[2023-06-28 18:28:51,184] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:28:51,186] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:28:51,186] [INFO] DQC Reference Directory: /var/lib/cwl/stgab34c727-b603-4ad8-972e-6f4e50889fb4/dqc_reference
[2023-06-28 18:28:52,469] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:28:52,470] [INFO] Task started: Prodigal
[2023-06-28 18:28:52,470] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e19e9f4-b205-4841-b0b6-4c33e3500cc4/GCA_017995765.1_ASM1799576v1_genomic.fna.gz | prodigal -d GCA_017995765.1_ASM1799576v1_genomic.fna/cds.fna -a GCA_017995765.1_ASM1799576v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:29:01,259] [INFO] Task succeeded: Prodigal
[2023-06-28 18:29:01,260] [INFO] Task started: HMMsearch
[2023-06-28 18:29:01,260] [INFO] Running command: hmmsearch --tblout GCA_017995765.1_ASM1799576v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab34c727-b603-4ad8-972e-6f4e50889fb4/dqc_reference/reference_markers.hmm GCA_017995765.1_ASM1799576v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:29:01,541] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:29:01,542] [INFO] Found 6/6 markers.
[2023-06-28 18:29:01,583] [INFO] Query marker FASTA was written to GCA_017995765.1_ASM1799576v1_genomic.fna/markers.fasta
[2023-06-28 18:29:01,584] [INFO] Task started: Blastn
[2023-06-28 18:29:01,584] [INFO] Running command: blastn -query GCA_017995765.1_ASM1799576v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab34c727-b603-4ad8-972e-6f4e50889fb4/dqc_reference/reference_markers.fasta -out GCA_017995765.1_ASM1799576v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:29:02,166] [INFO] Task succeeded: Blastn
[2023-06-28 18:29:02,170] [INFO] Selected 20 target genomes.
[2023-06-28 18:29:02,170] [INFO] Target genome list was writen to GCA_017995765.1_ASM1799576v1_genomic.fna/target_genomes.txt
[2023-06-28 18:29:02,204] [INFO] Task started: fastANI
[2023-06-28 18:29:02,204] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e19e9f4-b205-4841-b0b6-4c33e3500cc4/GCA_017995765.1_ASM1799576v1_genomic.fna.gz --refList GCA_017995765.1_ASM1799576v1_genomic.fna/target_genomes.txt --output GCA_017995765.1_ASM1799576v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:29:15,722] [INFO] Task succeeded: fastANI
[2023-06-28 18:29:15,722] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab34c727-b603-4ad8-972e-6f4e50889fb4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:29:15,723] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab34c727-b603-4ad8-972e-6f4e50889fb4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:29:15,725] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:29:15,726] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 18:29:15,726] [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
--------------------------------------------------------------------------------
[2023-06-28 18:29:15,728] [INFO] DFAST Taxonomy check result was written to GCA_017995765.1_ASM1799576v1_genomic.fna/tc_result.tsv
[2023-06-28 18:29:15,729] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:29:15,729] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:29:15,729] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab34c727-b603-4ad8-972e-6f4e50889fb4/dqc_reference/checkm_data
[2023-06-28 18:29:15,734] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:29:15,777] [INFO] Task started: CheckM
[2023-06-28 18:29:15,778] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017995765.1_ASM1799576v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017995765.1_ASM1799576v1_genomic.fna/checkm_input GCA_017995765.1_ASM1799576v1_genomic.fna/checkm_result
[2023-06-28 18:29:48,168] [INFO] Task succeeded: CheckM
[2023-06-28 18:29:48,170] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.61%
Contamintation: 10.61%
Strain heterogeneity: 55.56%
--------------------------------------------------------------------------------
[2023-06-28 18:29:48,202] [INFO] ===== Completeness check finished =====
[2023-06-28 18:29:48,202] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:29:48,203] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017995765.1_ASM1799576v1_genomic.fna/markers.fasta)
[2023-06-28 18:29:48,203] [INFO] Task started: Blastn
[2023-06-28 18:29:48,203] [INFO] Running command: blastn -query GCA_017995765.1_ASM1799576v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab34c727-b603-4ad8-972e-6f4e50889fb4/dqc_reference/reference_markers_gtdb.fasta -out GCA_017995765.1_ASM1799576v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:29:48,988] [INFO] Task succeeded: Blastn
[2023-06-28 18:29:48,993] [INFO] Selected 17 target genomes.
[2023-06-28 18:29:48,994] [INFO] Target genome list was writen to GCA_017995765.1_ASM1799576v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:29:49,008] [INFO] Task started: fastANI
[2023-06-28 18:29:49,008] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e19e9f4-b205-4841-b0b6-4c33e3500cc4/GCA_017995765.1_ASM1799576v1_genomic.fna.gz --refList GCA_017995765.1_ASM1799576v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017995765.1_ASM1799576v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:29:57,660] [INFO] Task succeeded: fastANI
[2023-06-28 18:29:57,675] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 18:29:57,676] [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_012797505.1	s__UBA8904 sp012797505	78.7624	164	1040	d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__Smithellaceae;g__UBA8904	95.0	99.21	98.97	0.84	0.84	5	-
GCA_003506745.1	s__UBA8904 sp003506745	77.9486	122	1040	d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__Smithellaceae;g__UBA8904	95.0	97.90	97.67	0.70	0.68	3	-
GCA_009773315.1	s__UBA8904 sp009773315	77.7572	186	1040	d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__Smithellaceae;g__UBA8904	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903904655.1	s__UBA8904 sp903904655	77.6369	171	1040	d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__Smithellaceae;g__UBA8904	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002382045.1	s__UBA8904 sp002382045	77.5083	199	1040	d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__Smithellaceae;g__UBA8904	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002070455.1	s__UBA8904 sp002070455	77.4724	128	1040	d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__Smithellaceae;g__UBA8904	95.0	98.81	98.81	0.78	0.78	2	-
GCA_002840435.1	s__UBA8904 sp002840435	77.433	216	1040	d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__Smithellaceae;g__UBA8904	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009668925.1	s__UBA8904 sp009668925	77.3606	159	1040	d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__Smithellaceae;g__UBA8904	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017860985.1	s__UBA8904 sp017860985	77.3571	95	1040	d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__Smithellaceae;g__UBA8904	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012729055.1	s__UBA8904 sp012729055	77.2153	165	1040	d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__Smithellaceae;g__UBA8904	95.0	99.58	99.58	0.94	0.94	2	-
GCA_002347685.1	s__UBA8904 sp002347685	77.0744	123	1040	d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__Smithellaceae;g__UBA8904	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003139775.1	s__Smithella sp003139775	76.8376	72	1040	d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__Smithellaceae;g__Smithella	95.0	99.83	99.63	0.95	0.94	14	-
GCA_003142535.1	s__Fen-1166 sp003142535	76.4861	57	1040	d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__Smithellaceae;g__Fen-1166	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 18:29:57,678] [INFO] GTDB search result was written to GCA_017995765.1_ASM1799576v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:29:57,679] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:29:57,682] [INFO] DFAST_QC result json was written to GCA_017995765.1_ASM1799576v1_genomic.fna/dqc_result.json
[2023-06-28 18:29:57,682] [INFO] DFAST_QC completed!
[2023-06-28 18:29:57,682] [INFO] Total running time: 0h1m6s