[2024-01-24 13:32:42,454] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:42,456] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:42,456] [INFO] DQC Reference Directory: /var/lib/cwl/stgc7a8026d-c5fb-47a3-9048-0e4b5f15dd72/dqc_reference
[2024-01-24 13:32:43,782] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:43,783] [INFO] Task started: Prodigal
[2024-01-24 13:32:43,783] [INFO] Running command: gunzip -c /var/lib/cwl/stgea4a83e1-81e2-494a-8971-3efb52b34a2c/GCF_000019665.1_ASM1966v1_genomic.fna.gz | prodigal -d GCF_000019665.1_ASM1966v1_genomic.fna/cds.fna -a GCF_000019665.1_ASM1966v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:55,214] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:55,214] [INFO] Task started: HMMsearch
[2024-01-24 13:32:55,214] [INFO] Running command: hmmsearch --tblout GCF_000019665.1_ASM1966v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc7a8026d-c5fb-47a3-9048-0e4b5f15dd72/dqc_reference/reference_markers.hmm GCF_000019665.1_ASM1966v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:55,423] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:55,424] [INFO] Found 6/6 markers.
[2024-01-24 13:32:55,470] [INFO] Query marker FASTA was written to GCF_000019665.1_ASM1966v1_genomic.fna/markers.fasta
[2024-01-24 13:32:55,471] [INFO] Task started: Blastn
[2024-01-24 13:32:55,471] [INFO] Running command: blastn -query GCF_000019665.1_ASM1966v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7a8026d-c5fb-47a3-9048-0e4b5f15dd72/dqc_reference/reference_markers.fasta -out GCF_000019665.1_ASM1966v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:56,083] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:56,086] [INFO] Selected 7 target genomes.
[2024-01-24 13:32:56,087] [INFO] Target genome list was writen to GCF_000019665.1_ASM1966v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:56,095] [INFO] Task started: fastANI
[2024-01-24 13:32:56,096] [INFO] Running command: fastANI --query /var/lib/cwl/stgea4a83e1-81e2-494a-8971-3efb52b34a2c/GCF_000019665.1_ASM1966v1_genomic.fna.gz --refList GCF_000019665.1_ASM1966v1_genomic.fna/target_genomes.txt --output GCF_000019665.1_ASM1966v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:00,753] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:00,753] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc7a8026d-c5fb-47a3-9048-0e4b5f15dd72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:00,753] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc7a8026d-c5fb-47a3-9048-0e4b5f15dd72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:00,755] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:33:00,755] [INFO] The taxonomy check result is classified as 'no_hit'.
[2024-01-24 13:33:00,755] [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 13:33:00,758] [INFO] DFAST Taxonomy check result was written to GCF_000019665.1_ASM1966v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:00,759] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:00,759] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:00,759] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc7a8026d-c5fb-47a3-9048-0e4b5f15dd72/dqc_reference/checkm_data
[2024-01-24 13:33:00,762] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:00,792] [INFO] Task started: CheckM
[2024-01-24 13:33:00,792] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000019665.1_ASM1966v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000019665.1_ASM1966v1_genomic.fna/checkm_input GCF_000019665.1_ASM1966v1_genomic.fna/checkm_result
[2024-01-24 13:33:35,770] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:35,771] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:35,787] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:35,788] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:35,788] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000019665.1_ASM1966v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:35,788] [INFO] Task started: Blastn
[2024-01-24 13:33:35,788] [INFO] Running command: blastn -query GCF_000019665.1_ASM1966v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7a8026d-c5fb-47a3-9048-0e4b5f15dd72/dqc_reference/reference_markers_gtdb.fasta -out GCF_000019665.1_ASM1966v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:36,534] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:36,537] [INFO] Selected 14 target genomes.
[2024-01-24 13:33:36,538] [INFO] Target genome list was writen to GCF_000019665.1_ASM1966v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:36,564] [INFO] Task started: fastANI
[2024-01-24 13:33:36,564] [INFO] Running command: fastANI --query /var/lib/cwl/stgea4a83e1-81e2-494a-8971-3efb52b34a2c/GCF_000019665.1_ASM1966v1_genomic.fna.gz --refList GCF_000019665.1_ASM1966v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000019665.1_ASM1966v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:42,515] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:42,520] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:42,520] [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_000019665.1	s__Methylacidiphilum infernorum	100.0	762	762	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Methylacidiphilales;f__Methylacidiphilaceae;g__Methylacidiphilum	95.0	96.14	96.14	0.95	0.95	2	conclusive
GCF_017310505.1	s__Methylacidiphilum sp004421255	78.4815	390	762	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Methylacidiphilales;f__Methylacidiphilaceae;g__Methylacidiphilum	95.0	98.58	98.58	0.94	0.94	2	-
GCA_000953475.1	s__Methylacidiphilum fumariolicum	76.9058	125	762	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Methylacidiphilales;f__Methylacidiphilaceae;g__Methylacidiphilum	95.0	99.98	99.97	1.00	1.00	6	-
GCF_007475525.1	s__Methylacidiphilum kamchatkense	76.4469	155	762	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Methylacidiphilales;f__Methylacidiphilaceae;g__Methylacidiphilum	95.0	99.97	99.97	1.00	1.00	2	-
GCF_004421185.1	s__Methylacidiphilum sp004421185	76.3633	140	762	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Methylacidiphilales;f__Methylacidiphilaceae;g__Methylacidiphilum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:42,521] [INFO] GTDB search result was written to GCF_000019665.1_ASM1966v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:42,522] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:42,524] [INFO] DFAST_QC result json was written to GCF_000019665.1_ASM1966v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:42,524] [INFO] DFAST_QC completed!
[2024-01-24 13:33:42,524] [INFO] Total running time: 0h1m0s