[2023-06-28 19:29:33,892] [INFO] DFAST_QC pipeline started.
[2023-06-28 19:29:33,896] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 19:29:33,897] [INFO] DQC Reference Directory: /var/lib/cwl/stg2547eae7-225f-4160-8fe3-20561d5ab355/dqc_reference
[2023-06-28 19:29:36,309] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 19:29:36,312] [INFO] Task started: Prodigal
[2023-06-28 19:29:36,313] [INFO] Running command: gunzip -c /var/lib/cwl/stgd78b1ba6-27c8-48af-98a9-1f3d17820e47/GCA_020047955.1_ASM2004795v1_genomic.fna.gz | prodigal -d GCA_020047955.1_ASM2004795v1_genomic.fna/cds.fna -a GCA_020047955.1_ASM2004795v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 19:29:39,071] [INFO] Task succeeded: Prodigal
[2023-06-28 19:29:39,072] [INFO] Task started: HMMsearch
[2023-06-28 19:29:39,072] [INFO] Running command: hmmsearch --tblout GCA_020047955.1_ASM2004795v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2547eae7-225f-4160-8fe3-20561d5ab355/dqc_reference/reference_markers.hmm GCA_020047955.1_ASM2004795v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 19:29:39,281] [INFO] Task succeeded: HMMsearch
[2023-06-28 19:29:39,283] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgd78b1ba6-27c8-48af-98a9-1f3d17820e47/GCA_020047955.1_ASM2004795v1_genomic.fna.gz]
[2023-06-28 19:29:39,307] [INFO] Query marker FASTA was written to GCA_020047955.1_ASM2004795v1_genomic.fna/markers.fasta
[2023-06-28 19:29:39,307] [INFO] Task started: Blastn
[2023-06-28 19:29:39,307] [INFO] Running command: blastn -query GCA_020047955.1_ASM2004795v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2547eae7-225f-4160-8fe3-20561d5ab355/dqc_reference/reference_markers.fasta -out GCA_020047955.1_ASM2004795v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:29:41,010] [INFO] Task succeeded: Blastn
[2023-06-28 19:29:41,019] [INFO] Selected 10 target genomes.
[2023-06-28 19:29:41,020] [INFO] Target genome list was writen to GCA_020047955.1_ASM2004795v1_genomic.fna/target_genomes.txt
[2023-06-28 19:29:41,026] [INFO] Task started: fastANI
[2023-06-28 19:29:41,026] [INFO] Running command: fastANI --query /var/lib/cwl/stgd78b1ba6-27c8-48af-98a9-1f3d17820e47/GCA_020047955.1_ASM2004795v1_genomic.fna.gz --refList GCA_020047955.1_ASM2004795v1_genomic.fna/target_genomes.txt --output GCA_020047955.1_ASM2004795v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 19:29:46,947] [INFO] Task succeeded: fastANI
[2023-06-28 19:29:46,948] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2547eae7-225f-4160-8fe3-20561d5ab355/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 19:29:46,948] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2547eae7-225f-4160-8fe3-20561d5ab355/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 19:29:46,951] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 19:29:46,951] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 19:29:46,951] [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 19:29:46,953] [INFO] DFAST Taxonomy check result was written to GCA_020047955.1_ASM2004795v1_genomic.fna/tc_result.tsv
[2023-06-28 19:29:46,954] [INFO] ===== Taxonomy check completed =====
[2023-06-28 19:29:46,954] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 19:29:46,954] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2547eae7-225f-4160-8fe3-20561d5ab355/dqc_reference/checkm_data
[2023-06-28 19:29:46,958] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 19:29:46,973] [INFO] Task started: CheckM
[2023-06-28 19:29:46,973] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020047955.1_ASM2004795v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020047955.1_ASM2004795v1_genomic.fna/checkm_input GCA_020047955.1_ASM2004795v1_genomic.fna/checkm_result
[2023-06-28 19:30:03,710] [INFO] Task succeeded: CheckM
[2023-06-28 19:30:03,711] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 19:30:03,731] [INFO] ===== Completeness check finished =====
[2023-06-28 19:30:03,732] [INFO] ===== Start GTDB Search =====
[2023-06-28 19:30:03,732] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020047955.1_ASM2004795v1_genomic.fna/markers.fasta)
[2023-06-28 19:30:03,732] [INFO] Task started: Blastn
[2023-06-28 19:30:03,733] [INFO] Running command: blastn -query GCA_020047955.1_ASM2004795v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2547eae7-225f-4160-8fe3-20561d5ab355/dqc_reference/reference_markers_gtdb.fasta -out GCA_020047955.1_ASM2004795v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:30:04,288] [INFO] Task succeeded: Blastn
[2023-06-28 19:30:04,292] [INFO] Selected 7 target genomes.
[2023-06-28 19:30:04,292] [INFO] Target genome list was writen to GCA_020047955.1_ASM2004795v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 19:30:04,300] [INFO] Task started: fastANI
[2023-06-28 19:30:04,301] [INFO] Running command: fastANI --query /var/lib/cwl/stgd78b1ba6-27c8-48af-98a9-1f3d17820e47/GCA_020047955.1_ASM2004795v1_genomic.fna.gz --refList GCA_020047955.1_ASM2004795v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020047955.1_ASM2004795v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 19:30:08,206] [INFO] Task succeeded: fastANI
[2023-06-28 19:30:08,217] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 19:30:08,218] [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_009773475.1	s__UBA2270 sp009773475	90.478	260	321	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__UBA2270	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019163335.1	s__UBA2270 sp019163335	86.2353	259	321	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__UBA2270	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013426795.1	s__UBA2270 sp013426795	84.3977	210	321	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__UBA2270	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002347085.1	s__UBA2270 sp002347085	78.2605	68	321	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__UBA2270	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013792135.1	s__UBA2270 sp002347745	77.6683	127	321	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__UBA2270	95.0	99.86	99.03	0.97	0.82	13	-
GCA_002424635.1	s__UBA2270 sp002424635	77.385	72	321	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__UBA2270	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 19:30:08,226] [INFO] GTDB search result was written to GCA_020047955.1_ASM2004795v1_genomic.fna/result_gtdb.tsv
[2023-06-28 19:30:08,227] [INFO] ===== GTDB Search completed =====
[2023-06-28 19:30:08,233] [INFO] DFAST_QC result json was written to GCA_020047955.1_ASM2004795v1_genomic.fna/dqc_result.json
[2023-06-28 19:30:08,233] [INFO] DFAST_QC completed!
[2023-06-28 19:30:08,234] [INFO] Total running time: 0h0m34s