[2024-01-24 13:32:55,501] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:55,503] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:55,503] [INFO] DQC Reference Directory: /var/lib/cwl/stg0581fa9f-8b4d-4f8e-be2c-a7ec8277db6d/dqc_reference
[2024-01-24 13:32:56,727] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:56,728] [INFO] Task started: Prodigal
[2024-01-24 13:32:56,728] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b6a9bee-dd34-4733-b25b-a6b026d6540e/GCF_000311985.1_ASM31198v1_genomic.fna.gz | prodigal -d GCF_000311985.1_ASM31198v1_genomic.fna/cds.fna -a GCF_000311985.1_ASM31198v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:01,739] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:01,739] [INFO] Task started: HMMsearch
[2024-01-24 13:33:01,740] [INFO] Running command: hmmsearch --tblout GCF_000311985.1_ASM31198v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0581fa9f-8b4d-4f8e-be2c-a7ec8277db6d/dqc_reference/reference_markers.hmm GCF_000311985.1_ASM31198v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:01,995] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:01,999] [INFO] Found 6/6 markers.
[2024-01-24 13:33:02,023] [INFO] Query marker FASTA was written to GCF_000311985.1_ASM31198v1_genomic.fna/markers.fasta
[2024-01-24 13:33:02,023] [INFO] Task started: Blastn
[2024-01-24 13:33:02,024] [INFO] Running command: blastn -query GCF_000311985.1_ASM31198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0581fa9f-8b4d-4f8e-be2c-a7ec8277db6d/dqc_reference/reference_markers.fasta -out GCF_000311985.1_ASM31198v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:02,631] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:02,634] [INFO] Selected 14 target genomes.
[2024-01-24 13:33:02,635] [INFO] Target genome list was writen to GCF_000311985.1_ASM31198v1_genomic.fna/target_genomes.txt
[2024-01-24 13:33:02,641] [INFO] Task started: fastANI
[2024-01-24 13:33:02,641] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b6a9bee-dd34-4733-b25b-a6b026d6540e/GCF_000311985.1_ASM31198v1_genomic.fna.gz --refList GCF_000311985.1_ASM31198v1_genomic.fna/target_genomes.txt --output GCF_000311985.1_ASM31198v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:08,984] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:08,985] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0581fa9f-8b4d-4f8e-be2c-a7ec8277db6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:08,985] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0581fa9f-8b4d-4f8e-be2c-a7ec8277db6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:08,990] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:08,990] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:08,990] [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
Kallipyga massiliensis	strain=ph2	GCA_000311985.1	1472764	1472764	type	True	99.9999	586	588	95	conclusive
Kallipyga gabonensis	strain=GM4	GCA_001286805.1	1686287	1686287	type	True	87.4262	429	588	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:08,994] [INFO] DFAST Taxonomy check result was written to GCF_000311985.1_ASM31198v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:08,997] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:08,998] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:08,998] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0581fa9f-8b4d-4f8e-be2c-a7ec8277db6d/dqc_reference/checkm_data
[2024-01-24 13:33:09,000] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:09,023] [INFO] Task started: CheckM
[2024-01-24 13:33:09,023] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000311985.1_ASM31198v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000311985.1_ASM31198v1_genomic.fna/checkm_input GCF_000311985.1_ASM31198v1_genomic.fna/checkm_result
[2024-01-24 13:33:31,372] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:31,374] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:31,399] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:31,400] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:31,400] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000311985.1_ASM31198v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:31,401] [INFO] Task started: Blastn
[2024-01-24 13:33:31,401] [INFO] Running command: blastn -query GCF_000311985.1_ASM31198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0581fa9f-8b4d-4f8e-be2c-a7ec8277db6d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000311985.1_ASM31198v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:32,248] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:32,253] [INFO] Selected 20 target genomes.
[2024-01-24 13:33:32,254] [INFO] Target genome list was writen to GCF_000311985.1_ASM31198v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:32,283] [INFO] Task started: fastANI
[2024-01-24 13:33:32,284] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b6a9bee-dd34-4733-b25b-a6b026d6540e/GCF_000311985.1_ASM31198v1_genomic.fna.gz --refList GCF_000311985.1_ASM31198v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000311985.1_ASM31198v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:39,571] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:39,579] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:39,579] [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_000311985.1	s__Kallipyga massiliensis	99.9999	586	588	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Kallipyga	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001286805.1	s__Kallipyga gabonensis	87.4262	429	588	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Kallipyga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000308275.2	s__Levyella massiliensis	85.749	57	588	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Levyella	95.0	98.23	98.23	0.93	0.93	2	-
GCF_900119705.1	s__Murdochiella vaginalis	83.1948	51	588	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Murdochiella	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:39,581] [INFO] GTDB search result was written to GCF_000311985.1_ASM31198v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:39,581] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:39,583] [INFO] DFAST_QC result json was written to GCF_000311985.1_ASM31198v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:39,583] [INFO] DFAST_QC completed!
[2024-01-24 13:33:39,583] [INFO] Total running time: 0h0m44s