[2023-06-18 11:02:56,352] [INFO] DFAST_QC pipeline started.
[2023-06-18 11:02:56,357] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 11:02:56,357] [INFO] DQC Reference Directory: /var/lib/cwl/stg34353282-a615-4486-85b5-dccfb27afdbb/dqc_reference
[2023-06-18 11:02:58,023] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 11:02:58,025] [INFO] Task started: Prodigal
[2023-06-18 11:02:58,025] [INFO] Running command: gunzip -c /var/lib/cwl/stg64058e61-48a9-4fff-813e-caa6bd79a2b5/GCA_018896115.1_ASM1889611v1_genomic.fna.gz | prodigal -d GCA_018896115.1_ASM1889611v1_genomic.fna/cds.fna -a GCA_018896115.1_ASM1889611v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 11:02:59,984] [INFO] Task succeeded: Prodigal
[2023-06-18 11:02:59,984] [INFO] Task started: HMMsearch
[2023-06-18 11:02:59,985] [INFO] Running command: hmmsearch --tblout GCA_018896115.1_ASM1889611v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34353282-a615-4486-85b5-dccfb27afdbb/dqc_reference/reference_markers.hmm GCA_018896115.1_ASM1889611v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 11:03:00,228] [INFO] Task succeeded: HMMsearch
[2023-06-18 11:03:00,229] [INFO] Found 6/6 markers.
[2023-06-18 11:03:00,250] [INFO] Query marker FASTA was written to GCA_018896115.1_ASM1889611v1_genomic.fna/markers.fasta
[2023-06-18 11:03:00,250] [INFO] Task started: Blastn
[2023-06-18 11:03:00,251] [INFO] Running command: blastn -query GCA_018896115.1_ASM1889611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34353282-a615-4486-85b5-dccfb27afdbb/dqc_reference/reference_markers.fasta -out GCA_018896115.1_ASM1889611v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:03:02,719] [INFO] Task succeeded: Blastn
[2023-06-18 11:03:02,724] [INFO] Selected 10 target genomes.
[2023-06-18 11:03:02,725] [INFO] Target genome list was writen to GCA_018896115.1_ASM1889611v1_genomic.fna/target_genomes.txt
[2023-06-18 11:03:02,728] [INFO] Task started: fastANI
[2023-06-18 11:03:02,729] [INFO] Running command: fastANI --query /var/lib/cwl/stg64058e61-48a9-4fff-813e-caa6bd79a2b5/GCA_018896115.1_ASM1889611v1_genomic.fna.gz --refList GCA_018896115.1_ASM1889611v1_genomic.fna/target_genomes.txt --output GCA_018896115.1_ASM1889611v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 11:03:07,123] [INFO] Task succeeded: fastANI
[2023-06-18 11:03:07,123] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34353282-a615-4486-85b5-dccfb27afdbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 11:03:07,124] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34353282-a615-4486-85b5-dccfb27afdbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 11:03:07,126] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 11:03:07,126] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 11:03:07,127] [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
--------------------------------------------------------------------------------
[2023-06-18 11:03:07,129] [INFO] DFAST Taxonomy check result was written to GCA_018896115.1_ASM1889611v1_genomic.fna/tc_result.tsv
[2023-06-18 11:03:07,130] [INFO] ===== Taxonomy check completed =====
[2023-06-18 11:03:07,130] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 11:03:07,130] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34353282-a615-4486-85b5-dccfb27afdbb/dqc_reference/checkm_data
[2023-06-18 11:03:07,134] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 11:03:07,153] [INFO] Task started: CheckM
[2023-06-18 11:03:07,153] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018896115.1_ASM1889611v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018896115.1_ASM1889611v1_genomic.fna/checkm_input GCA_018896115.1_ASM1889611v1_genomic.fna/checkm_result
[2023-06-18 11:03:21,818] [INFO] Task succeeded: CheckM
[2023-06-18 11:03:21,820] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 11:03:21,847] [INFO] ===== Completeness check finished =====
[2023-06-18 11:03:21,848] [INFO] ===== Start GTDB Search =====
[2023-06-18 11:03:21,848] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018896115.1_ASM1889611v1_genomic.fna/markers.fasta)
[2023-06-18 11:03:21,849] [INFO] Task started: Blastn
[2023-06-18 11:03:21,849] [INFO] Running command: blastn -query GCA_018896115.1_ASM1889611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34353282-a615-4486-85b5-dccfb27afdbb/dqc_reference/reference_markers_gtdb.fasta -out GCA_018896115.1_ASM1889611v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:03:22,713] [INFO] Task succeeded: Blastn
[2023-06-18 11:03:22,718] [INFO] Selected 14 target genomes.
[2023-06-18 11:03:22,718] [INFO] Target genome list was writen to GCA_018896115.1_ASM1889611v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 11:03:22,727] [INFO] Task started: fastANI
[2023-06-18 11:03:22,727] [INFO] Running command: fastANI --query /var/lib/cwl/stg64058e61-48a9-4fff-813e-caa6bd79a2b5/GCA_018896115.1_ASM1889611v1_genomic.fna.gz --refList GCA_018896115.1_ASM1889611v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018896115.1_ASM1889611v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 11:03:28,104] [INFO] Task succeeded: fastANI
[2023-06-18 11:03:28,113] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 11:03:28,114] [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_018897535.1	s__UASB340 sp018897535	99.7977	286	342	d__Bacteria;p__Dependentiae;c__Babeliae;o__Babeliales;f__UASB340;g__UASB340	95.0	99.90	99.90	0.96	0.96	2	conclusive
GCA_001468925.1	s__UASB340 sp001468925	94.8227	271	342	d__Bacteria;p__Dependentiae;c__Babeliae;o__Babeliales;f__UASB340;g__UASB340	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000989185.1	s__UASB340 sp000989185	78.0007	145	342	d__Bacteria;p__Dependentiae;c__Babeliae;o__Babeliales;f__UASB340;g__UASB340	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014728525.1	s__WJLJ01 sp014728525	76.9256	76	342	d__Bacteria;p__Dependentiae;c__Babeliae;o__Babeliales;f__UASB340;g__WJLJ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 11:03:28,116] [INFO] GTDB search result was written to GCA_018896115.1_ASM1889611v1_genomic.fna/result_gtdb.tsv
[2023-06-18 11:03:28,119] [INFO] ===== GTDB Search completed =====
[2023-06-18 11:03:28,121] [INFO] DFAST_QC result json was written to GCA_018896115.1_ASM1889611v1_genomic.fna/dqc_result.json
[2023-06-18 11:03:28,121] [INFO] DFAST_QC completed!
[2023-06-18 11:03:28,122] [INFO] Total running time: 0h0m32s