[2023-06-17 01:16:01,842] [INFO] DFAST_QC pipeline started.
[2023-06-17 01:16:01,844] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 01:16:01,845] [INFO] DQC Reference Directory: /var/lib/cwl/stgaad51ce1-7063-4eb2-a124-5f512cf3086a/dqc_reference
[2023-06-17 01:16:04,460] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 01:16:04,461] [INFO] Task started: Prodigal
[2023-06-17 01:16:04,462] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ae659f9-7498-4a96-bb9e-aa041a85fe53/GCA_905188045.1_ERR1430432-mag-bin.14_genomic.fna.gz | prodigal -d GCA_905188045.1_ERR1430432-mag-bin.14_genomic.fna/cds.fna -a GCA_905188045.1_ERR1430432-mag-bin.14_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 01:16:07,998] [INFO] Task succeeded: Prodigal
[2023-06-17 01:16:07,998] [INFO] Task started: HMMsearch
[2023-06-17 01:16:07,998] [INFO] Running command: hmmsearch --tblout GCA_905188045.1_ERR1430432-mag-bin.14_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaad51ce1-7063-4eb2-a124-5f512cf3086a/dqc_reference/reference_markers.hmm GCA_905188045.1_ERR1430432-mag-bin.14_genomic.fna/protein.faa > /dev/null
[2023-06-17 01:16:08,238] [INFO] Task succeeded: HMMsearch
[2023-06-17 01:16:08,240] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg9ae659f9-7498-4a96-bb9e-aa041a85fe53/GCA_905188045.1_ERR1430432-mag-bin.14_genomic.fna.gz]
[2023-06-17 01:16:08,261] [INFO] Query marker FASTA was written to GCA_905188045.1_ERR1430432-mag-bin.14_genomic.fna/markers.fasta
[2023-06-17 01:16:08,262] [INFO] Task started: Blastn
[2023-06-17 01:16:08,262] [INFO] Running command: blastn -query GCA_905188045.1_ERR1430432-mag-bin.14_genomic.fna/markers.fasta -db /var/lib/cwl/stgaad51ce1-7063-4eb2-a124-5f512cf3086a/dqc_reference/reference_markers.fasta -out GCA_905188045.1_ERR1430432-mag-bin.14_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:16:09,348] [INFO] Task succeeded: Blastn
[2023-06-17 01:16:09,355] [INFO] Selected 14 target genomes.
[2023-06-17 01:16:09,358] [INFO] Target genome list was writen to GCA_905188045.1_ERR1430432-mag-bin.14_genomic.fna/target_genomes.txt
[2023-06-17 01:16:09,365] [INFO] Task started: fastANI
[2023-06-17 01:16:09,365] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ae659f9-7498-4a96-bb9e-aa041a85fe53/GCA_905188045.1_ERR1430432-mag-bin.14_genomic.fna.gz --refList GCA_905188045.1_ERR1430432-mag-bin.14_genomic.fna/target_genomes.txt --output GCA_905188045.1_ERR1430432-mag-bin.14_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 01:16:16,108] [INFO] Task succeeded: fastANI
[2023-06-17 01:16:16,109] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaad51ce1-7063-4eb2-a124-5f512cf3086a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 01:16:16,109] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaad51ce1-7063-4eb2-a124-5f512cf3086a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 01:16:16,111] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 01:16:16,111] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 01:16:16,111] [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
--------------------------------------------------------------------------------
[2023-06-17 01:16:16,113] [INFO] DFAST Taxonomy check result was written to GCA_905188045.1_ERR1430432-mag-bin.14_genomic.fna/tc_result.tsv
[2023-06-17 01:16:16,114] [INFO] ===== Taxonomy check completed =====
[2023-06-17 01:16:16,114] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 01:16:16,114] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaad51ce1-7063-4eb2-a124-5f512cf3086a/dqc_reference/checkm_data
[2023-06-17 01:16:16,122] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 01:16:16,140] [INFO] Task started: CheckM
[2023-06-17 01:16:16,141] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905188045.1_ERR1430432-mag-bin.14_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905188045.1_ERR1430432-mag-bin.14_genomic.fna/checkm_input GCA_905188045.1_ERR1430432-mag-bin.14_genomic.fna/checkm_result
[2023-06-17 01:16:33,654] [INFO] Task succeeded: CheckM
[2023-06-17 01:16:33,655] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 01:16:33,673] [INFO] ===== Completeness check finished =====
[2023-06-17 01:16:33,673] [INFO] ===== Start GTDB Search =====
[2023-06-17 01:16:33,674] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905188045.1_ERR1430432-mag-bin.14_genomic.fna/markers.fasta)
[2023-06-17 01:16:33,674] [INFO] Task started: Blastn
[2023-06-17 01:16:33,674] [INFO] Running command: blastn -query GCA_905188045.1_ERR1430432-mag-bin.14_genomic.fna/markers.fasta -db /var/lib/cwl/stgaad51ce1-7063-4eb2-a124-5f512cf3086a/dqc_reference/reference_markers_gtdb.fasta -out GCA_905188045.1_ERR1430432-mag-bin.14_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:16:34,251] [INFO] Task succeeded: Blastn
[2023-06-17 01:16:34,257] [INFO] Selected 12 target genomes.
[2023-06-17 01:16:34,257] [INFO] Target genome list was writen to GCA_905188045.1_ERR1430432-mag-bin.14_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 01:16:34,263] [INFO] Task started: fastANI
[2023-06-17 01:16:34,263] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ae659f9-7498-4a96-bb9e-aa041a85fe53/GCA_905188045.1_ERR1430432-mag-bin.14_genomic.fna.gz --refList GCA_905188045.1_ERR1430432-mag-bin.14_genomic.fna/target_genomes_gtdb.txt --output GCA_905188045.1_ERR1430432-mag-bin.14_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 01:16:38,672] [INFO] Task succeeded: fastANI
[2023-06-17 01:16:38,682] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 01:16:38,682] [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_900549495.1	s__Faecousia sp900549495	82.5657	136	397	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	96.75	96.75	0.74	0.74	2	-
GCA_900546075.1	s__Faecousia sp900546075	81.0076	119	397	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	97.06	96.74	0.84	0.78	6	-
GCA_900549705.1	s__Faecousia sp900549705	80.8928	137	397	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	96.98	96.52	0.84	0.77	3	-
GCA_900547405.1	s__Faecousia sp900547405	80.8045	95	397	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	97.15	96.95	0.86	0.86	5	-
GCA_000434635.1	s__Faecousia sp000434635	80.787	131	397	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	97.30	97.16	0.81	0.81	4	-
GCA_900544945.1	s__Faecousia sp900544945	80.0164	93	397	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	96.60	96.52	0.82	0.81	4	-
GCA_900770015.1	s__Faecousia sp900770015	79.9424	106	397	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002437585.1	s__Faecousia sp002437585	79.6227	111	397	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	99.35	99.16	0.96	0.95	3	-
GCA_004562395.1	s__Faecousia sp004562395	79.5418	77	397	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016302405.1	s__Faecousia sp016302405	78.7046	82	397	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017436785.1	s__Faecousia sp017436785	78.4026	81	397	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 01:16:38,684] [INFO] GTDB search result was written to GCA_905188045.1_ERR1430432-mag-bin.14_genomic.fna/result_gtdb.tsv
[2023-06-17 01:16:38,685] [INFO] ===== GTDB Search completed =====
[2023-06-17 01:16:38,688] [INFO] DFAST_QC result json was written to GCA_905188045.1_ERR1430432-mag-bin.14_genomic.fna/dqc_result.json
[2023-06-17 01:16:38,689] [INFO] DFAST_QC completed!
[2023-06-17 01:16:38,689] [INFO] Total running time: 0h0m37s