[2023-06-27 10:20:04,465] [INFO] DFAST_QC pipeline started.
[2023-06-27 10:20:04,468] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 10:20:04,468] [INFO] DQC Reference Directory: /var/lib/cwl/stgadf11bec-1d69-421b-8cce-0e1338efc2f2/dqc_reference
[2023-06-27 10:20:05,733] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 10:20:05,734] [INFO] Task started: Prodigal
[2023-06-27 10:20:05,734] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd757c70-5bf7-4098-9500-4d792adac7ef/GCA_026708135.1_ASM2670813v1_genomic.fna.gz | prodigal -d GCA_026708135.1_ASM2670813v1_genomic.fna/cds.fna -a GCA_026708135.1_ASM2670813v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 10:20:15,504] [INFO] Task succeeded: Prodigal
[2023-06-27 10:20:15,505] [INFO] Task started: HMMsearch
[2023-06-27 10:20:15,505] [INFO] Running command: hmmsearch --tblout GCA_026708135.1_ASM2670813v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgadf11bec-1d69-421b-8cce-0e1338efc2f2/dqc_reference/reference_markers.hmm GCA_026708135.1_ASM2670813v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 10:20:15,778] [INFO] Task succeeded: HMMsearch
[2023-06-27 10:20:15,780] [INFO] Found 6/6 markers.
[2023-06-27 10:20:15,822] [INFO] Query marker FASTA was written to GCA_026708135.1_ASM2670813v1_genomic.fna/markers.fasta
[2023-06-27 10:20:15,823] [INFO] Task started: Blastn
[2023-06-27 10:20:15,823] [INFO] Running command: blastn -query GCA_026708135.1_ASM2670813v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgadf11bec-1d69-421b-8cce-0e1338efc2f2/dqc_reference/reference_markers.fasta -out GCA_026708135.1_ASM2670813v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 10:20:16,480] [INFO] Task succeeded: Blastn
[2023-06-27 10:20:16,486] [INFO] Selected 22 target genomes.
[2023-06-27 10:20:16,486] [INFO] Target genome list was writen to GCA_026708135.1_ASM2670813v1_genomic.fna/target_genomes.txt
[2023-06-27 10:20:16,495] [INFO] Task started: fastANI
[2023-06-27 10:20:16,495] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd757c70-5bf7-4098-9500-4d792adac7ef/GCA_026708135.1_ASM2670813v1_genomic.fna.gz --refList GCA_026708135.1_ASM2670813v1_genomic.fna/target_genomes.txt --output GCA_026708135.1_ASM2670813v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 10:20:31,782] [INFO] Task succeeded: fastANI
[2023-06-27 10:20:31,783] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgadf11bec-1d69-421b-8cce-0e1338efc2f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 10:20:31,783] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgadf11bec-1d69-421b-8cce-0e1338efc2f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 10:20:31,785] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 10:20:31,785] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 10:20:31,786] [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
--------------------------------------------------------------------------------
[2023-06-27 10:20:31,794] [INFO] DFAST Taxonomy check result was written to GCA_026708135.1_ASM2670813v1_genomic.fna/tc_result.tsv
[2023-06-27 10:20:31,795] [INFO] ===== Taxonomy check completed =====
[2023-06-27 10:20:31,795] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 10:20:31,795] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgadf11bec-1d69-421b-8cce-0e1338efc2f2/dqc_reference/checkm_data
[2023-06-27 10:20:31,798] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 10:20:31,839] [INFO] Task started: CheckM
[2023-06-27 10:20:31,839] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026708135.1_ASM2670813v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026708135.1_ASM2670813v1_genomic.fna/checkm_input GCA_026708135.1_ASM2670813v1_genomic.fna/checkm_result
[2023-06-27 10:21:04,882] [INFO] Task succeeded: CheckM
[2023-06-27 10:21:04,884] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 10:21:04,906] [INFO] ===== Completeness check finished =====
[2023-06-27 10:21:04,906] [INFO] ===== Start GTDB Search =====
[2023-06-27 10:21:04,906] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026708135.1_ASM2670813v1_genomic.fna/markers.fasta)
[2023-06-27 10:21:04,907] [INFO] Task started: Blastn
[2023-06-27 10:21:04,907] [INFO] Running command: blastn -query GCA_026708135.1_ASM2670813v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgadf11bec-1d69-421b-8cce-0e1338efc2f2/dqc_reference/reference_markers_gtdb.fasta -out GCA_026708135.1_ASM2670813v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 10:21:05,692] [INFO] Task succeeded: Blastn
[2023-06-27 10:21:05,697] [INFO] Selected 21 target genomes.
[2023-06-27 10:21:05,697] [INFO] Target genome list was writen to GCA_026708135.1_ASM2670813v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 10:21:05,739] [INFO] Task started: fastANI
[2023-06-27 10:21:05,739] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd757c70-5bf7-4098-9500-4d792adac7ef/GCA_026708135.1_ASM2670813v1_genomic.fna.gz --refList GCA_026708135.1_ASM2670813v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026708135.1_ASM2670813v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 10:21:21,283] [INFO] Task succeeded: fastANI
[2023-06-27 10:21:21,296] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 10:21:21,297] [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_012270545.1	s__UBA6055 sp012270545	80.8208	702	1104	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__UBA6055	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523705.1	s__UBA6055 sp011523705	80.79	775	1104	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__UBA6055	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523545.1	s__UBA6055 sp011523545	80.1546	743	1104	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__UBA6055	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523515.1	s__UBA6055 sp011523515	78.695	501	1104	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__UBA6055	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523735.1	s__UBA6055 sp011523735	78.6162	484	1104	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__UBA6055	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009841405.1	s__UBA6055 sp009841405	78.4843	501	1104	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__UBA6055	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525385.1	s__UBA6055 sp011525385	78.0245	415	1104	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__UBA6055	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 10:21:21,318] [INFO] GTDB search result was written to GCA_026708135.1_ASM2670813v1_genomic.fna/result_gtdb.tsv
[2023-06-27 10:21:21,319] [INFO] ===== GTDB Search completed =====
[2023-06-27 10:21:21,323] [INFO] DFAST_QC result json was written to GCA_026708135.1_ASM2670813v1_genomic.fna/dqc_result.json
[2023-06-27 10:21:21,323] [INFO] DFAST_QC completed!
[2023-06-27 10:21:21,323] [INFO] Total running time: 0h1m17s