[2023-06-30 03:32:46,466] [INFO] DFAST_QC pipeline started.
[2023-06-30 03:32:46,476] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 03:32:46,477] [INFO] DQC Reference Directory: /var/lib/cwl/stg148139c1-4a55-48fd-893b-8efcf948b3cb/dqc_reference
[2023-06-30 03:32:47,722] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 03:32:47,723] [INFO] Task started: Prodigal
[2023-06-30 03:32:47,724] [INFO] Running command: gunzip -c /var/lib/cwl/stg646e50ac-0864-4886-93ee-9910ac7e29e4/GCA_943845895.1_20200430_Bin_METABAT_120_1-contigs.fa_genomic.fna.gz | prodigal -d GCA_943845895.1_20200430_Bin_METABAT_120_1-contigs.fa_genomic.fna/cds.fna -a GCA_943845895.1_20200430_Bin_METABAT_120_1-contigs.fa_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 03:32:54,625] [INFO] Task succeeded: Prodigal
[2023-06-30 03:32:54,625] [INFO] Task started: HMMsearch
[2023-06-30 03:32:54,625] [INFO] Running command: hmmsearch --tblout GCA_943845895.1_20200430_Bin_METABAT_120_1-contigs.fa_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg148139c1-4a55-48fd-893b-8efcf948b3cb/dqc_reference/reference_markers.hmm GCA_943845895.1_20200430_Bin_METABAT_120_1-contigs.fa_genomic.fna/protein.faa > /dev/null
[2023-06-30 03:32:54,859] [INFO] Task succeeded: HMMsearch
[2023-06-30 03:32:54,860] [INFO] Found 6/6 markers.
[2023-06-30 03:32:54,881] [INFO] Query marker FASTA was written to GCA_943845895.1_20200430_Bin_METABAT_120_1-contigs.fa_genomic.fna/markers.fasta
[2023-06-30 03:32:54,882] [INFO] Task started: Blastn
[2023-06-30 03:32:54,882] [INFO] Running command: blastn -query GCA_943845895.1_20200430_Bin_METABAT_120_1-contigs.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg148139c1-4a55-48fd-893b-8efcf948b3cb/dqc_reference/reference_markers.fasta -out GCA_943845895.1_20200430_Bin_METABAT_120_1-contigs.fa_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:32:55,504] [INFO] Task succeeded: Blastn
[2023-06-30 03:32:55,509] [INFO] Selected 32 target genomes.
[2023-06-30 03:32:55,510] [INFO] Target genome list was writen to GCA_943845895.1_20200430_Bin_METABAT_120_1-contigs.fa_genomic.fna/target_genomes.txt
[2023-06-30 03:32:55,512] [INFO] Task started: fastANI
[2023-06-30 03:32:55,512] [INFO] Running command: fastANI --query /var/lib/cwl/stg646e50ac-0864-4886-93ee-9910ac7e29e4/GCA_943845895.1_20200430_Bin_METABAT_120_1-contigs.fa_genomic.fna.gz --refList GCA_943845895.1_20200430_Bin_METABAT_120_1-contigs.fa_genomic.fna/target_genomes.txt --output GCA_943845895.1_20200430_Bin_METABAT_120_1-contigs.fa_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 03:33:11,947] [INFO] Task succeeded: fastANI
[2023-06-30 03:33:11,948] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg148139c1-4a55-48fd-893b-8efcf948b3cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 03:33:11,948] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg148139c1-4a55-48fd-893b-8efcf948b3cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 03:33:11,950] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 03:33:11,950] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 03:33:11,950] [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
--------------------------------------------------------------------------------
[2023-06-30 03:33:11,953] [INFO] DFAST Taxonomy check result was written to GCA_943845895.1_20200430_Bin_METABAT_120_1-contigs.fa_genomic.fna/tc_result.tsv
[2023-06-30 03:33:11,954] [INFO] ===== Taxonomy check completed =====
[2023-06-30 03:33:11,954] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 03:33:11,955] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg148139c1-4a55-48fd-893b-8efcf948b3cb/dqc_reference/checkm_data
[2023-06-30 03:33:11,959] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 03:33:11,983] [INFO] Task started: CheckM
[2023-06-30 03:33:11,983] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_943845895.1_20200430_Bin_METABAT_120_1-contigs.fa_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_943845895.1_20200430_Bin_METABAT_120_1-contigs.fa_genomic.fna/checkm_input GCA_943845895.1_20200430_Bin_METABAT_120_1-contigs.fa_genomic.fna/checkm_result
[2023-06-30 03:33:38,178] [INFO] Task succeeded: CheckM
[2023-06-30 03:33:38,180] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 03:33:38,203] [INFO] ===== Completeness check finished =====
[2023-06-30 03:33:38,203] [INFO] ===== Start GTDB Search =====
[2023-06-30 03:33:38,203] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_943845895.1_20200430_Bin_METABAT_120_1-contigs.fa_genomic.fna/markers.fasta)
[2023-06-30 03:33:38,204] [INFO] Task started: Blastn
[2023-06-30 03:33:38,204] [INFO] Running command: blastn -query GCA_943845895.1_20200430_Bin_METABAT_120_1-contigs.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg148139c1-4a55-48fd-893b-8efcf948b3cb/dqc_reference/reference_markers_gtdb.fasta -out GCA_943845895.1_20200430_Bin_METABAT_120_1-contigs.fa_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:33:39,024] [INFO] Task succeeded: Blastn
[2023-06-30 03:33:39,028] [INFO] Selected 20 target genomes.
[2023-06-30 03:33:39,028] [INFO] Target genome list was writen to GCA_943845895.1_20200430_Bin_METABAT_120_1-contigs.fa_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 03:33:39,032] [INFO] Task started: fastANI
[2023-06-30 03:33:39,032] [INFO] Running command: fastANI --query /var/lib/cwl/stg646e50ac-0864-4886-93ee-9910ac7e29e4/GCA_943845895.1_20200430_Bin_METABAT_120_1-contigs.fa_genomic.fna.gz --refList GCA_943845895.1_20200430_Bin_METABAT_120_1-contigs.fa_genomic.fna/target_genomes_gtdb.txt --output GCA_943845895.1_20200430_Bin_METABAT_120_1-contigs.fa_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 03:33:46,262] [INFO] Task succeeded: fastANI
[2023-06-30 03:33:46,277] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 03:33:46,277] [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_011526285.1	s__UBA7428 sp011526285	77.8495	174	611	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478905.1	s__UBA7428 sp905478905	77.7647	159	611	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	98.97	98.97	0.80	0.80	2	-
GCA_011526275.1	s__UBA7428 sp011526275	77.7266	176	611	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181615.1	s__UBA7428 sp905181615	77.1168	83	611	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	99.59	99.59	0.98	0.98	2	-
GCA_003023645.1	s__UBA7428 sp003023645	77.0308	84	611	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	99.50	99.50	0.87	0.87	2	-
GCA_011526335.1	s__UBA7428 sp011526335	76.9427	94	611	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608425.1	s__UBA7428 sp018608425	76.7855	67	611	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002477625.1	s__UBA7428 sp002477625	76.4033	75	611	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	98.28	97.25	0.74	0.68	4	-
GCA_002708445.1	s__UBA7428 sp002708445	76.1979	59	611	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 03:33:46,279] [INFO] GTDB search result was written to GCA_943845895.1_20200430_Bin_METABAT_120_1-contigs.fa_genomic.fna/result_gtdb.tsv
[2023-06-30 03:33:46,280] [INFO] ===== GTDB Search completed =====
[2023-06-30 03:33:46,282] [INFO] DFAST_QC result json was written to GCA_943845895.1_20200430_Bin_METABAT_120_1-contigs.fa_genomic.fna/dqc_result.json
[2023-06-30 03:33:46,282] [INFO] DFAST_QC completed!
[2023-06-30 03:33:46,282] [INFO] Total running time: 0h0m60s