[2023-06-28 11:36:59,630] [INFO] DFAST_QC pipeline started.
[2023-06-28 11:36:59,632] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 11:36:59,632] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c933cf8-723c-4a36-99ba-0ec77769de66/dqc_reference
[2023-06-28 11:37:00,776] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 11:37:00,777] [INFO] Task started: Prodigal
[2023-06-28 11:37:00,777] [INFO] Running command: gunzip -c /var/lib/cwl/stgb6b06a47-f255-49c7-8e45-8720b6484ea3/GCA_944326545.1_BRZ_MM_bin19_genomic.fna.gz | prodigal -d GCA_944326545.1_BRZ_MM_bin19_genomic.fna/cds.fna -a GCA_944326545.1_BRZ_MM_bin19_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 11:37:04,608] [INFO] Task succeeded: Prodigal
[2023-06-28 11:37:04,608] [INFO] Task started: HMMsearch
[2023-06-28 11:37:04,608] [INFO] Running command: hmmsearch --tblout GCA_944326545.1_BRZ_MM_bin19_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c933cf8-723c-4a36-99ba-0ec77769de66/dqc_reference/reference_markers.hmm GCA_944326545.1_BRZ_MM_bin19_genomic.fna/protein.faa > /dev/null
[2023-06-28 11:37:04,776] [INFO] Task succeeded: HMMsearch
[2023-06-28 11:37:04,777] [INFO] Found 6/6 markers.
[2023-06-28 11:37:04,796] [INFO] Query marker FASTA was written to GCA_944326545.1_BRZ_MM_bin19_genomic.fna/markers.fasta
[2023-06-28 11:37:04,797] [INFO] Task started: Blastn
[2023-06-28 11:37:04,797] [INFO] Running command: blastn -query GCA_944326545.1_BRZ_MM_bin19_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c933cf8-723c-4a36-99ba-0ec77769de66/dqc_reference/reference_markers.fasta -out GCA_944326545.1_BRZ_MM_bin19_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 11:37:05,304] [INFO] Task succeeded: Blastn
[2023-06-28 11:37:05,307] [INFO] Selected 17 target genomes.
[2023-06-28 11:37:05,307] [INFO] Target genome list was writen to GCA_944326545.1_BRZ_MM_bin19_genomic.fna/target_genomes.txt
[2023-06-28 11:37:05,312] [INFO] Task started: fastANI
[2023-06-28 11:37:05,312] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6b06a47-f255-49c7-8e45-8720b6484ea3/GCA_944326545.1_BRZ_MM_bin19_genomic.fna.gz --refList GCA_944326545.1_BRZ_MM_bin19_genomic.fna/target_genomes.txt --output GCA_944326545.1_BRZ_MM_bin19_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 11:37:13,888] [INFO] Task succeeded: fastANI
[2023-06-28 11:37:13,888] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c933cf8-723c-4a36-99ba-0ec77769de66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 11:37:13,888] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c933cf8-723c-4a36-99ba-0ec77769de66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 11:37:13,890] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 11:37:13,890] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 11:37:13,890] [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 11:37:13,891] [INFO] DFAST Taxonomy check result was written to GCA_944326545.1_BRZ_MM_bin19_genomic.fna/tc_result.tsv
[2023-06-28 11:37:13,892] [INFO] ===== Taxonomy check completed =====
[2023-06-28 11:37:13,892] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 11:37:13,892] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c933cf8-723c-4a36-99ba-0ec77769de66/dqc_reference/checkm_data
[2023-06-28 11:37:13,894] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 11:37:13,918] [INFO] Task started: CheckM
[2023-06-28 11:37:13,918] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944326545.1_BRZ_MM_bin19_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944326545.1_BRZ_MM_bin19_genomic.fna/checkm_input GCA_944326545.1_BRZ_MM_bin19_genomic.fna/checkm_result
[2023-06-28 11:37:30,855] [INFO] Task succeeded: CheckM
[2023-06-28 11:37:30,856] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 11:37:30,868] [INFO] ===== Completeness check finished =====
[2023-06-28 11:37:30,869] [INFO] ===== Start GTDB Search =====
[2023-06-28 11:37:30,869] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944326545.1_BRZ_MM_bin19_genomic.fna/markers.fasta)
[2023-06-28 11:37:30,869] [INFO] Task started: Blastn
[2023-06-28 11:37:30,869] [INFO] Running command: blastn -query GCA_944326545.1_BRZ_MM_bin19_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c933cf8-723c-4a36-99ba-0ec77769de66/dqc_reference/reference_markers_gtdb.fasta -out GCA_944326545.1_BRZ_MM_bin19_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 11:37:31,577] [INFO] Task succeeded: Blastn
[2023-06-28 11:37:31,580] [INFO] Selected 22 target genomes.
[2023-06-28 11:37:31,580] [INFO] Target genome list was writen to GCA_944326545.1_BRZ_MM_bin19_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 11:37:31,597] [INFO] Task started: fastANI
[2023-06-28 11:37:31,597] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6b06a47-f255-49c7-8e45-8720b6484ea3/GCA_944326545.1_BRZ_MM_bin19_genomic.fna.gz --refList GCA_944326545.1_BRZ_MM_bin19_genomic.fna/target_genomes_gtdb.txt --output GCA_944326545.1_BRZ_MM_bin19_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 11:37:38,645] [INFO] Task succeeded: fastANI
[2023-06-28 11:37:38,655] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 11:37:38,656] [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_000980375.1	s__Limenecus avicola	78.9762	284	719	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Limenecus	95.0	98.45	97.78	0.95	0.92	8	-
GCA_018362895.1	s__Limenecus sp018362895	78.8592	265	719	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Limenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900547585.1	s__Spyradomonas sp900547585	77.8228	86	719	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Spyradomonas	95.0	99.89	99.89	0.88	0.88	2	-
GCA_900547155.1	s__Spyradomonas excrementavium	77.6085	86	719	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Spyradomonas	95.0	99.06	98.43	0.95	0.94	4	-
GCA_900761225.1	s__Stercorousia sp900761225	76.9288	70	719	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003258735.1	s__Zag111 sp003258735	76.8554	68	719	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	98.31	98.12	0.91	0.82	5	-
GCA_000433095.1	s__Stercorousia sp000433095	76.802	76	719	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	99.53	99.13	0.95	0.93	3	-
GCA_902797965.1	s__CAG-196 sp902797965	76.7997	53	719	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_900555325.1	s__Zag111 sp900555325	76.7606	51	719	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	99.12	99.12	0.81	0.81	2	-
GCA_900752845.1	s__Stercorousia sp900752845	76.7521	58	719	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	99.76	99.76	0.83	0.83	2	-
GCA_015152455.1	s__SIG32 sp015152455	76.6578	62	719	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__SIG32	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017470245.1	s__Avigastranaerophilus sp017470245	76.558	79	719	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Avigastranaerophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017467305.1	s__Avigastranaerophilus sp017467305	76.5126	60	719	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Avigastranaerophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018716565.1	s__Avigastranaerophilus faecigallinarum	76.4578	73	719	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Avigastranaerophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017694215.1	s__Scatousia excrementipullorum	76.4494	50	719	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Scatousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902788575.1	s__CAG-196 sp902788575	76.4063	53	719	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 11:37:38,657] [INFO] GTDB search result was written to GCA_944326545.1_BRZ_MM_bin19_genomic.fna/result_gtdb.tsv
[2023-06-28 11:37:38,658] [INFO] ===== GTDB Search completed =====
[2023-06-28 11:37:38,660] [INFO] DFAST_QC result json was written to GCA_944326545.1_BRZ_MM_bin19_genomic.fna/dqc_result.json
[2023-06-28 11:37:38,661] [INFO] DFAST_QC completed!
[2023-06-28 11:37:38,661] [INFO] Total running time: 0h0m39s