[2023-06-28 17:35:38,617] [INFO] DFAST_QC pipeline started.
[2023-06-28 17:35:38,619] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 17:35:38,620] [INFO] DQC Reference Directory: /var/lib/cwl/stg43f3da05-5ca1-4814-9524-d07904e6f2c3/dqc_reference
[2023-06-28 17:35:39,914] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 17:35:39,916] [INFO] Task started: Prodigal
[2023-06-28 17:35:39,916] [INFO] Running command: gunzip -c /var/lib/cwl/stg2ad7fd28-29f3-4c93-91c0-c815e9b1925c/GCA_944322885.1_E02_bin142_genomic.fna.gz | prodigal -d GCA_944322885.1_E02_bin142_genomic.fna/cds.fna -a GCA_944322885.1_E02_bin142_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 17:35:43,473] [INFO] Task succeeded: Prodigal
[2023-06-28 17:35:43,473] [INFO] Task started: HMMsearch
[2023-06-28 17:35:43,473] [INFO] Running command: hmmsearch --tblout GCA_944322885.1_E02_bin142_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43f3da05-5ca1-4814-9524-d07904e6f2c3/dqc_reference/reference_markers.hmm GCA_944322885.1_E02_bin142_genomic.fna/protein.faa > /dev/null
[2023-06-28 17:35:43,692] [INFO] Task succeeded: HMMsearch
[2023-06-28 17:35:43,693] [INFO] Found 6/6 markers.
[2023-06-28 17:35:43,712] [INFO] Query marker FASTA was written to GCA_944322885.1_E02_bin142_genomic.fna/markers.fasta
[2023-06-28 17:35:43,713] [INFO] Task started: Blastn
[2023-06-28 17:35:43,713] [INFO] Running command: blastn -query GCA_944322885.1_E02_bin142_genomic.fna/markers.fasta -db /var/lib/cwl/stg43f3da05-5ca1-4814-9524-d07904e6f2c3/dqc_reference/reference_markers.fasta -out GCA_944322885.1_E02_bin142_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:35:44,369] [INFO] Task succeeded: Blastn
[2023-06-28 17:35:44,374] [INFO] Selected 27 target genomes.
[2023-06-28 17:35:44,374] [INFO] Target genome list was writen to GCA_944322885.1_E02_bin142_genomic.fna/target_genomes.txt
[2023-06-28 17:35:44,384] [INFO] Task started: fastANI
[2023-06-28 17:35:44,384] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ad7fd28-29f3-4c93-91c0-c815e9b1925c/GCA_944322885.1_E02_bin142_genomic.fna.gz --refList GCA_944322885.1_E02_bin142_genomic.fna/target_genomes.txt --output GCA_944322885.1_E02_bin142_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 17:35:57,383] [INFO] Task succeeded: fastANI
[2023-06-28 17:35:57,384] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43f3da05-5ca1-4814-9524-d07904e6f2c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 17:35:57,384] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43f3da05-5ca1-4814-9524-d07904e6f2c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 17:35:57,385] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 17:35:57,386] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 17:35:57,386] [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 17:35:57,387] [INFO] DFAST Taxonomy check result was written to GCA_944322885.1_E02_bin142_genomic.fna/tc_result.tsv
[2023-06-28 17:35:57,388] [INFO] ===== Taxonomy check completed =====
[2023-06-28 17:35:57,388] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 17:35:57,389] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43f3da05-5ca1-4814-9524-d07904e6f2c3/dqc_reference/checkm_data
[2023-06-28 17:35:57,391] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 17:35:57,417] [INFO] Task started: CheckM
[2023-06-28 17:35:57,418] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944322885.1_E02_bin142_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944322885.1_E02_bin142_genomic.fna/checkm_input GCA_944322885.1_E02_bin142_genomic.fna/checkm_result
[2023-06-28 17:36:16,450] [INFO] Task succeeded: CheckM
[2023-06-28 17:36:16,452] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 17:36:16,477] [INFO] ===== Completeness check finished =====
[2023-06-28 17:36:16,478] [INFO] ===== Start GTDB Search =====
[2023-06-28 17:36:16,478] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944322885.1_E02_bin142_genomic.fna/markers.fasta)
[2023-06-28 17:36:16,478] [INFO] Task started: Blastn
[2023-06-28 17:36:16,479] [INFO] Running command: blastn -query GCA_944322885.1_E02_bin142_genomic.fna/markers.fasta -db /var/lib/cwl/stg43f3da05-5ca1-4814-9524-d07904e6f2c3/dqc_reference/reference_markers_gtdb.fasta -out GCA_944322885.1_E02_bin142_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:36:17,274] [INFO] Task succeeded: Blastn
[2023-06-28 17:36:17,280] [INFO] Selected 16 target genomes.
[2023-06-28 17:36:17,281] [INFO] Target genome list was writen to GCA_944322885.1_E02_bin142_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 17:36:17,299] [INFO] Task started: fastANI
[2023-06-28 17:36:17,300] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ad7fd28-29f3-4c93-91c0-c815e9b1925c/GCA_944322885.1_E02_bin142_genomic.fna.gz --refList GCA_944322885.1_E02_bin142_genomic.fna/target_genomes_gtdb.txt --output GCA_944322885.1_E02_bin142_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 17:36:23,109] [INFO] Task succeeded: fastANI
[2023-06-28 17:36:23,130] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 17:36:23,131] [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_900551675.1	s__Stercorousia sp900551675	80.4866	345	599	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	100.00	100.00	0.98	0.98	2	-
GCA_905216055.1	s__Stercorousia sp905216055	80.073	352	599	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000438175.1	s__Stercorousia faecigallinarum	79.9754	356	599	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	98.53	97.95	0.88	0.85	4	-
GCA_900555175.1	s__Stercorousia sp900555175	79.9227	207	599	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	100.00	100.00	0.94	0.94	2	-
GCA_900761225.1	s__Stercorousia sp900761225	79.6525	330	599	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905212085.1	s__Stercorousia sp905212085	79.5442	315	599	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000437435.1	s__Stercorousia sp000437435	79.3239	343	599	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	97.52	97.52	0.91	0.91	3	-
GCA_000433095.1	s__Stercorousia sp000433095	79.03	328	599	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	99.53	99.13	0.95	0.93	3	-
GCA_900752845.1	s__Stercorousia sp900752845	78.9304	256	599	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	99.76	99.76	0.83	0.83	2	-
GCA_001765415.1	s__Stercorousia sp001765415	78.5501	252	599	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	98.74	98.70	0.94	0.93	5	-
GCA_900556295.1	s__Stercorousia sp900556295	78.4721	169	599	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	97.71	97.55	0.83	0.77	3	-
GCA_003150395.1	s__Scatenecus sp003150395	78.1163	183	599	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Scatenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902794035.1	s__UBA2813 sp902794035	77.6868	91	599	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2813	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902763805.1	s__CAG-196 sp902763805	77.3349	75	599	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__CAG-196	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902761735.1	s__UBA1221 sp902761735	77.1344	106	599	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA1221	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016280955.1	s__CAG-196 sp016280955	76.754	89	599	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__CAG-196	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 17:36:23,133] [INFO] GTDB search result was written to GCA_944322885.1_E02_bin142_genomic.fna/result_gtdb.tsv
[2023-06-28 17:36:23,133] [INFO] ===== GTDB Search completed =====
[2023-06-28 17:36:23,137] [INFO] DFAST_QC result json was written to GCA_944322885.1_E02_bin142_genomic.fna/dqc_result.json
[2023-06-28 17:36:23,137] [INFO] DFAST_QC completed!
[2023-06-28 17:36:23,137] [INFO] Total running time: 0h0m45s