[2023-06-30 10:22:08,714] [INFO] DFAST_QC pipeline started.
[2023-06-30 10:22:08,721] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 10:22:08,722] [INFO] DQC Reference Directory: /var/lib/cwl/stged839dcb-df11-4242-b9e5-3cc320fe63c9/dqc_reference
[2023-06-30 10:22:10,007] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 10:22:10,008] [INFO] Task started: Prodigal
[2023-06-30 10:22:10,008] [INFO] Running command: gunzip -c /var/lib/cwl/stgb4044b43-3272-4b83-9025-259ebc169fa4/GCA_024691145.1_ASM2469114v1_genomic.fna.gz | prodigal -d GCA_024691145.1_ASM2469114v1_genomic.fna/cds.fna -a GCA_024691145.1_ASM2469114v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 10:22:14,894] [INFO] Task succeeded: Prodigal
[2023-06-30 10:22:14,895] [INFO] Task started: HMMsearch
[2023-06-30 10:22:14,895] [INFO] Running command: hmmsearch --tblout GCA_024691145.1_ASM2469114v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged839dcb-df11-4242-b9e5-3cc320fe63c9/dqc_reference/reference_markers.hmm GCA_024691145.1_ASM2469114v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 10:22:15,233] [INFO] Task succeeded: HMMsearch
[2023-06-30 10:22:15,235] [INFO] Found 6/6 markers.
[2023-06-30 10:22:15,279] [INFO] Query marker FASTA was written to GCA_024691145.1_ASM2469114v1_genomic.fna/markers.fasta
[2023-06-30 10:22:15,279] [INFO] Task started: Blastn
[2023-06-30 10:22:15,279] [INFO] Running command: blastn -query GCA_024691145.1_ASM2469114v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged839dcb-df11-4242-b9e5-3cc320fe63c9/dqc_reference/reference_markers.fasta -out GCA_024691145.1_ASM2469114v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:22:15,936] [INFO] Task succeeded: Blastn
[2023-06-30 10:22:15,940] [INFO] Selected 31 target genomes.
[2023-06-30 10:22:15,940] [INFO] Target genome list was writen to GCA_024691145.1_ASM2469114v1_genomic.fna/target_genomes.txt
[2023-06-30 10:22:15,946] [INFO] Task started: fastANI
[2023-06-30 10:22:15,946] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4044b43-3272-4b83-9025-259ebc169fa4/GCA_024691145.1_ASM2469114v1_genomic.fna.gz --refList GCA_024691145.1_ASM2469114v1_genomic.fna/target_genomes.txt --output GCA_024691145.1_ASM2469114v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 10:22:31,568] [INFO] Task succeeded: fastANI
[2023-06-30 10:22:31,568] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged839dcb-df11-4242-b9e5-3cc320fe63c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 10:22:31,569] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged839dcb-df11-4242-b9e5-3cc320fe63c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 10:22:31,571] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 10:22:31,571] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 10:22:31,571] [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
--------------------------------------------------------------------------------
[2023-06-30 10:22:31,574] [INFO] DFAST Taxonomy check result was written to GCA_024691145.1_ASM2469114v1_genomic.fna/tc_result.tsv
[2023-06-30 10:22:31,576] [INFO] ===== Taxonomy check completed =====
[2023-06-30 10:22:31,577] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 10:22:31,577] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged839dcb-df11-4242-b9e5-3cc320fe63c9/dqc_reference/checkm_data
[2023-06-30 10:22:31,582] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 10:22:31,617] [INFO] Task started: CheckM
[2023-06-30 10:22:31,617] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024691145.1_ASM2469114v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024691145.1_ASM2469114v1_genomic.fna/checkm_input GCA_024691145.1_ASM2469114v1_genomic.fna/checkm_result
[2023-06-30 10:22:53,731] [INFO] Task succeeded: CheckM
[2023-06-30 10:22:53,732] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 10:22:53,758] [INFO] ===== Completeness check finished =====
[2023-06-30 10:22:53,759] [INFO] ===== Start GTDB Search =====
[2023-06-30 10:22:53,759] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024691145.1_ASM2469114v1_genomic.fna/markers.fasta)
[2023-06-30 10:22:53,760] [INFO] Task started: Blastn
[2023-06-30 10:22:53,760] [INFO] Running command: blastn -query GCA_024691145.1_ASM2469114v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged839dcb-df11-4242-b9e5-3cc320fe63c9/dqc_reference/reference_markers_gtdb.fasta -out GCA_024691145.1_ASM2469114v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:22:54,736] [INFO] Task succeeded: Blastn
[2023-06-30 10:22:54,741] [INFO] Selected 34 target genomes.
[2023-06-30 10:22:54,741] [INFO] Target genome list was writen to GCA_024691145.1_ASM2469114v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 10:22:54,760] [INFO] Task started: fastANI
[2023-06-30 10:22:54,760] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4044b43-3272-4b83-9025-259ebc169fa4/GCA_024691145.1_ASM2469114v1_genomic.fna.gz --refList GCA_024691145.1_ASM2469114v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024691145.1_ASM2469114v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 10:23:11,932] [INFO] Task succeeded: fastANI
[2023-06-30 10:23:11,943] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 10:23:11,943] [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
GCA_900314555.1	s__CAG-603 sp900314555	77.1913	63	755	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-603	95.0	100.00	100.00	0.99	0.99	2	-
GCA_015057455.1	s__SIG301 sp015057455	77.0022	74	755	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__SIG301	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018918265.1	s__Falcatimonas sp018918265	76.9206	69	755	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Falcatimonas	95.0	98.30	98.30	0.93	0.93	2	-
GCA_016282745.1	s__SIG293 sp016282745	76.4081	60	755	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__SIG293	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016591975.1	s__TB5 sp016591975	76.3964	55	755	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__TB5	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 10:23:11,945] [INFO] GTDB search result was written to GCA_024691145.1_ASM2469114v1_genomic.fna/result_gtdb.tsv
[2023-06-30 10:23:11,946] [INFO] ===== GTDB Search completed =====
[2023-06-30 10:23:11,949] [INFO] DFAST_QC result json was written to GCA_024691145.1_ASM2469114v1_genomic.fna/dqc_result.json
[2023-06-30 10:23:11,949] [INFO] DFAST_QC completed!
[2023-06-30 10:23:11,949] [INFO] Total running time: 0h1m3s