[2023-06-28 11:01:39,886] [INFO] DFAST_QC pipeline started.
[2023-06-28 11:01:39,888] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 11:01:39,889] [INFO] DQC Reference Directory: /var/lib/cwl/stgca7dc59a-f530-4337-84c2-eb2050c1f322/dqc_reference
[2023-06-28 11:01:41,249] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 11:01:41,251] [INFO] Task started: Prodigal
[2023-06-28 11:01:41,251] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3fc7ff9-47d3-430d-841b-5f89b9091af9/GCA_020059545.1_ASM2005954v1_genomic.fna.gz | prodigal -d GCA_020059545.1_ASM2005954v1_genomic.fna/cds.fna -a GCA_020059545.1_ASM2005954v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 11:01:52,188] [INFO] Task succeeded: Prodigal
[2023-06-28 11:01:52,189] [INFO] Task started: HMMsearch
[2023-06-28 11:01:52,189] [INFO] Running command: hmmsearch --tblout GCA_020059545.1_ASM2005954v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca7dc59a-f530-4337-84c2-eb2050c1f322/dqc_reference/reference_markers.hmm GCA_020059545.1_ASM2005954v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 11:01:52,500] [INFO] Task succeeded: HMMsearch
[2023-06-28 11:01:52,501] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgf3fc7ff9-47d3-430d-841b-5f89b9091af9/GCA_020059545.1_ASM2005954v1_genomic.fna.gz]
[2023-06-28 11:01:52,537] [INFO] Query marker FASTA was written to GCA_020059545.1_ASM2005954v1_genomic.fna/markers.fasta
[2023-06-28 11:01:52,537] [INFO] Task started: Blastn
[2023-06-28 11:01:52,538] [INFO] Running command: blastn -query GCA_020059545.1_ASM2005954v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca7dc59a-f530-4337-84c2-eb2050c1f322/dqc_reference/reference_markers.fasta -out GCA_020059545.1_ASM2005954v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 11:01:53,165] [INFO] Task succeeded: Blastn
[2023-06-28 11:01:53,182] [INFO] Selected 21 target genomes.
[2023-06-28 11:01:53,182] [INFO] Target genome list was writen to GCA_020059545.1_ASM2005954v1_genomic.fna/target_genomes.txt
[2023-06-28 11:01:53,186] [INFO] Task started: fastANI
[2023-06-28 11:01:53,187] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3fc7ff9-47d3-430d-841b-5f89b9091af9/GCA_020059545.1_ASM2005954v1_genomic.fna.gz --refList GCA_020059545.1_ASM2005954v1_genomic.fna/target_genomes.txt --output GCA_020059545.1_ASM2005954v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 11:02:08,871] [INFO] Task succeeded: fastANI
[2023-06-28 11:02:08,871] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca7dc59a-f530-4337-84c2-eb2050c1f322/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 11:02:08,872] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca7dc59a-f530-4337-84c2-eb2050c1f322/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 11:02:08,873] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 11:02:08,873] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 11:02:08,873] [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 11:02:08,875] [INFO] DFAST Taxonomy check result was written to GCA_020059545.1_ASM2005954v1_genomic.fna/tc_result.tsv
[2023-06-28 11:02:08,876] [INFO] ===== Taxonomy check completed =====
[2023-06-28 11:02:08,876] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 11:02:08,876] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca7dc59a-f530-4337-84c2-eb2050c1f322/dqc_reference/checkm_data
[2023-06-28 11:02:08,879] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 11:02:08,922] [INFO] Task started: CheckM
[2023-06-28 11:02:08,922] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020059545.1_ASM2005954v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020059545.1_ASM2005954v1_genomic.fna/checkm_input GCA_020059545.1_ASM2005954v1_genomic.fna/checkm_result
[2023-06-28 11:02:44,940] [INFO] Task succeeded: CheckM
[2023-06-28 11:02:44,941] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 11:02:44,966] [INFO] ===== Completeness check finished =====
[2023-06-28 11:02:44,966] [INFO] ===== Start GTDB Search =====
[2023-06-28 11:02:44,967] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020059545.1_ASM2005954v1_genomic.fna/markers.fasta)
[2023-06-28 11:02:44,967] [INFO] Task started: Blastn
[2023-06-28 11:02:44,967] [INFO] Running command: blastn -query GCA_020059545.1_ASM2005954v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca7dc59a-f530-4337-84c2-eb2050c1f322/dqc_reference/reference_markers_gtdb.fasta -out GCA_020059545.1_ASM2005954v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 11:02:45,733] [INFO] Task succeeded: Blastn
[2023-06-28 11:02:45,739] [INFO] Selected 29 target genomes.
[2023-06-28 11:02:45,739] [INFO] Target genome list was writen to GCA_020059545.1_ASM2005954v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 11:02:45,753] [INFO] Task started: fastANI
[2023-06-28 11:02:45,753] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3fc7ff9-47d3-430d-841b-5f89b9091af9/GCA_020059545.1_ASM2005954v1_genomic.fna.gz --refList GCA_020059545.1_ASM2005954v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020059545.1_ASM2005954v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 11:03:01,383] [INFO] Task succeeded: fastANI
[2023-06-28 11:03:01,391] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 11:03:01,391] [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_011368195.1	s__DSWF01 sp011368195	77.111	50	1255	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA4823;g__DSWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016935755.1	s__JAFGQI01 sp016935755	76.3935	51	1255	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA4823;g__JAFGQI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002428565.1	s__UBA6092 sp002428565	76.2074	54	1255	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA4823;g__UBA6092	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 11:03:01,393] [INFO] GTDB search result was written to GCA_020059545.1_ASM2005954v1_genomic.fna/result_gtdb.tsv
[2023-06-28 11:03:01,394] [INFO] ===== GTDB Search completed =====
[2023-06-28 11:03:01,396] [INFO] DFAST_QC result json was written to GCA_020059545.1_ASM2005954v1_genomic.fna/dqc_result.json
[2023-06-28 11:03:01,396] [INFO] DFAST_QC completed!
[2023-06-28 11:03:01,396] [INFO] Total running time: 0h1m22s