_015352425.1_ASM1535242v1_genomic.fna/tc_result.tsv
[2024-01-25 18:51:26,065] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:51:26,066] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:51:26,066] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90f9afde-34f4-49ed-bf37-dcdbb51ab918/dqc_reference/checkm_data
[2024-01-25 18:51:26,066] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:51:26,120] [INFO] Task started: CheckM
[2024-01-25 18:51:26,120] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015352425.1_ASM1535242v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015352425.1_ASM1535242v1_genomic.fna/checkm_input GCF_015352425.1_ASM1535242v1_genomic.fna/checkm_result
[2024-01-25 18:52:00,868] [INFO] Task succeeded: CheckM
[2024-01-25 18:52:00,869] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:52:00,885] [INFO] ===== Completeness check finished =====
[2024-01-25 18:52:00,885] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:52:00,886] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015352425.1_ASM1535242v1_genomic.fna/markers.fasta)
[2024-01-25 18:52:00,886] [INFO] Task started: Blastn
[2024-01-25 18:52:00,886] [INFO] Running command: blastn -query GCF_015352425.1_ASM1535242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90f9afde-34f4-49ed-bf37-dcdbb51ab918/dqc_reference/reference_markers_gtdb.fasta -out GCF_015352425.1_ASM1535242v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:52:01,852] [INFO] Task succeeded: Blastn
[2024-01-25 18:52:01,856] [INFO] Selected 16 target genomes.
[2024-01-25 18:52:01,856] [INFO] Target genome list was writen to GCF_015352425.1_ASM1535242v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:52:01,879] [INFO] Task started: fastANI
[2024-01-25 18:52:01,879] [INFO] Running command: fastANI --query /var/lib/cwl/stgeac9e2b7-b0a3-4b56-b558-ccd2ade3e357/GCF_015352425.1_ASM1535242v1_genomic.fna.gz --refList GCF_015352425.1_ASM1535242v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015352425.1_ASM1535242v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:52:12,600] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:12,606] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:52:12,606] [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_015352425.1	s__Fusibacter_A sp015352425	100.0	1730	1734	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Acidaminobacteraceae;g__Fusibacter_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001748365.1	s__Fusibacter_A sp001748365	81.0852	887	1734	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Acidaminobacteraceae;g__Fusibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002452745.1	s__Fusibacter_A sp002452745	78.3929	255	1734	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Acidaminobacteraceae;g__Fusibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908355.1	s__Fusibacter_C tunisiensis	77.6819	85	1734	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Acidaminobacteraceae;g__Fusibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859095.1	s__Fusibacter_C sp014859095	77.2195	64	1734	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Acidaminobacteraceae;g__Fusibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897605.1	s__Fusibacter_C sp001897605	76.9702	85	1734	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Acidaminobacteraceae;g__Fusibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018390735.1	s__Fusibacter paucivorans	76.8087	88	1734	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Acidaminobacteraceae;g__Fusibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002441045.1	s__Fusibacter_C sp002441045	76.165	69	1734	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Acidaminobacteraceae;g__Fusibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016342415.1	s__JABXKX01 sp016342415	75.5135	63	1734	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Acidaminobacteraceae;g__JABXKX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:52:12,608] [INFO] GTDB search result was written to GCF_015352425.1_ASM1535242v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:52:12,609] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:52:12,611] [INFO] DFAST_QC result json was written to GCF_015352425.1_ASM1535242v1_genomic.fna/dqc_result.json
[2024-01-25 18:52:12,611] [INFO] DFAST_QC completed!
[2024-01-25 18:52:12,611] [INFO] Total running time: 0h1m7s