[2023-06-28 10:54:13,057] [INFO] DFAST_QC pipeline started.
[2023-06-28 10:54:13,064] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 10:54:13,065] [INFO] DQC Reference Directory: /var/lib/cwl/stgc636afa4-42b3-419a-acde-aca49975f135/dqc_reference
[2023-06-28 10:54:15,681] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 10:54:15,683] [INFO] Task started: Prodigal
[2023-06-28 10:54:15,683] [INFO] Running command: gunzip -c /var/lib/cwl/stg6bd5d1f2-68d2-4a47-a9ad-0943cb093249/GCA_015058085.1_ASM1505808v1_genomic.fna.gz | prodigal -d GCA_015058085.1_ASM1505808v1_genomic.fna/cds.fna -a GCA_015058085.1_ASM1505808v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 10:54:19,409] [INFO] Task succeeded: Prodigal
[2023-06-28 10:54:19,409] [INFO] Task started: HMMsearch
[2023-06-28 10:54:19,409] [INFO] Running command: hmmsearch --tblout GCA_015058085.1_ASM1505808v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc636afa4-42b3-419a-acde-aca49975f135/dqc_reference/reference_markers.hmm GCA_015058085.1_ASM1505808v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 10:54:19,655] [INFO] Task succeeded: HMMsearch
[2023-06-28 10:54:19,659] [INFO] Found 6/6 markers.
[2023-06-28 10:54:19,692] [INFO] Query marker FASTA was written to GCA_015058085.1_ASM1505808v1_genomic.fna/markers.fasta
[2023-06-28 10:54:19,693] [INFO] Task started: Blastn
[2023-06-28 10:54:19,693] [INFO] Running command: blastn -query GCA_015058085.1_ASM1505808v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc636afa4-42b3-419a-acde-aca49975f135/dqc_reference/reference_markers.fasta -out GCA_015058085.1_ASM1505808v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:54:20,639] [INFO] Task succeeded: Blastn
[2023-06-28 10:54:20,643] [INFO] Selected 21 target genomes.
[2023-06-28 10:54:20,643] [INFO] Target genome list was writen to GCA_015058085.1_ASM1505808v1_genomic.fna/target_genomes.txt
[2023-06-28 10:54:20,701] [INFO] Task started: fastANI
[2023-06-28 10:54:20,702] [INFO] Running command: fastANI --query /var/lib/cwl/stg6bd5d1f2-68d2-4a47-a9ad-0943cb093249/GCA_015058085.1_ASM1505808v1_genomic.fna.gz --refList GCA_015058085.1_ASM1505808v1_genomic.fna/target_genomes.txt --output GCA_015058085.1_ASM1505808v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 10:54:33,328] [INFO] Task succeeded: fastANI
[2023-06-28 10:54:33,329] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc636afa4-42b3-419a-acde-aca49975f135/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 10:54:33,329] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc636afa4-42b3-419a-acde-aca49975f135/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 10:54:33,330] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 10:54:33,330] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 10:54:33,331] [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 10:54:33,333] [INFO] DFAST Taxonomy check result was written to GCA_015058085.1_ASM1505808v1_genomic.fna/tc_result.tsv
[2023-06-28 10:54:33,334] [INFO] ===== Taxonomy check completed =====
[2023-06-28 10:54:33,334] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 10:54:33,334] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc636afa4-42b3-419a-acde-aca49975f135/dqc_reference/checkm_data
[2023-06-28 10:54:33,338] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 10:54:33,363] [INFO] Task started: CheckM
[2023-06-28 10:54:33,363] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015058085.1_ASM1505808v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015058085.1_ASM1505808v1_genomic.fna/checkm_input GCA_015058085.1_ASM1505808v1_genomic.fna/checkm_result
[2023-06-28 10:54:52,055] [INFO] Task succeeded: CheckM
[2023-06-28 10:54:52,057] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 10:54:52,081] [INFO] ===== Completeness check finished =====
[2023-06-28 10:54:52,081] [INFO] ===== Start GTDB Search =====
[2023-06-28 10:54:52,082] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015058085.1_ASM1505808v1_genomic.fna/markers.fasta)
[2023-06-28 10:54:52,082] [INFO] Task started: Blastn
[2023-06-28 10:54:52,082] [INFO] Running command: blastn -query GCA_015058085.1_ASM1505808v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc636afa4-42b3-419a-acde-aca49975f135/dqc_reference/reference_markers_gtdb.fasta -out GCA_015058085.1_ASM1505808v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:54:52,919] [INFO] Task succeeded: Blastn
[2023-06-28 10:54:52,925] [INFO] Selected 11 target genomes.
[2023-06-28 10:54:52,925] [INFO] Target genome list was writen to GCA_015058085.1_ASM1505808v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 10:54:52,963] [INFO] Task started: fastANI
[2023-06-28 10:54:52,964] [INFO] Running command: fastANI --query /var/lib/cwl/stg6bd5d1f2-68d2-4a47-a9ad-0943cb093249/GCA_015058085.1_ASM1505808v1_genomic.fna.gz --refList GCA_015058085.1_ASM1505808v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015058085.1_ASM1505808v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 10:54:56,874] [INFO] Task succeeded: fastANI
[2023-06-28 10:54:56,882] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 10:54:56,882] [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_902778565.1	s__RUG754 sp902778565	97.3131	375	479	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__RUG754	95.0	97.09	96.81	0.82	0.78	4	conclusive
GCA_902780845.1	s__RUG754 sp902780845	82.4022	276	479	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__RUG754	95.0	97.56	96.37	0.79	0.76	5	-
GCA_017394515.1	s__RUG754 sp017394515	81.9465	283	479	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__RUG754	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017538125.1	s__RUG754 sp017538125	79.6911	202	479	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__RUG754	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016284485.1	s__RUG754 sp016284485	79.0381	139	479	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__RUG754	95.0	98.64	98.64	0.79	0.79	2	-
GCA_900315895.1	s__RUG754 sp900315895	78.4234	142	479	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__RUG754	95.0	98.21	97.66	0.90	0.87	8	-
GCA_905235115.1	s__RUG754 sp905235115	78.091	146	479	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__RUG754	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 10:54:56,884] [INFO] GTDB search result was written to GCA_015058085.1_ASM1505808v1_genomic.fna/result_gtdb.tsv
[2023-06-28 10:54:56,885] [INFO] ===== GTDB Search completed =====
[2023-06-28 10:54:56,888] [INFO] DFAST_QC result json was written to GCA_015058085.1_ASM1505808v1_genomic.fna/dqc_result.json
[2023-06-28 10:54:56,888] [INFO] DFAST_QC completed!
[2023-06-28 10:54:56,888] [INFO] Total running time: 0h0m44s