[2023-06-29 20:10:54,570] [INFO] DFAST_QC pipeline started.
[2023-06-29 20:10:54,572] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 20:10:54,573] [INFO] DQC Reference Directory: /var/lib/cwl/stgccd4cd78-ab9b-45c7-9cf3-67427dd176f3/dqc_reference
[2023-06-29 20:10:55,836] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 20:10:55,837] [INFO] Task started: Prodigal
[2023-06-29 20:10:55,837] [INFO] Running command: gunzip -c /var/lib/cwl/stg0f1fd634-160f-4900-b7a3-47e3bd8fb432/GCA_007244375.1_ASM724437v1_genomic.fna.gz | prodigal -d GCA_007244375.1_ASM724437v1_genomic.fna/cds.fna -a GCA_007244375.1_ASM724437v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 20:11:02,951] [INFO] Task succeeded: Prodigal
[2023-06-29 20:11:02,951] [INFO] Task started: HMMsearch
[2023-06-29 20:11:02,952] [INFO] Running command: hmmsearch --tblout GCA_007244375.1_ASM724437v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgccd4cd78-ab9b-45c7-9cf3-67427dd176f3/dqc_reference/reference_markers.hmm GCA_007244375.1_ASM724437v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 20:11:03,210] [INFO] Task succeeded: HMMsearch
[2023-06-29 20:11:03,212] [INFO] Found 6/6 markers.
[2023-06-29 20:11:03,240] [INFO] Query marker FASTA was written to GCA_007244375.1_ASM724437v1_genomic.fna/markers.fasta
[2023-06-29 20:11:03,241] [INFO] Task started: Blastn
[2023-06-29 20:11:03,241] [INFO] Running command: blastn -query GCA_007244375.1_ASM724437v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgccd4cd78-ab9b-45c7-9cf3-67427dd176f3/dqc_reference/reference_markers.fasta -out GCA_007244375.1_ASM724437v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:11:03,805] [INFO] Task succeeded: Blastn
[2023-06-29 20:11:03,809] [INFO] Selected 17 target genomes.
[2023-06-29 20:11:03,809] [INFO] Target genome list was writen to GCA_007244375.1_ASM724437v1_genomic.fna/target_genomes.txt
[2023-06-29 20:11:03,814] [INFO] Task started: fastANI
[2023-06-29 20:11:03,814] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f1fd634-160f-4900-b7a3-47e3bd8fb432/GCA_007244375.1_ASM724437v1_genomic.fna.gz --refList GCA_007244375.1_ASM724437v1_genomic.fna/target_genomes.txt --output GCA_007244375.1_ASM724437v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 20:11:14,229] [INFO] Task succeeded: fastANI
[2023-06-29 20:11:14,230] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgccd4cd78-ab9b-45c7-9cf3-67427dd176f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 20:11:14,230] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgccd4cd78-ab9b-45c7-9cf3-67427dd176f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 20:11:14,233] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 20:11:14,233] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 20:11:14,233] [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 20:11:14,236] [INFO] DFAST Taxonomy check result was written to GCA_007244375.1_ASM724437v1_genomic.fna/tc_result.tsv
[2023-06-29 20:11:14,237] [INFO] ===== Taxonomy check completed =====
[2023-06-29 20:11:14,237] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 20:11:14,237] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgccd4cd78-ab9b-45c7-9cf3-67427dd176f3/dqc_reference/checkm_data
[2023-06-29 20:11:14,241] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 20:11:14,280] [INFO] Task started: CheckM
[2023-06-29 20:11:14,280] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_007244375.1_ASM724437v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_007244375.1_ASM724437v1_genomic.fna/checkm_input GCA_007244375.1_ASM724437v1_genomic.fna/checkm_result
[2023-06-29 20:11:42,418] [INFO] Task succeeded: CheckM
[2023-06-29 20:11:42,419] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 20:11:42,443] [INFO] ===== Completeness check finished =====
[2023-06-29 20:11:42,443] [INFO] ===== Start GTDB Search =====
[2023-06-29 20:11:42,444] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_007244375.1_ASM724437v1_genomic.fna/markers.fasta)
[2023-06-29 20:11:42,444] [INFO] Task started: Blastn
[2023-06-29 20:11:42,444] [INFO] Running command: blastn -query GCA_007244375.1_ASM724437v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgccd4cd78-ab9b-45c7-9cf3-67427dd176f3/dqc_reference/reference_markers_gtdb.fasta -out GCA_007244375.1_ASM724437v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:11:43,243] [INFO] Task succeeded: Blastn
[2023-06-29 20:11:43,251] [INFO] Selected 13 target genomes.
[2023-06-29 20:11:43,251] [INFO] Target genome list was writen to GCA_007244375.1_ASM724437v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 20:11:43,260] [INFO] Task started: fastANI
[2023-06-29 20:11:43,260] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f1fd634-160f-4900-b7a3-47e3bd8fb432/GCA_007244375.1_ASM724437v1_genomic.fna.gz --refList GCA_007244375.1_ASM724437v1_genomic.fna/target_genomes_gtdb.txt --output GCA_007244375.1_ASM724437v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 20:11:50,344] [INFO] Task succeeded: fastANI
[2023-06-29 20:11:50,359] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 20:11:50,360] [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_007244375.1	s__Smithella sp001412345	100.0	1003	1005	d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__Smithellaceae;g__Smithella	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCA_001683985.1	s__Smithella sp001683985	91.387	636	1005	d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__Smithellaceae;g__Smithella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000747625.2	s__Smithella sp000747625	82.8385	522	1005	d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__Smithellaceae;g__Smithella	95.0	99.54	99.39	0.89	0.85	4	-
GCA_000753945.1	s__Smithella sp000753945	82.3925	241	1005	d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__Smithellaceae;g__Smithella	95.0	98.83	98.58	0.79	0.73	4	-
GCA_002840505.1	s__Smithella sp002840505	82.176	687	1005	d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__Smithellaceae;g__Smithella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002327415.1	s__Smithella sp002327415	80.7899	329	1005	d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__Smithellaceae;g__Smithella	95.0	98.51	98.51	0.75	0.75	2	-
GCA_002840555.1	s__Smithella sp002840555	78.1606	343	1005	d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__Smithellaceae;g__Smithella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018056685.1	s__Smithella sp018056685	77.9747	232	1005	d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__Smithellaceae;g__Smithella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017993615.1	s__Smithella sp017993615	77.91	198	1005	d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__Smithellaceae;g__Smithella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016928765.1	s__UBA4810 sp016928765	76.1244	73	1005	d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__Smithellaceae;g__UBA4810	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 20:11:50,362] [INFO] GTDB search result was written to GCA_007244375.1_ASM724437v1_genomic.fna/result_gtdb.tsv
[2023-06-29 20:11:50,362] [INFO] ===== GTDB Search completed =====
[2023-06-29 20:11:50,365] [INFO] DFAST_QC result json was written to GCA_007244375.1_ASM724437v1_genomic.fna/dqc_result.json
[2023-06-29 20:11:50,365] [INFO] DFAST_QC completed!
[2023-06-29 20:11:50,365] [INFO] Total running time: 0h0m56s