[2023-06-05 18:35:07,427] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:35:07,431] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:35:07,431] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c656a27-8bdc-4eb0-9a24-cd75040844c7/dqc_reference
[2023-06-05 18:35:09,320] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:35:09,320] [INFO] Task started: Prodigal
[2023-06-05 18:35:09,321] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0ab5b08-d478-4377-8845-a765af66f1e2/GCA_934726245.1_ERR7746436_bin.122_genomic.fna.gz | prodigal -d GCA_934726245.1_ERR7746436_bin.122_genomic.fna/cds.fna -a GCA_934726245.1_ERR7746436_bin.122_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:35:12,680] [INFO] Task succeeded: Prodigal
[2023-06-05 18:35:12,681] [INFO] Task started: HMMsearch
[2023-06-05 18:35:12,681] [INFO] Running command: hmmsearch --tblout GCA_934726245.1_ERR7746436_bin.122_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c656a27-8bdc-4eb0-9a24-cd75040844c7/dqc_reference/reference_markers.hmm GCA_934726245.1_ERR7746436_bin.122_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:35:12,868] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:35:12,870] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc0ab5b08-d478-4377-8845-a765af66f1e2/GCA_934726245.1_ERR7746436_bin.122_genomic.fna.gz]
[2023-06-05 18:35:12,904] [INFO] Query marker FASTA was written to GCA_934726245.1_ERR7746436_bin.122_genomic.fna/markers.fasta
[2023-06-05 18:35:12,905] [INFO] Task started: Blastn
[2023-06-05 18:35:12,905] [INFO] Running command: blastn -query GCA_934726245.1_ERR7746436_bin.122_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c656a27-8bdc-4eb0-9a24-cd75040844c7/dqc_reference/reference_markers.fasta -out GCA_934726245.1_ERR7746436_bin.122_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:35:13,471] [INFO] Task succeeded: Blastn
[2023-06-05 18:35:13,475] [INFO] Selected 12 target genomes.
[2023-06-05 18:35:13,475] [INFO] Target genome list was writen to GCA_934726245.1_ERR7746436_bin.122_genomic.fna/target_genomes.txt
[2023-06-05 18:35:13,483] [INFO] Task started: fastANI
[2023-06-05 18:35:13,484] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0ab5b08-d478-4377-8845-a765af66f1e2/GCA_934726245.1_ERR7746436_bin.122_genomic.fna.gz --refList GCA_934726245.1_ERR7746436_bin.122_genomic.fna/target_genomes.txt --output GCA_934726245.1_ERR7746436_bin.122_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:35:17,917] [INFO] Task succeeded: fastANI
[2023-06-05 18:35:17,917] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c656a27-8bdc-4eb0-9a24-cd75040844c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:35:17,918] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c656a27-8bdc-4eb0-9a24-cd75040844c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:35:17,919] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:35:17,919] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 18:35:17,919] [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
--------------------------------------------------------------------------------
[2023-06-05 18:35:17,930] [INFO] DFAST Taxonomy check result was written to GCA_934726245.1_ERR7746436_bin.122_genomic.fna/tc_result.tsv
[2023-06-05 18:35:17,931] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:35:17,931] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:35:17,931] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c656a27-8bdc-4eb0-9a24-cd75040844c7/dqc_reference/checkm_data
[2023-06-05 18:35:17,934] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:35:17,957] [INFO] Task started: CheckM
[2023-06-05 18:35:17,957] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934726245.1_ERR7746436_bin.122_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934726245.1_ERR7746436_bin.122_genomic.fna/checkm_input GCA_934726245.1_ERR7746436_bin.122_genomic.fna/checkm_result
[2023-06-05 18:35:35,549] [INFO] Task succeeded: CheckM
[2023-06-05 18:35:35,550] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:35:35,571] [INFO] ===== Completeness check finished =====
[2023-06-05 18:35:35,572] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:35:35,572] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934726245.1_ERR7746436_bin.122_genomic.fna/markers.fasta)
[2023-06-05 18:35:35,572] [INFO] Task started: Blastn
[2023-06-05 18:35:35,572] [INFO] Running command: blastn -query GCA_934726245.1_ERR7746436_bin.122_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c656a27-8bdc-4eb0-9a24-cd75040844c7/dqc_reference/reference_markers_gtdb.fasta -out GCA_934726245.1_ERR7746436_bin.122_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:35:36,388] [INFO] Task succeeded: Blastn
[2023-06-05 18:35:36,392] [INFO] Selected 13 target genomes.
[2023-06-05 18:35:36,392] [INFO] Target genome list was writen to GCA_934726245.1_ERR7746436_bin.122_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:35:36,396] [INFO] Task started: fastANI
[2023-06-05 18:35:36,396] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0ab5b08-d478-4377-8845-a765af66f1e2/GCA_934726245.1_ERR7746436_bin.122_genomic.fna.gz --refList GCA_934726245.1_ERR7746436_bin.122_genomic.fna/target_genomes_gtdb.txt --output GCA_934726245.1_ERR7746436_bin.122_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:35:40,846] [INFO] Task succeeded: fastANI
[2023-06-05 18:35:40,857] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:35:40,858] [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_003258725.1	s__UBA6984 sp003258725	98.4611	533	582	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA6984	95.0	98.56	98.53	0.92	0.92	3	conclusive
GCA_900550295.1	s__UBA6984 sp900550295	86.1421	411	582	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA6984	95.0	99.30	99.12	0.94	0.93	3	-
GCA_002297005.1	s__UBA791 sp002297005	80.7228	198	582	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA791	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905235155.1	s__UBA6984 sp905235155	78.7671	257	582	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA6984	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002450015.1	s__UBA6984 sp002450015	78.6979	190	582	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA6984	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017512405.1	s__UBA6984 sp017512405	78.5845	212	582	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA6984	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017405375.1	s__UBA6984 sp017405375	78.4618	155	582	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA6984	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002369055.1	s__UBA6984 sp002369055	78.3473	170	582	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA6984	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905236205.1	s__UBA6984 sp905236205	78.1366	194	582	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA6984	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902803265.1	s__UBA791 sp902803265	77.9645	110	582	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA791	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900766355.1	s__UMGS1585 sp900766355	77.3625	97	582	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UMGS1585	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902797985.1	s__UBA2883 sp902797985	77.3196	76	582	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2883	95.0	98.86	98.86	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2023-06-05 18:35:40,860] [INFO] GTDB search result was written to GCA_934726245.1_ERR7746436_bin.122_genomic.fna/result_gtdb.tsv
[2023-06-05 18:35:40,860] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:35:40,875] [INFO] DFAST_QC result json was written to GCA_934726245.1_ERR7746436_bin.122_genomic.fna/dqc_result.json
[2023-06-05 18:35:40,875] [INFO] DFAST_QC completed!
[2023-06-05 18:35:40,875] [INFO] Total running time: 0h0m33s