[2023-06-29 03:29:07,787] [INFO] DFAST_QC pipeline started.
[2023-06-29 03:29:07,793] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 03:29:07,793] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a3f651b-2e6c-4167-b8d7-26cce3f0bb76/dqc_reference
[2023-06-29 03:29:10,072] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 03:29:10,073] [INFO] Task started: Prodigal
[2023-06-29 03:29:10,073] [INFO] Running command: gunzip -c /var/lib/cwl/stg9292ab37-207c-4a5b-9e9b-24acf202323d/GCA_020532285.1_ASM2053228v1_genomic.fna.gz | prodigal -d GCA_020532285.1_ASM2053228v1_genomic.fna/cds.fna -a GCA_020532285.1_ASM2053228v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 03:29:16,616] [INFO] Task succeeded: Prodigal
[2023-06-29 03:29:16,616] [INFO] Task started: HMMsearch
[2023-06-29 03:29:16,616] [INFO] Running command: hmmsearch --tblout GCA_020532285.1_ASM2053228v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a3f651b-2e6c-4167-b8d7-26cce3f0bb76/dqc_reference/reference_markers.hmm GCA_020532285.1_ASM2053228v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 03:29:16,869] [INFO] Task succeeded: HMMsearch
[2023-06-29 03:29:16,871] [INFO] Found 6/6 markers.
[2023-06-29 03:29:16,896] [INFO] Query marker FASTA was written to GCA_020532285.1_ASM2053228v1_genomic.fna/markers.fasta
[2023-06-29 03:29:16,896] [INFO] Task started: Blastn
[2023-06-29 03:29:16,896] [INFO] Running command: blastn -query GCA_020532285.1_ASM2053228v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a3f651b-2e6c-4167-b8d7-26cce3f0bb76/dqc_reference/reference_markers.fasta -out GCA_020532285.1_ASM2053228v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 03:29:17,517] [INFO] Task succeeded: Blastn
[2023-06-29 03:29:17,524] [INFO] Selected 25 target genomes.
[2023-06-29 03:29:17,524] [INFO] Target genome list was writen to GCA_020532285.1_ASM2053228v1_genomic.fna/target_genomes.txt
[2023-06-29 03:29:17,530] [INFO] Task started: fastANI
[2023-06-29 03:29:17,530] [INFO] Running command: fastANI --query /var/lib/cwl/stg9292ab37-207c-4a5b-9e9b-24acf202323d/GCA_020532285.1_ASM2053228v1_genomic.fna.gz --refList GCA_020532285.1_ASM2053228v1_genomic.fna/target_genomes.txt --output GCA_020532285.1_ASM2053228v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 03:29:36,175] [INFO] Task succeeded: fastANI
[2023-06-29 03:29:36,175] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a3f651b-2e6c-4167-b8d7-26cce3f0bb76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 03:29:36,176] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a3f651b-2e6c-4167-b8d7-26cce3f0bb76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 03:29:36,177] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 03:29:36,177] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 03:29:36,177] [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
--------------------------------------------------------------------------------
[2023-06-29 03:29:36,180] [INFO] DFAST Taxonomy check result was written to GCA_020532285.1_ASM2053228v1_genomic.fna/tc_result.tsv
[2023-06-29 03:29:36,181] [INFO] ===== Taxonomy check completed =====
[2023-06-29 03:29:36,181] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 03:29:36,181] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a3f651b-2e6c-4167-b8d7-26cce3f0bb76/dqc_reference/checkm_data
[2023-06-29 03:29:36,184] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 03:29:36,215] [INFO] Task started: CheckM
[2023-06-29 03:29:36,216] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020532285.1_ASM2053228v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020532285.1_ASM2053228v1_genomic.fna/checkm_input GCA_020532285.1_ASM2053228v1_genomic.fna/checkm_result
[2023-06-29 03:30:01,903] [INFO] Task succeeded: CheckM
[2023-06-29 03:30:01,904] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 03:30:01,943] [INFO] ===== Completeness check finished =====
[2023-06-29 03:30:01,944] [INFO] ===== Start GTDB Search =====
[2023-06-29 03:30:01,944] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020532285.1_ASM2053228v1_genomic.fna/markers.fasta)
[2023-06-29 03:30:01,945] [INFO] Task started: Blastn
[2023-06-29 03:30:01,945] [INFO] Running command: blastn -query GCA_020532285.1_ASM2053228v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a3f651b-2e6c-4167-b8d7-26cce3f0bb76/dqc_reference/reference_markers_gtdb.fasta -out GCA_020532285.1_ASM2053228v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 03:30:02,721] [INFO] Task succeeded: Blastn
[2023-06-29 03:30:02,727] [INFO] Selected 19 target genomes.
[2023-06-29 03:30:02,727] [INFO] Target genome list was writen to GCA_020532285.1_ASM2053228v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 03:30:02,797] [INFO] Task started: fastANI
[2023-06-29 03:30:02,797] [INFO] Running command: fastANI --query /var/lib/cwl/stg9292ab37-207c-4a5b-9e9b-24acf202323d/GCA_020532285.1_ASM2053228v1_genomic.fna.gz --refList GCA_020532285.1_ASM2053228v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020532285.1_ASM2053228v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 03:30:11,614] [INFO] Task succeeded: fastANI
[2023-06-29 03:30:11,626] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 03:30:11,626] [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_012522635.1	s__Syntrophosphaera sp012522635	99.1867	515	692	d__Bacteria;p__Cloacimonadota;c__Cloacimonadia;o__Cloacimonadales;f__Cloacimonadaceae;g__Syntrophosphaera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012728875.1	s__Syntrophosphaera sp012728875	84.4648	528	692	d__Bacteria;p__Cloacimonadota;c__Cloacimonadia;o__Cloacimonadales;f__Cloacimonadaceae;g__Syntrophosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012516855.1	s__Syntrophosphaera sp012516855	77.2869	169	692	d__Bacteria;p__Cloacimonadota;c__Cloacimonadia;o__Cloacimonadales;f__Cloacimonadaceae;g__Syntrophosphaera	95.0	98.46	98.46	0.92	0.92	2	-
GCA_017995495.1	s__Syntrophosphaera sp017995495	77.241	114	692	d__Bacteria;p__Cloacimonadota;c__Cloacimonadia;o__Cloacimonadales;f__Cloacimonadaceae;g__Syntrophosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002391675.1	s__UBA3900 sp002391675	76.6354	55	692	d__Bacteria;p__Cloacimonadota;c__Cloacimonadia;o__Cloacimonadales;f__Cloacimonadaceae;g__UBA3900	95.0	98.99	98.12	0.91	0.89	3	-
--------------------------------------------------------------------------------
[2023-06-29 03:30:11,628] [INFO] GTDB search result was written to GCA_020532285.1_ASM2053228v1_genomic.fna/result_gtdb.tsv
[2023-06-29 03:30:11,629] [INFO] ===== GTDB Search completed =====
[2023-06-29 03:30:11,633] [INFO] DFAST_QC result json was written to GCA_020532285.1_ASM2053228v1_genomic.fna/dqc_result.json
[2023-06-29 03:30:11,634] [INFO] DFAST_QC completed!
[2023-06-29 03:30:11,634] [INFO] Total running time: 0h1m4s