[2023-07-01 05:37:47,018] [INFO] DFAST_QC pipeline started.
[2023-07-01 05:37:47,020] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 05:37:47,020] [INFO] DQC Reference Directory: /var/lib/cwl/stgf88b4f74-3633-4a76-81ab-e992e7b98937/dqc_reference
[2023-07-01 05:37:48,231] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 05:37:48,231] [INFO] Task started: Prodigal
[2023-07-01 05:37:48,232] [INFO] Running command: gunzip -c /var/lib/cwl/stg63364b2f-3ebc-4e39-aadf-ff93a4bc61d6/GCA_024404115.1_ASM2440411v1_genomic.fna.gz | prodigal -d GCA_024404115.1_ASM2440411v1_genomic.fna/cds.fna -a GCA_024404115.1_ASM2440411v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 05:37:54,042] [INFO] Task succeeded: Prodigal
[2023-07-01 05:37:54,042] [INFO] Task started: HMMsearch
[2023-07-01 05:37:54,043] [INFO] Running command: hmmsearch --tblout GCA_024404115.1_ASM2440411v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf88b4f74-3633-4a76-81ab-e992e7b98937/dqc_reference/reference_markers.hmm GCA_024404115.1_ASM2440411v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 05:37:54,319] [INFO] Task succeeded: HMMsearch
[2023-07-01 05:37:54,321] [INFO] Found 6/6 markers.
[2023-07-01 05:37:54,348] [INFO] Query marker FASTA was written to GCA_024404115.1_ASM2440411v1_genomic.fna/markers.fasta
[2023-07-01 05:37:54,348] [INFO] Task started: Blastn
[2023-07-01 05:37:54,348] [INFO] Running command: blastn -query GCA_024404115.1_ASM2440411v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf88b4f74-3633-4a76-81ab-e992e7b98937/dqc_reference/reference_markers.fasta -out GCA_024404115.1_ASM2440411v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 05:37:54,976] [INFO] Task succeeded: Blastn
[2023-07-01 05:37:54,981] [INFO] Selected 13 target genomes.
[2023-07-01 05:37:54,981] [INFO] Target genome list was writen to GCA_024404115.1_ASM2440411v1_genomic.fna/target_genomes.txt
[2023-07-01 05:37:54,983] [INFO] Task started: fastANI
[2023-07-01 05:37:54,983] [INFO] Running command: fastANI --query /var/lib/cwl/stg63364b2f-3ebc-4e39-aadf-ff93a4bc61d6/GCA_024404115.1_ASM2440411v1_genomic.fna.gz --refList GCA_024404115.1_ASM2440411v1_genomic.fna/target_genomes.txt --output GCA_024404115.1_ASM2440411v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 05:38:01,910] [INFO] Task succeeded: fastANI
[2023-07-01 05:38:01,911] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf88b4f74-3633-4a76-81ab-e992e7b98937/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 05:38:01,911] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf88b4f74-3633-4a76-81ab-e992e7b98937/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 05:38:01,918] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 05:38:01,919] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-07-01 05:38:01,919] [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
--------------------------------------------------------------------------------
[2023-07-01 05:38:01,921] [INFO] DFAST Taxonomy check result was written to GCA_024404115.1_ASM2440411v1_genomic.fna/tc_result.tsv
[2023-07-01 05:38:01,922] [INFO] ===== Taxonomy check completed =====
[2023-07-01 05:38:01,922] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 05:38:01,923] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf88b4f74-3633-4a76-81ab-e992e7b98937/dqc_reference/checkm_data
[2023-07-01 05:38:01,928] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 05:38:01,956] [INFO] Task started: CheckM
[2023-07-01 05:38:01,957] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024404115.1_ASM2440411v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024404115.1_ASM2440411v1_genomic.fna/checkm_input GCA_024404115.1_ASM2440411v1_genomic.fna/checkm_result
[2023-07-01 05:38:26,596] [INFO] Task succeeded: CheckM
[2023-07-01 05:38:26,598] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.85%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 05:38:26,619] [INFO] ===== Completeness check finished =====
[2023-07-01 05:38:26,619] [INFO] ===== Start GTDB Search =====
[2023-07-01 05:38:26,620] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024404115.1_ASM2440411v1_genomic.fna/markers.fasta)
[2023-07-01 05:38:26,620] [INFO] Task started: Blastn
[2023-07-01 05:38:26,620] [INFO] Running command: blastn -query GCA_024404115.1_ASM2440411v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf88b4f74-3633-4a76-81ab-e992e7b98937/dqc_reference/reference_markers_gtdb.fasta -out GCA_024404115.1_ASM2440411v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 05:38:27,634] [INFO] Task succeeded: Blastn
[2023-07-01 05:38:27,639] [INFO] Selected 14 target genomes.
[2023-07-01 05:38:27,639] [INFO] Target genome list was writen to GCA_024404115.1_ASM2440411v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 05:38:27,648] [INFO] Task started: fastANI
[2023-07-01 05:38:27,648] [INFO] Running command: fastANI --query /var/lib/cwl/stg63364b2f-3ebc-4e39-aadf-ff93a4bc61d6/GCA_024404115.1_ASM2440411v1_genomic.fna.gz --refList GCA_024404115.1_ASM2440411v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024404115.1_ASM2440411v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 05:38:33,564] [INFO] Task succeeded: fastANI
[2023-07-01 05:38:33,581] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-07-01 05:38:33,582] [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_017465465.1	s__CAG-488 sp017465465	78.7896	232	786	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017461625.1	s__CAG-488 sp017461625	78.7343	158	786	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017935265.1	s__CAG-488 sp017935265	78.2103	173	786	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902789095.1	s__CAG-488 sp902789095	77.8031	166	786	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900539465.1	s__CAG-488 sp900539465	77.648	171	786	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488	95.0	99.25	98.53	0.96	0.93	3	-
GCA_017522225.1	s__CAG-488 sp017522225	77.4524	80	786	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017625835.1	s__CAG-488 sp017625835	77.4269	83	786	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017380575.1	s__CAG-488 sp017380575	77.3758	118	786	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017481575.1	s__CAG-488 sp017481575	77.317	101	786	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017379935.1	s__CAG-488 sp017379935	77.0817	84	786	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002315505.1	s__CAG-488 sp002315505	76.9016	123	786	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017942105.1	s__CAG-488 sp017942105	76.6969	90	786	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 05:38:33,584] [INFO] GTDB search result was written to GCA_024404115.1_ASM2440411v1_genomic.fna/result_gtdb.tsv
[2023-07-01 05:38:33,584] [INFO] ===== GTDB Search completed =====
[2023-07-01 05:38:33,587] [INFO] DFAST_QC result json was written to GCA_024404115.1_ASM2440411v1_genomic.fna/dqc_result.json
[2023-07-01 05:38:33,587] [INFO] DFAST_QC completed!
[2023-07-01 05:38:33,588] [INFO] Total running time: 0h0m47s