[2023-06-28 17:15:31,604] [INFO] DFAST_QC pipeline started.
[2023-06-28 17:15:31,608] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 17:15:31,608] [INFO] DQC Reference Directory: /var/lib/cwl/stga7410a5c-ba60-4da9-88b7-378bb82b677b/dqc_reference
[2023-06-28 17:15:33,319] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 17:15:33,319] [INFO] Task started: Prodigal
[2023-06-28 17:15:33,320] [INFO] Running command: gunzip -c /var/lib/cwl/stg884727da-d07a-4d14-8bef-108d72a97976/GCA_944358405.1_E07_bin200_genomic.fna.gz | prodigal -d GCA_944358405.1_E07_bin200_genomic.fna/cds.fna -a GCA_944358405.1_E07_bin200_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 17:15:35,137] [INFO] Task succeeded: Prodigal
[2023-06-28 17:15:35,138] [INFO] Task started: HMMsearch
[2023-06-28 17:15:35,138] [INFO] Running command: hmmsearch --tblout GCA_944358405.1_E07_bin200_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7410a5c-ba60-4da9-88b7-378bb82b677b/dqc_reference/reference_markers.hmm GCA_944358405.1_E07_bin200_genomic.fna/protein.faa > /dev/null
[2023-06-28 17:15:35,353] [INFO] Task succeeded: HMMsearch
[2023-06-28 17:15:35,355] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg884727da-d07a-4d14-8bef-108d72a97976/GCA_944358405.1_E07_bin200_genomic.fna.gz]
[2023-06-28 17:15:35,370] [INFO] Query marker FASTA was written to GCA_944358405.1_E07_bin200_genomic.fna/markers.fasta
[2023-06-28 17:15:35,370] [INFO] Task started: Blastn
[2023-06-28 17:15:35,370] [INFO] Running command: blastn -query GCA_944358405.1_E07_bin200_genomic.fna/markers.fasta -db /var/lib/cwl/stga7410a5c-ba60-4da9-88b7-378bb82b677b/dqc_reference/reference_markers.fasta -out GCA_944358405.1_E07_bin200_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:15:37,331] [INFO] Task succeeded: Blastn
[2023-06-28 17:15:37,334] [INFO] Selected 21 target genomes.
[2023-06-28 17:15:37,335] [INFO] Target genome list was writen to GCA_944358405.1_E07_bin200_genomic.fna/target_genomes.txt
[2023-06-28 17:15:37,347] [INFO] Task started: fastANI
[2023-06-28 17:15:37,347] [INFO] Running command: fastANI --query /var/lib/cwl/stg884727da-d07a-4d14-8bef-108d72a97976/GCA_944358405.1_E07_bin200_genomic.fna.gz --refList GCA_944358405.1_E07_bin200_genomic.fna/target_genomes.txt --output GCA_944358405.1_E07_bin200_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 17:15:47,079] [INFO] Task succeeded: fastANI
[2023-06-28 17:15:47,079] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7410a5c-ba60-4da9-88b7-378bb82b677b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 17:15:47,080] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7410a5c-ba60-4da9-88b7-378bb82b677b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 17:15:47,081] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 17:15:47,081] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 17:15:47,081] [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 17:15:47,083] [INFO] DFAST Taxonomy check result was written to GCA_944358405.1_E07_bin200_genomic.fna/tc_result.tsv
[2023-06-28 17:15:47,083] [INFO] ===== Taxonomy check completed =====
[2023-06-28 17:15:47,083] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 17:15:47,084] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7410a5c-ba60-4da9-88b7-378bb82b677b/dqc_reference/checkm_data
[2023-06-28 17:15:47,086] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 17:15:47,104] [INFO] Task started: CheckM
[2023-06-28 17:15:47,104] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944358405.1_E07_bin200_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944358405.1_E07_bin200_genomic.fna/checkm_input GCA_944358405.1_E07_bin200_genomic.fna/checkm_result
[2023-06-28 17:16:00,563] [INFO] Task succeeded: CheckM
[2023-06-28 17:16:00,564] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.11%
Contamintation: 1.04%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-28 17:16:00,578] [INFO] ===== Completeness check finished =====
[2023-06-28 17:16:00,578] [INFO] ===== Start GTDB Search =====
[2023-06-28 17:16:00,579] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944358405.1_E07_bin200_genomic.fna/markers.fasta)
[2023-06-28 17:16:00,579] [INFO] Task started: Blastn
[2023-06-28 17:16:00,579] [INFO] Running command: blastn -query GCA_944358405.1_E07_bin200_genomic.fna/markers.fasta -db /var/lib/cwl/stga7410a5c-ba60-4da9-88b7-378bb82b677b/dqc_reference/reference_markers_gtdb.fasta -out GCA_944358405.1_E07_bin200_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:16:01,411] [INFO] Task succeeded: Blastn
[2023-06-28 17:16:01,414] [INFO] Selected 20 target genomes.
[2023-06-28 17:16:01,415] [INFO] Target genome list was writen to GCA_944358405.1_E07_bin200_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 17:16:01,417] [INFO] Task started: fastANI
[2023-06-28 17:16:01,417] [INFO] Running command: fastANI --query /var/lib/cwl/stg884727da-d07a-4d14-8bef-108d72a97976/GCA_944358405.1_E07_bin200_genomic.fna.gz --refList GCA_944358405.1_E07_bin200_genomic.fna/target_genomes_gtdb.txt --output GCA_944358405.1_E07_bin200_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 17:16:06,319] [INFO] Task succeeded: fastANI
[2023-06-28 17:16:06,338] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 17:16:06,338] [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_017886705.1	s__Faecimonas sp017886705	78.8158	146	403	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018712565.1	s__Faecimonas gallistercoris	78.7811	129	403	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecimonas	95.0	99.98	99.98	0.85	0.85	2	-
GCA_900554315.1	s__Faecimonas sp900554315	78.2028	118	403	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecimonas	95.0	99.99	99.97	0.89	0.78	3	-
GCA_900753325.1	s__CAG-877 sp900753325	77.9423	105	403	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-877	95.0	99.65	99.65	0.68	0.68	2	-
GCA_900768815.1	s__CAG-877 sp900768815	77.9117	123	403	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-877	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015059435.1	s__Faecimonas sp015059435	77.9068	92	403	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017622175.1	s__CAG-877 sp017622175	77.865	105	403	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-877	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017409785.1	s__CAG-877 sp017409785	77.8346	110	403	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-877	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000433455.1	s__CAG-877 sp000433455	77.8025	121	403	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-877	95.0	97.81	97.70	0.90	0.89	3	-
GCA_910589335.1	s__UBA3789 sp910589335	77.656	108	403	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905209745.1	s__Faecimonas sp905209745	77.6449	74	403	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017519965.1	s__RUG14891 sp017519965	77.4098	78	403	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG14891	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543055.1	s__UBA3789 sp900543055	77.3138	85	403	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	98.54	97.21	0.78	0.56	4	-
GCA_910585335.1	s__MGBC119817 sp910585335	77.1893	60	403	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__MGBC119817	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902796215.1	s__UBA3789 sp902796215	77.0588	70	403	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902768065.1	s__UBA3789 sp902768065	77.0466	65	403	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902797265.1	s__UBA3789 sp902797265	76.8723	85	403	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017405445.1	s__UBA3789 sp017405445	76.7939	75	403	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017511375.1	s__UBA3789 sp017511375	76.7658	62	403	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 17:16:06,342] [INFO] GTDB search result was written to GCA_944358405.1_E07_bin200_genomic.fna/result_gtdb.tsv
[2023-06-28 17:16:06,343] [INFO] ===== GTDB Search completed =====
[2023-06-28 17:16:06,346] [INFO] DFAST_QC result json was written to GCA_944358405.1_E07_bin200_genomic.fna/dqc_result.json
[2023-06-28 17:16:06,346] [INFO] DFAST_QC completed!
[2023-06-28 17:16:06,346] [INFO] Total running time: 0h0m35s