[2023-06-04 23:34:15,193] [INFO] DFAST_QC pipeline started.
[2023-06-04 23:34:15,196] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 23:34:15,196] [INFO] DQC Reference Directory: /var/lib/cwl/stg46f19cde-ef5d-4232-89e1-367a61df15b2/dqc_reference
[2023-06-04 23:34:16,377] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 23:34:16,378] [INFO] Task started: Prodigal
[2023-06-04 23:34:16,378] [INFO] Running command: gunzip -c /var/lib/cwl/stg86e88e96-5aeb-494a-8da7-0d95a8d040d1/GCA_934487025.1_ERR7745388_bin.125_genomic.fna.gz | prodigal -d GCA_934487025.1_ERR7745388_bin.125_genomic.fna/cds.fna -a GCA_934487025.1_ERR7745388_bin.125_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 23:34:20,491] [INFO] Task succeeded: Prodigal
[2023-06-04 23:34:20,492] [INFO] Task started: HMMsearch
[2023-06-04 23:34:20,492] [INFO] Running command: hmmsearch --tblout GCA_934487025.1_ERR7745388_bin.125_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46f19cde-ef5d-4232-89e1-367a61df15b2/dqc_reference/reference_markers.hmm GCA_934487025.1_ERR7745388_bin.125_genomic.fna/protein.faa > /dev/null
[2023-06-04 23:34:20,692] [INFO] Task succeeded: HMMsearch
[2023-06-04 23:34:20,693] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg86e88e96-5aeb-494a-8da7-0d95a8d040d1/GCA_934487025.1_ERR7745388_bin.125_genomic.fna.gz]
[2023-06-04 23:34:20,716] [INFO] Query marker FASTA was written to GCA_934487025.1_ERR7745388_bin.125_genomic.fna/markers.fasta
[2023-06-04 23:34:20,716] [INFO] Task started: Blastn
[2023-06-04 23:34:20,716] [INFO] Running command: blastn -query GCA_934487025.1_ERR7745388_bin.125_genomic.fna/markers.fasta -db /var/lib/cwl/stg46f19cde-ef5d-4232-89e1-367a61df15b2/dqc_reference/reference_markers.fasta -out GCA_934487025.1_ERR7745388_bin.125_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 23:34:21,302] [INFO] Task succeeded: Blastn
[2023-06-04 23:34:21,307] [INFO] Selected 8 target genomes.
[2023-06-04 23:34:21,307] [INFO] Target genome list was writen to GCA_934487025.1_ERR7745388_bin.125_genomic.fna/target_genomes.txt
[2023-06-04 23:34:21,323] [INFO] Task started: fastANI
[2023-06-04 23:34:21,323] [INFO] Running command: fastANI --query /var/lib/cwl/stg86e88e96-5aeb-494a-8da7-0d95a8d040d1/GCA_934487025.1_ERR7745388_bin.125_genomic.fna.gz --refList GCA_934487025.1_ERR7745388_bin.125_genomic.fna/target_genomes.txt --output GCA_934487025.1_ERR7745388_bin.125_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 23:34:26,140] [INFO] Task succeeded: fastANI
[2023-06-04 23:34:26,141] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46f19cde-ef5d-4232-89e1-367a61df15b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 23:34:26,141] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46f19cde-ef5d-4232-89e1-367a61df15b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 23:34:26,143] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 23:34:26,144] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 23:34:26,144] [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
--------------------------------------------------------------------------------
[2023-06-04 23:34:26,146] [INFO] DFAST Taxonomy check result was written to GCA_934487025.1_ERR7745388_bin.125_genomic.fna/tc_result.tsv
[2023-06-04 23:34:26,147] [INFO] ===== Taxonomy check completed =====
[2023-06-04 23:34:26,147] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 23:34:26,148] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46f19cde-ef5d-4232-89e1-367a61df15b2/dqc_reference/checkm_data
[2023-06-04 23:34:26,152] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 23:34:26,180] [INFO] Task started: CheckM
[2023-06-04 23:34:26,181] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934487025.1_ERR7745388_bin.125_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934487025.1_ERR7745388_bin.125_genomic.fna/checkm_input GCA_934487025.1_ERR7745388_bin.125_genomic.fna/checkm_result
[2023-06-04 23:34:45,108] [INFO] Task succeeded: CheckM
[2023-06-04 23:34:45,110] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.76%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 23:34:45,131] [INFO] ===== Completeness check finished =====
[2023-06-04 23:34:45,131] [INFO] ===== Start GTDB Search =====
[2023-06-04 23:34:45,132] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934487025.1_ERR7745388_bin.125_genomic.fna/markers.fasta)
[2023-06-04 23:34:45,132] [INFO] Task started: Blastn
[2023-06-04 23:34:45,132] [INFO] Running command: blastn -query GCA_934487025.1_ERR7745388_bin.125_genomic.fna/markers.fasta -db /var/lib/cwl/stg46f19cde-ef5d-4232-89e1-367a61df15b2/dqc_reference/reference_markers_gtdb.fasta -out GCA_934487025.1_ERR7745388_bin.125_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 23:34:45,987] [INFO] Task succeeded: Blastn
[2023-06-04 23:34:45,992] [INFO] Selected 8 target genomes.
[2023-06-04 23:34:45,992] [INFO] Target genome list was writen to GCA_934487025.1_ERR7745388_bin.125_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 23:34:45,996] [INFO] Task started: fastANI
[2023-06-04 23:34:45,996] [INFO] Running command: fastANI --query /var/lib/cwl/stg86e88e96-5aeb-494a-8da7-0d95a8d040d1/GCA_934487025.1_ERR7745388_bin.125_genomic.fna.gz --refList GCA_934487025.1_ERR7745388_bin.125_genomic.fna/target_genomes_gtdb.txt --output GCA_934487025.1_ERR7745388_bin.125_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 23:34:49,314] [INFO] Task succeeded: fastANI
[2023-06-04 23:34:49,323] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 23:34:49,323] [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_900555785.1	s__UMGS1865 sp900555785	96.4412	283	399	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1865	95.0	97.99	97.50	0.81	0.71	3	conclusive
GCA_900768535.1	s__UMGS1865 sp900768535	82.4933	266	399	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1865	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900547725.1	s__UMGS1865 sp900547725	81.7284	231	399	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1865	95.0	97.94	97.81	0.84	0.81	3	-
GCA_002438075.1	s__UMGS1865 sp002438075	81.6347	231	399	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1865	95.0	99.71	99.71	0.83	0.83	2	-
GCA_905201895.1	s__UMGS1865 sp905201895	77.2485	66	399	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1865	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015064525.1	s__UMGS1865 sp015064525	77.0466	51	399	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1865	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 23:34:49,326] [INFO] GTDB search result was written to GCA_934487025.1_ERR7745388_bin.125_genomic.fna/result_gtdb.tsv
[2023-06-04 23:34:49,326] [INFO] ===== GTDB Search completed =====
[2023-06-04 23:34:49,329] [INFO] DFAST_QC result json was written to GCA_934487025.1_ERR7745388_bin.125_genomic.fna/dqc_result.json
[2023-06-04 23:34:49,329] [INFO] DFAST_QC completed!
[2023-06-04 23:34:49,329] [INFO] Total running time: 0h0m34s