[2023-06-27 06:05:25,436] [INFO] DFAST_QC pipeline started.
[2023-06-27 06:05:25,438] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 06:05:25,439] [INFO] DQC Reference Directory: /var/lib/cwl/stg861ce807-03cf-4b3a-8e76-7e2d67dad86a/dqc_reference
[2023-06-27 06:05:27,078] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 06:05:27,079] [INFO] Task started: Prodigal
[2023-06-27 06:05:27,079] [INFO] Running command: gunzip -c /var/lib/cwl/stg94f7d539-1d35-411c-85b7-a76090b9abb5/GCA_002449935.1_ASM244993v1_genomic.fna.gz | prodigal -d GCA_002449935.1_ASM244993v1_genomic.fna/cds.fna -a GCA_002449935.1_ASM244993v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 06:05:32,570] [INFO] Task succeeded: Prodigal
[2023-06-27 06:05:32,571] [INFO] Task started: HMMsearch
[2023-06-27 06:05:32,571] [INFO] Running command: hmmsearch --tblout GCA_002449935.1_ASM244993v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg861ce807-03cf-4b3a-8e76-7e2d67dad86a/dqc_reference/reference_markers.hmm GCA_002449935.1_ASM244993v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 06:05:32,804] [INFO] Task succeeded: HMMsearch
[2023-06-27 06:05:32,806] [INFO] Found 6/6 markers.
[2023-06-27 06:05:32,848] [INFO] Query marker FASTA was written to GCA_002449935.1_ASM244993v1_genomic.fna/markers.fasta
[2023-06-27 06:05:32,849] [INFO] Task started: Blastn
[2023-06-27 06:05:32,849] [INFO] Running command: blastn -query GCA_002449935.1_ASM244993v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg861ce807-03cf-4b3a-8e76-7e2d67dad86a/dqc_reference/reference_markers.fasta -out GCA_002449935.1_ASM244993v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:05:33,477] [INFO] Task succeeded: Blastn
[2023-06-27 06:05:33,481] [INFO] Selected 30 target genomes.
[2023-06-27 06:05:33,481] [INFO] Target genome list was writen to GCA_002449935.1_ASM244993v1_genomic.fna/target_genomes.txt
[2023-06-27 06:05:33,485] [INFO] Task started: fastANI
[2023-06-27 06:05:33,486] [INFO] Running command: fastANI --query /var/lib/cwl/stg94f7d539-1d35-411c-85b7-a76090b9abb5/GCA_002449935.1_ASM244993v1_genomic.fna.gz --refList GCA_002449935.1_ASM244993v1_genomic.fna/target_genomes.txt --output GCA_002449935.1_ASM244993v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 06:05:59,768] [INFO] Task succeeded: fastANI
[2023-06-27 06:05:59,769] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg861ce807-03cf-4b3a-8e76-7e2d67dad86a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 06:05:59,769] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg861ce807-03cf-4b3a-8e76-7e2d67dad86a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 06:05:59,771] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 06:05:59,771] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 06:05:59,771] [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 06:05:59,780] [INFO] DFAST Taxonomy check result was written to GCA_002449935.1_ASM244993v1_genomic.fna/tc_result.tsv
[2023-06-27 06:05:59,781] [INFO] ===== Taxonomy check completed =====
[2023-06-27 06:05:59,781] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 06:05:59,781] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg861ce807-03cf-4b3a-8e76-7e2d67dad86a/dqc_reference/checkm_data
[2023-06-27 06:05:59,786] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 06:05:59,815] [INFO] Task started: CheckM
[2023-06-27 06:05:59,815] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002449935.1_ASM244993v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002449935.1_ASM244993v1_genomic.fna/checkm_input GCA_002449935.1_ASM244993v1_genomic.fna/checkm_result
[2023-06-27 06:06:22,264] [INFO] Task succeeded: CheckM
[2023-06-27 06:06:22,265] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.39%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 06:06:22,287] [INFO] ===== Completeness check finished =====
[2023-06-27 06:06:22,287] [INFO] ===== Start GTDB Search =====
[2023-06-27 06:06:22,287] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002449935.1_ASM244993v1_genomic.fna/markers.fasta)
[2023-06-27 06:06:22,288] [INFO] Task started: Blastn
[2023-06-27 06:06:22,288] [INFO] Running command: blastn -query GCA_002449935.1_ASM244993v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg861ce807-03cf-4b3a-8e76-7e2d67dad86a/dqc_reference/reference_markers_gtdb.fasta -out GCA_002449935.1_ASM244993v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:06:23,230] [INFO] Task succeeded: Blastn
[2023-06-27 06:06:23,235] [INFO] Selected 9 target genomes.
[2023-06-27 06:06:23,235] [INFO] Target genome list was writen to GCA_002449935.1_ASM244993v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 06:06:23,247] [INFO] Task started: fastANI
[2023-06-27 06:06:23,247] [INFO] Running command: fastANI --query /var/lib/cwl/stg94f7d539-1d35-411c-85b7-a76090b9abb5/GCA_002449935.1_ASM244993v1_genomic.fna.gz --refList GCA_002449935.1_ASM244993v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002449935.1_ASM244993v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 06:06:27,837] [INFO] Task succeeded: fastANI
[2023-06-27 06:06:27,851] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 06:06:27,852] [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_002391225.1	s__UBA4246 sp002391225	95.735	605	678	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA4246	95.0	95.72	95.65	0.85	0.82	4	conclusive
GCA_902790015.1	s__UBA4246 sp902790015	80.9405	329	678	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA4246	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902760595.1	s__UBA4246 sp902760595	78.9684	185	678	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA4246	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902789795.1	s__UBA4246 sp902789795	78.422	203	678	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA4246	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017430225.1	s__UBA4246 sp017430225	78.2867	143	678	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA4246	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017469085.1	s__UBA4246 sp017469085	78.1117	124	678	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA4246	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902766515.1	s__UBA4246 sp902766515	77.8797	130	678	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA4246	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905236495.1	s__RUG563 sp905236495	77.0165	77	678	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG563	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 06:06:27,854] [INFO] GTDB search result was written to GCA_002449935.1_ASM244993v1_genomic.fna/result_gtdb.tsv
[2023-06-27 06:06:27,855] [INFO] ===== GTDB Search completed =====
[2023-06-27 06:06:27,858] [INFO] DFAST_QC result json was written to GCA_002449935.1_ASM244993v1_genomic.fna/dqc_result.json
[2023-06-27 06:06:27,859] [INFO] DFAST_QC completed!
[2023-06-27 06:06:27,859] [INFO] Total running time: 0h1m2s