[2024-01-24 13:22:10,270] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:10,282] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:10,283] [INFO] DQC Reference Directory: /var/lib/cwl/stgfeb1d0dd-dda1-4517-9a22-7f74c5f64fdc/dqc_reference
[2024-01-24 13:22:11,588] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:11,589] [INFO] Task started: Prodigal
[2024-01-24 13:22:11,589] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf270bcc-9833-4c89-988f-c2d64ee1abeb/GCF_009768935.1_ASM976893v1_genomic.fna.gz | prodigal -d GCF_009768935.1_ASM976893v1_genomic.fna/cds.fna -a GCF_009768935.1_ASM976893v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:19,797] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:19,797] [INFO] Task started: HMMsearch
[2024-01-24 13:22:19,797] [INFO] Running command: hmmsearch --tblout GCF_009768935.1_ASM976893v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfeb1d0dd-dda1-4517-9a22-7f74c5f64fdc/dqc_reference/reference_markers.hmm GCF_009768935.1_ASM976893v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:20,053] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:20,054] [INFO] Found 6/6 markers.
[2024-01-24 13:22:20,106] [INFO] Query marker FASTA was written to GCF_009768935.1_ASM976893v1_genomic.fna/markers.fasta
[2024-01-24 13:22:20,106] [INFO] Task started: Blastn
[2024-01-24 13:22:20,106] [INFO] Running command: blastn -query GCF_009768935.1_ASM976893v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfeb1d0dd-dda1-4517-9a22-7f74c5f64fdc/dqc_reference/reference_markers.fasta -out GCF_009768935.1_ASM976893v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:20,697] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:20,704] [INFO] Selected 12 target genomes.
[2024-01-24 13:22:20,704] [INFO] Target genome list was writen to GCF_009768935.1_ASM976893v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:20,723] [INFO] Task started: fastANI
[2024-01-24 13:22:20,723] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf270bcc-9833-4c89-988f-c2d64ee1abeb/GCF_009768935.1_ASM976893v1_genomic.fna.gz --refList GCF_009768935.1_ASM976893v1_genomic.fna/target_genomes.txt --output GCF_009768935.1_ASM976893v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:30,943] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:30,944] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfeb1d0dd-dda1-4517-9a22-7f74c5f64fdc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:30,944] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfeb1d0dd-dda1-4517-9a22-7f74c5f64fdc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:30,946] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:22:30,946] [INFO] The taxonomy check result is classified as 'no_hit'.
[2024-01-24 13:22:30,946] [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
--------------------------------------------------------------------------------
[2024-01-24 13:22:30,947] [INFO] DFAST Taxonomy check result was written to GCF_009768935.1_ASM976893v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:30,948] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:30,948] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:30,948] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfeb1d0dd-dda1-4517-9a22-7f74c5f64fdc/dqc_reference/checkm_data
[2024-01-24 13:22:30,951] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:30,983] [INFO] Task started: CheckM
[2024-01-24 13:22:30,983] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009768935.1_ASM976893v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009768935.1_ASM976893v1_genomic.fna/checkm_input GCF_009768935.1_ASM976893v1_genomic.fna/checkm_result
[2024-01-24 13:23:01,912] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:01,913] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 12.50%
Strain heterogeneity: 83.33%
--------------------------------------------------------------------------------
[2024-01-24 13:23:01,937] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:01,938] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:01,938] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009768935.1_ASM976893v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:01,939] [INFO] Task started: Blastn
[2024-01-24 13:23:01,939] [INFO] Running command: blastn -query GCF_009768935.1_ASM976893v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfeb1d0dd-dda1-4517-9a22-7f74c5f64fdc/dqc_reference/reference_markers_gtdb.fasta -out GCF_009768935.1_ASM976893v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:02,738] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:02,742] [INFO] Selected 21 target genomes.
[2024-01-24 13:23:02,742] [INFO] Target genome list was writen to GCF_009768935.1_ASM976893v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:02,807] [INFO] Task started: fastANI
[2024-01-24 13:23:02,807] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf270bcc-9833-4c89-988f-c2d64ee1abeb/GCF_009768935.1_ASM976893v1_genomic.fna.gz --refList GCF_009768935.1_ASM976893v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009768935.1_ASM976893v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:14,857] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:14,870] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:14,870] [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_009768935.1	s__Rectinema subterraneum	100.0	873	882	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__UBA8932;g__Rectinema	95.0	99.42	99.25	0.95	0.93	6	conclusive
GCA_015657395.1	s__Rectinema sp015657395	78.5747	227	882	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__UBA8932;g__Rectinema	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002425765.1	s__Rectinema sp002425765	78.2422	188	882	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__UBA8932;g__Rectinema	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002441395.1	s__Rectinema sp002441395	78.2118	200	882	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__UBA8932;g__Rectinema	95.0	99.50	99.28	0.93	0.89	3	-
GCA_011368145.1	s__Rectinema sp011368145	77.7936	174	882	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__UBA8932;g__Rectinema	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002070755.1	s__Rectinema sp002070755	76.8055	65	882	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__UBA8932;g__Rectinema	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:14,872] [INFO] GTDB search result was written to GCF_009768935.1_ASM976893v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:14,873] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:14,880] [INFO] DFAST_QC result json was written to GCF_009768935.1_ASM976893v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:14,880] [INFO] DFAST_QC completed!
[2024-01-24 13:23:14,880] [INFO] Total running time: 0h1m5s