[2023-06-28 10:00:50,309] [INFO] DFAST_QC pipeline started.
[2023-06-28 10:00:50,314] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 10:00:50,314] [INFO] DQC Reference Directory: /var/lib/cwl/stg1298594a-7634-4dbb-9856-0765f9e22fc1/dqc_reference
[2023-06-28 10:00:51,809] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 10:00:51,810] [INFO] Task started: Prodigal
[2023-06-28 10:00:51,810] [INFO] Running command: gunzip -c /var/lib/cwl/stg0fb681cc-3b87-43c4-a57a-84d29f6fc362/GCA_017989735.1_ASM1798973v1_genomic.fna.gz | prodigal -d GCA_017989735.1_ASM1798973v1_genomic.fna/cds.fna -a GCA_017989735.1_ASM1798973v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 10:00:55,424] [INFO] Task succeeded: Prodigal
[2023-06-28 10:00:55,425] [INFO] Task started: HMMsearch
[2023-06-28 10:00:55,425] [INFO] Running command: hmmsearch --tblout GCA_017989735.1_ASM1798973v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1298594a-7634-4dbb-9856-0765f9e22fc1/dqc_reference/reference_markers.hmm GCA_017989735.1_ASM1798973v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 10:00:55,607] [INFO] Task succeeded: HMMsearch
[2023-06-28 10:00:55,610] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg0fb681cc-3b87-43c4-a57a-84d29f6fc362/GCA_017989735.1_ASM1798973v1_genomic.fna.gz]
[2023-06-28 10:00:55,637] [INFO] Query marker FASTA was written to GCA_017989735.1_ASM1798973v1_genomic.fna/markers.fasta
[2023-06-28 10:00:55,638] [INFO] Task started: Blastn
[2023-06-28 10:00:55,638] [INFO] Running command: blastn -query GCA_017989735.1_ASM1798973v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1298594a-7634-4dbb-9856-0765f9e22fc1/dqc_reference/reference_markers.fasta -out GCA_017989735.1_ASM1798973v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:00:56,323] [INFO] Task succeeded: Blastn
[2023-06-28 10:00:56,335] [INFO] Selected 17 target genomes.
[2023-06-28 10:00:56,336] [INFO] Target genome list was writen to GCA_017989735.1_ASM1798973v1_genomic.fna/target_genomes.txt
[2023-06-28 10:00:56,338] [INFO] Task started: fastANI
[2023-06-28 10:00:56,338] [INFO] Running command: fastANI --query /var/lib/cwl/stg0fb681cc-3b87-43c4-a57a-84d29f6fc362/GCA_017989735.1_ASM1798973v1_genomic.fna.gz --refList GCA_017989735.1_ASM1798973v1_genomic.fna/target_genomes.txt --output GCA_017989735.1_ASM1798973v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 10:01:11,085] [INFO] Task succeeded: fastANI
[2023-06-28 10:01:11,086] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1298594a-7634-4dbb-9856-0765f9e22fc1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 10:01:11,086] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1298594a-7634-4dbb-9856-0765f9e22fc1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 10:01:11,089] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 10:01:11,089] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 10:01:11,089] [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 10:01:11,092] [INFO] DFAST Taxonomy check result was written to GCA_017989735.1_ASM1798973v1_genomic.fna/tc_result.tsv
[2023-06-28 10:01:11,093] [INFO] ===== Taxonomy check completed =====
[2023-06-28 10:01:11,093] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 10:01:11,094] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1298594a-7634-4dbb-9856-0765f9e22fc1/dqc_reference/checkm_data
[2023-06-28 10:01:11,098] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 10:01:11,119] [INFO] Task started: CheckM
[2023-06-28 10:01:11,119] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017989735.1_ASM1798973v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017989735.1_ASM1798973v1_genomic.fna/checkm_input GCA_017989735.1_ASM1798973v1_genomic.fna/checkm_result
[2023-06-28 10:01:29,048] [INFO] Task succeeded: CheckM
[2023-06-28 10:01:29,050] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 20.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 10:01:29,074] [INFO] ===== Completeness check finished =====
[2023-06-28 10:01:29,075] [INFO] ===== Start GTDB Search =====
[2023-06-28 10:01:29,075] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017989735.1_ASM1798973v1_genomic.fna/markers.fasta)
[2023-06-28 10:01:29,076] [INFO] Task started: Blastn
[2023-06-28 10:01:29,076] [INFO] Running command: blastn -query GCA_017989735.1_ASM1798973v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1298594a-7634-4dbb-9856-0765f9e22fc1/dqc_reference/reference_markers_gtdb.fasta -out GCA_017989735.1_ASM1798973v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:01:30,128] [INFO] Task succeeded: Blastn
[2023-06-28 10:01:30,134] [INFO] Selected 16 target genomes.
[2023-06-28 10:01:30,135] [INFO] Target genome list was writen to GCA_017989735.1_ASM1798973v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 10:01:30,140] [INFO] Task started: fastANI
[2023-06-28 10:01:30,140] [INFO] Running command: fastANI --query /var/lib/cwl/stg0fb681cc-3b87-43c4-a57a-84d29f6fc362/GCA_017989735.1_ASM1798973v1_genomic.fna.gz --refList GCA_017989735.1_ASM1798973v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017989735.1_ASM1798973v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 10:01:42,005] [INFO] Task succeeded: fastANI
[2023-06-28 10:01:42,013] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 10:01:42,013] [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_016794465.1	s__JAGNNG01 sp016794465	95.804	310	321	d__Bacteria;p__Myxococcota;c__Polyangia;o__Palsa-1104;f__JAEUJZ01;g__JAGNNG01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016794365.1	s__JAGNNG01 sp016794365	80.8975	256	321	d__Bacteria;p__Myxococcota;c__Polyangia;o__Palsa-1104;f__JAEUJZ01;g__JAGNNG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017990795.1	s__JAGNNG01 sp017990795	80.8236	56	321	d__Bacteria;p__Myxococcota;c__Polyangia;o__Palsa-1104;f__JAEUJZ01;g__JAGNNG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794505.1	s__JAEUJZ01 sp016794505	76.5069	75	321	d__Bacteria;p__Myxococcota;c__Polyangia;o__Palsa-1104;f__JAEUJZ01;g__JAEUJZ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 10:01:42,015] [INFO] GTDB search result was written to GCA_017989735.1_ASM1798973v1_genomic.fna/result_gtdb.tsv
[2023-06-28 10:01:42,016] [INFO] ===== GTDB Search completed =====
[2023-06-28 10:01:42,019] [INFO] DFAST_QC result json was written to GCA_017989735.1_ASM1798973v1_genomic.fna/dqc_result.json
[2023-06-28 10:01:42,019] [INFO] DFAST_QC completed!
[2023-06-28 10:01:42,019] [INFO] Total running time: 0h0m52s