[2023-06-29 13:43:20,693] [INFO] DFAST_QC pipeline started.
[2023-06-29 13:43:20,695] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 13:43:20,696] [INFO] DQC Reference Directory: /var/lib/cwl/stg268337b7-80a5-44be-80d6-f15079431189/dqc_reference
[2023-06-29 13:43:22,141] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 13:43:22,142] [INFO] Task started: Prodigal
[2023-06-29 13:43:22,142] [INFO] Running command: gunzip -c /var/lib/cwl/stgf1dc36b2-7596-49dc-bccf-d864e22eccb7/GCA_011041355.1_ASM1104135v1_genomic.fna.gz | prodigal -d GCA_011041355.1_ASM1104135v1_genomic.fna/cds.fna -a GCA_011041355.1_ASM1104135v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 13:43:23,593] [INFO] Task succeeded: Prodigal
[2023-06-29 13:43:23,594] [INFO] Task started: HMMsearch
[2023-06-29 13:43:23,594] [INFO] Running command: hmmsearch --tblout GCA_011041355.1_ASM1104135v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg268337b7-80a5-44be-80d6-f15079431189/dqc_reference/reference_markers.hmm GCA_011041355.1_ASM1104135v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 13:43:23,792] [INFO] Task succeeded: HMMsearch
[2023-06-29 13:43:23,794] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgf1dc36b2-7596-49dc-bccf-d864e22eccb7/GCA_011041355.1_ASM1104135v1_genomic.fna.gz]
[2023-06-29 13:43:23,809] [INFO] Query marker FASTA was written to GCA_011041355.1_ASM1104135v1_genomic.fna/markers.fasta
[2023-06-29 13:43:23,810] [INFO] Task started: Blastn
[2023-06-29 13:43:23,810] [INFO] Running command: blastn -query GCA_011041355.1_ASM1104135v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg268337b7-80a5-44be-80d6-f15079431189/dqc_reference/reference_markers.fasta -out GCA_011041355.1_ASM1104135v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:43:24,285] [INFO] Task succeeded: Blastn
[2023-06-29 13:43:24,289] [INFO] Selected 5 target genomes.
[2023-06-29 13:43:24,289] [INFO] Target genome list was writen to GCA_011041355.1_ASM1104135v1_genomic.fna/target_genomes.txt
[2023-06-29 13:43:24,290] [INFO] Task started: fastANI
[2023-06-29 13:43:24,290] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1dc36b2-7596-49dc-bccf-d864e22eccb7/GCA_011041355.1_ASM1104135v1_genomic.fna.gz --refList GCA_011041355.1_ASM1104135v1_genomic.fna/target_genomes.txt --output GCA_011041355.1_ASM1104135v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 13:43:26,197] [INFO] Task succeeded: fastANI
[2023-06-29 13:43:26,198] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg268337b7-80a5-44be-80d6-f15079431189/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 13:43:26,198] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg268337b7-80a5-44be-80d6-f15079431189/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 13:43:26,200] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 13:43:26,200] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 13:43:26,200] [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
--------------------------------------------------------------------------------
[2023-06-29 13:43:26,202] [INFO] DFAST Taxonomy check result was written to GCA_011041355.1_ASM1104135v1_genomic.fna/tc_result.tsv
[2023-06-29 13:43:26,202] [INFO] ===== Taxonomy check completed =====
[2023-06-29 13:43:26,202] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 13:43:26,203] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg268337b7-80a5-44be-80d6-f15079431189/dqc_reference/checkm_data
[2023-06-29 13:43:26,205] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 13:43:26,217] [INFO] Task started: CheckM
[2023-06-29 13:43:26,218] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_011041355.1_ASM1104135v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_011041355.1_ASM1104135v1_genomic.fna/checkm_input GCA_011041355.1_ASM1104135v1_genomic.fna/checkm_result
[2023-06-29 13:43:39,546] [INFO] Task succeeded: CheckM
[2023-06-29 13:43:39,547] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.32%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 13:43:39,565] [INFO] ===== Completeness check finished =====
[2023-06-29 13:43:39,566] [INFO] ===== Start GTDB Search =====
[2023-06-29 13:43:39,566] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_011041355.1_ASM1104135v1_genomic.fna/markers.fasta)
[2023-06-29 13:43:39,567] [INFO] Task started: Blastn
[2023-06-29 13:43:39,567] [INFO] Running command: blastn -query GCA_011041355.1_ASM1104135v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg268337b7-80a5-44be-80d6-f15079431189/dqc_reference/reference_markers_gtdb.fasta -out GCA_011041355.1_ASM1104135v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:43:40,014] [INFO] Task succeeded: Blastn
[2023-06-29 13:43:40,019] [INFO] Selected 11 target genomes.
[2023-06-29 13:43:40,019] [INFO] Target genome list was writen to GCA_011041355.1_ASM1104135v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 13:43:40,026] [INFO] Task started: fastANI
[2023-06-29 13:43:40,026] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1dc36b2-7596-49dc-bccf-d864e22eccb7/GCA_011041355.1_ASM1104135v1_genomic.fna.gz --refList GCA_011041355.1_ASM1104135v1_genomic.fna/target_genomes_gtdb.txt --output GCA_011041355.1_ASM1104135v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 13:43:41,863] [INFO] Task succeeded: fastANI
[2023-06-29 13:43:41,866] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 13:43:41,867] [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_002897655.1	s__BMS3ABIN17 sp002897655	99.5844	140	204	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Pacearchaeales;f__GW2011-AR1;g__BMS3ABIN17	95.0	99.86	99.86	0.85	0.85	2	conclusive
--------------------------------------------------------------------------------
[2023-06-29 13:43:41,869] [INFO] GTDB search result was written to GCA_011041355.1_ASM1104135v1_genomic.fna/result_gtdb.tsv
[2023-06-29 13:43:41,869] [INFO] ===== GTDB Search completed =====
[2023-06-29 13:43:41,872] [INFO] DFAST_QC result json was written to GCA_011041355.1_ASM1104135v1_genomic.fna/dqc_result.json
[2023-06-29 13:43:41,872] [INFO] DFAST_QC completed!
[2023-06-29 13:43:41,873] [INFO] Total running time: 0h0m21s