[2023-06-28 08:11:22,453] [INFO] DFAST_QC pipeline started.
[2023-06-28 08:11:22,454] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 08:11:22,454] [INFO] DQC Reference Directory: /var/lib/cwl/stg63966acb-8b26-4117-88cd-164d1501f34f/dqc_reference
[2023-06-28 08:11:25,672] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 08:11:25,674] [INFO] Task started: Prodigal
[2023-06-28 08:11:25,675] [INFO] Running command: gunzip -c /var/lib/cwl/stg7e540e2c-6295-47c6-af7c-0fc816de513d/GCA_019310125.1_ASM1931012v1_genomic.fna.gz | prodigal -d GCA_019310125.1_ASM1931012v1_genomic.fna/cds.fna -a GCA_019310125.1_ASM1931012v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 08:11:33,631] [INFO] Task succeeded: Prodigal
[2023-06-28 08:11:33,631] [INFO] Task started: HMMsearch
[2023-06-28 08:11:33,632] [INFO] Running command: hmmsearch --tblout GCA_019310125.1_ASM1931012v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63966acb-8b26-4117-88cd-164d1501f34f/dqc_reference/reference_markers.hmm GCA_019310125.1_ASM1931012v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 08:11:33,905] [INFO] Task succeeded: HMMsearch
[2023-06-28 08:11:33,906] [INFO] Found 6/6 markers.
[2023-06-28 08:11:33,944] [INFO] Query marker FASTA was written to GCA_019310125.1_ASM1931012v1_genomic.fna/markers.fasta
[2023-06-28 08:11:33,944] [INFO] Task started: Blastn
[2023-06-28 08:11:33,945] [INFO] Running command: blastn -query GCA_019310125.1_ASM1931012v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63966acb-8b26-4117-88cd-164d1501f34f/dqc_reference/reference_markers.fasta -out GCA_019310125.1_ASM1931012v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 08:11:34,527] [INFO] Task succeeded: Blastn
[2023-06-28 08:11:34,533] [INFO] Selected 23 target genomes.
[2023-06-28 08:11:34,533] [INFO] Target genome list was writen to GCA_019310125.1_ASM1931012v1_genomic.fna/target_genomes.txt
[2023-06-28 08:11:34,540] [INFO] Task started: fastANI
[2023-06-28 08:11:34,540] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e540e2c-6295-47c6-af7c-0fc816de513d/GCA_019310125.1_ASM1931012v1_genomic.fna.gz --refList GCA_019310125.1_ASM1931012v1_genomic.fna/target_genomes.txt --output GCA_019310125.1_ASM1931012v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 08:11:49,505] [INFO] Task succeeded: fastANI
[2023-06-28 08:11:49,506] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63966acb-8b26-4117-88cd-164d1501f34f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 08:11:49,506] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63966acb-8b26-4117-88cd-164d1501f34f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 08:11:49,508] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 08:11:49,508] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 08:11:49,508] [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 08:11:49,510] [INFO] DFAST Taxonomy check result was written to GCA_019310125.1_ASM1931012v1_genomic.fna/tc_result.tsv
[2023-06-28 08:11:49,510] [INFO] ===== Taxonomy check completed =====
[2023-06-28 08:11:49,510] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 08:11:49,511] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63966acb-8b26-4117-88cd-164d1501f34f/dqc_reference/checkm_data
[2023-06-28 08:11:49,513] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 08:11:49,553] [INFO] Task started: CheckM
[2023-06-28 08:11:49,553] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019310125.1_ASM1931012v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019310125.1_ASM1931012v1_genomic.fna/checkm_input GCA_019310125.1_ASM1931012v1_genomic.fna/checkm_result
[2023-06-28 08:12:18,938] [INFO] Task succeeded: CheckM
[2023-06-28 08:12:18,940] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 08:12:18,961] [INFO] ===== Completeness check finished =====
[2023-06-28 08:12:18,962] [INFO] ===== Start GTDB Search =====
[2023-06-28 08:12:18,962] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019310125.1_ASM1931012v1_genomic.fna/markers.fasta)
[2023-06-28 08:12:18,963] [INFO] Task started: Blastn
[2023-06-28 08:12:18,963] [INFO] Running command: blastn -query GCA_019310125.1_ASM1931012v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63966acb-8b26-4117-88cd-164d1501f34f/dqc_reference/reference_markers_gtdb.fasta -out GCA_019310125.1_ASM1931012v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 08:12:19,703] [INFO] Task succeeded: Blastn
[2023-06-28 08:12:19,708] [INFO] Selected 20 target genomes.
[2023-06-28 08:12:19,708] [INFO] Target genome list was writen to GCA_019310125.1_ASM1931012v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 08:12:19,720] [INFO] Task started: fastANI
[2023-06-28 08:12:19,720] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e540e2c-6295-47c6-af7c-0fc816de513d/GCA_019310125.1_ASM1931012v1_genomic.fna.gz --refList GCA_019310125.1_ASM1931012v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019310125.1_ASM1931012v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 08:12:34,995] [INFO] Task succeeded: fastANI
[2023-06-28 08:12:35,004] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 08:12:35,004] [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_001751005.1	s__S5133MH16 sp001751005	88.577	459	983	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA11574;g__S5133MH16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004193595.1	s__S5133MH16 sp004193595	87.9185	750	983	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA11574;g__S5133MH16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002868985.1	s__UBA11574 sp002868985	77.9642	191	983	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA11574;g__UBA11574	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012974475.1	s__JAAXQD01 sp012974475	77.8233	213	983	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA11574;g__JAAXQD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382665.1	s__Desulfatibia profunda	77.1417	145	983	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA11574;g__Desulfatibia	95.0	99.67	99.67	0.86	0.86	2	-
GCA_013203195.1	s__Desulfatibia_A sp013203195	77.1245	110	983	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA11574;g__Desulfatibia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004193555.1	s__ETH-SRB1 sp004193555	77.0619	95	983	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__ETH-SRB1;g__ETH-SRB1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014381545.1	s__Desulfaltia bathyphila	76.2155	61	983	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__ETH-SRB1;g__Desulfaltia	95.0	99.82	99.78	0.90	0.90	3	-
--------------------------------------------------------------------------------
[2023-06-28 08:12:35,006] [INFO] GTDB search result was written to GCA_019310125.1_ASM1931012v1_genomic.fna/result_gtdb.tsv
[2023-06-28 08:12:35,006] [INFO] ===== GTDB Search completed =====
[2023-06-28 08:12:35,009] [INFO] DFAST_QC result json was written to GCA_019310125.1_ASM1931012v1_genomic.fna/dqc_result.json
[2023-06-28 08:12:35,009] [INFO] DFAST_QC completed!
[2023-06-28 08:12:35,009] [INFO] Total running time: 0h1m13s