[2023-06-28 22:52:01,171] [INFO] DFAST_QC pipeline started.
[2023-06-28 22:52:01,176] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 22:52:01,176] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9541bcd-8c50-4262-bb11-3267fd9dfe84/dqc_reference
[2023-06-28 22:52:03,178] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 22:52:03,179] [INFO] Task started: Prodigal
[2023-06-28 22:52:03,179] [INFO] Running command: gunzip -c /var/lib/cwl/stg4471d99c-a5e3-4fe2-9e1e-8a359bedf88f/GCA_017411085.1_ASM1741108v1_genomic.fna.gz | prodigal -d GCA_017411085.1_ASM1741108v1_genomic.fna/cds.fna -a GCA_017411085.1_ASM1741108v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 22:52:06,831] [INFO] Task succeeded: Prodigal
[2023-06-28 22:52:06,831] [INFO] Task started: HMMsearch
[2023-06-28 22:52:06,831] [INFO] Running command: hmmsearch --tblout GCA_017411085.1_ASM1741108v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9541bcd-8c50-4262-bb11-3267fd9dfe84/dqc_reference/reference_markers.hmm GCA_017411085.1_ASM1741108v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 22:52:06,983] [INFO] Task succeeded: HMMsearch
[2023-06-28 22:52:06,984] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg4471d99c-a5e3-4fe2-9e1e-8a359bedf88f/GCA_017411085.1_ASM1741108v1_genomic.fna.gz]
[2023-06-28 22:52:07,005] [INFO] Query marker FASTA was written to GCA_017411085.1_ASM1741108v1_genomic.fna/markers.fasta
[2023-06-28 22:52:07,006] [INFO] Task started: Blastn
[2023-06-28 22:52:07,006] [INFO] Running command: blastn -query GCA_017411085.1_ASM1741108v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9541bcd-8c50-4262-bb11-3267fd9dfe84/dqc_reference/reference_markers.fasta -out GCA_017411085.1_ASM1741108v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:52:07,970] [INFO] Task succeeded: Blastn
[2023-06-28 22:52:07,974] [INFO] Selected 18 target genomes.
[2023-06-28 22:52:07,975] [INFO] Target genome list was writen to GCA_017411085.1_ASM1741108v1_genomic.fna/target_genomes.txt
[2023-06-28 22:52:07,982] [INFO] Task started: fastANI
[2023-06-28 22:52:07,983] [INFO] Running command: fastANI --query /var/lib/cwl/stg4471d99c-a5e3-4fe2-9e1e-8a359bedf88f/GCA_017411085.1_ASM1741108v1_genomic.fna.gz --refList GCA_017411085.1_ASM1741108v1_genomic.fna/target_genomes.txt --output GCA_017411085.1_ASM1741108v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 22:52:19,217] [INFO] Task succeeded: fastANI
[2023-06-28 22:52:19,218] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9541bcd-8c50-4262-bb11-3267fd9dfe84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 22:52:19,218] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9541bcd-8c50-4262-bb11-3267fd9dfe84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 22:52:19,220] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 22:52:19,220] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 22:52:19,220] [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
--------------------------------------------------------------------------------
[2023-06-28 22:52:19,222] [INFO] DFAST Taxonomy check result was written to GCA_017411085.1_ASM1741108v1_genomic.fna/tc_result.tsv
[2023-06-28 22:52:19,223] [INFO] ===== Taxonomy check completed =====
[2023-06-28 22:52:19,223] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 22:52:19,223] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9541bcd-8c50-4262-bb11-3267fd9dfe84/dqc_reference/checkm_data
[2023-06-28 22:52:19,226] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 22:52:19,248] [INFO] Task started: CheckM
[2023-06-28 22:52:19,249] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017411085.1_ASM1741108v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017411085.1_ASM1741108v1_genomic.fna/checkm_input GCA_017411085.1_ASM1741108v1_genomic.fna/checkm_result
[2023-06-28 22:52:36,328] [INFO] Task succeeded: CheckM
[2023-06-28 22:52:36,330] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 48.96%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 22:52:36,351] [INFO] ===== Completeness check finished =====
[2023-06-28 22:52:36,351] [INFO] ===== Start GTDB Search =====
[2023-06-28 22:52:36,351] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017411085.1_ASM1741108v1_genomic.fna/markers.fasta)
[2023-06-28 22:52:36,351] [INFO] Task started: Blastn
[2023-06-28 22:52:36,351] [INFO] Running command: blastn -query GCA_017411085.1_ASM1741108v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9541bcd-8c50-4262-bb11-3267fd9dfe84/dqc_reference/reference_markers_gtdb.fasta -out GCA_017411085.1_ASM1741108v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:52:36,775] [INFO] Task succeeded: Blastn
[2023-06-28 22:52:36,779] [INFO] Selected 9 target genomes.
[2023-06-28 22:52:36,779] [INFO] Target genome list was writen to GCA_017411085.1_ASM1741108v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 22:52:36,783] [INFO] Task started: fastANI
[2023-06-28 22:52:36,783] [INFO] Running command: fastANI --query /var/lib/cwl/stg4471d99c-a5e3-4fe2-9e1e-8a359bedf88f/GCA_017411085.1_ASM1741108v1_genomic.fna.gz --refList GCA_017411085.1_ASM1741108v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017411085.1_ASM1741108v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 22:52:41,813] [INFO] Task succeeded: fastANI
[2023-06-28 22:52:41,821] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 22:52:41,822] [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_902783705.1	s__UMGS1696 sp902783705	95.5932	289	358	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1696	95.0	97.08	97.08	0.83	0.83	2	conclusive
GCA_017540285.1	s__UMGS1696 sp017540285	88.0696	269	358	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1696	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017412675.1	s__UMGS1696 sp017412675	86.6894	297	358	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1696	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017550315.1	s__UMGS1696 sp017550315	86.0845	299	358	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1696	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902782445.1	s__UMGS1696 sp902782445	79.845	216	358	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1696	95.0	97.30	97.10	0.87	0.82	3	-
GCA_015065385.1	s__UMGS1696 sp015065385	79.296	217	358	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1696	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017540175.1	s__UMGS1696 sp902773525	79.1511	201	358	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1696	95.0	98.81	98.75	0.96	0.96	3	-
GCA_902761695.1	s__UMGS1696 sp902761695	78.7344	171	358	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1696	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 22:52:41,824] [INFO] GTDB search result was written to GCA_017411085.1_ASM1741108v1_genomic.fna/result_gtdb.tsv
[2023-06-28 22:52:41,824] [INFO] ===== GTDB Search completed =====
[2023-06-28 22:52:41,827] [INFO] DFAST_QC result json was written to GCA_017411085.1_ASM1741108v1_genomic.fna/dqc_result.json
[2023-06-28 22:52:41,828] [INFO] DFAST_QC completed!
[2023-06-28 22:52:41,828] [INFO] Total running time: 0h0m41s