[2023-06-05 12:31:18,677] [INFO] DFAST_QC pipeline started.
[2023-06-05 12:31:18,679] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 12:31:18,680] [INFO] DQC Reference Directory: /var/lib/cwl/stg06b27e53-314e-4033-8c44-135a3e71f558/dqc_reference
[2023-06-05 12:31:19,870] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 12:31:19,871] [INFO] Task started: Prodigal
[2023-06-05 12:31:19,871] [INFO] Running command: gunzip -c /var/lib/cwl/stg1edba66a-60c1-4415-9d70-aaab0517128e/GCA_934591745.1_ERR7738223_bin.268_genomic.fna.gz | prodigal -d GCA_934591745.1_ERR7738223_bin.268_genomic.fna/cds.fna -a GCA_934591745.1_ERR7738223_bin.268_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 12:31:24,375] [INFO] Task succeeded: Prodigal
[2023-06-05 12:31:24,375] [INFO] Task started: HMMsearch
[2023-06-05 12:31:24,375] [INFO] Running command: hmmsearch --tblout GCA_934591745.1_ERR7738223_bin.268_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06b27e53-314e-4033-8c44-135a3e71f558/dqc_reference/reference_markers.hmm GCA_934591745.1_ERR7738223_bin.268_genomic.fna/protein.faa > /dev/null
[2023-06-05 12:31:24,576] [INFO] Task succeeded: HMMsearch
[2023-06-05 12:31:24,578] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1edba66a-60c1-4415-9d70-aaab0517128e/GCA_934591745.1_ERR7738223_bin.268_genomic.fna.gz]
[2023-06-05 12:31:24,599] [INFO] Query marker FASTA was written to GCA_934591745.1_ERR7738223_bin.268_genomic.fna/markers.fasta
[2023-06-05 12:31:24,600] [INFO] Task started: Blastn
[2023-06-05 12:31:24,600] [INFO] Running command: blastn -query GCA_934591745.1_ERR7738223_bin.268_genomic.fna/markers.fasta -db /var/lib/cwl/stg06b27e53-314e-4033-8c44-135a3e71f558/dqc_reference/reference_markers.fasta -out GCA_934591745.1_ERR7738223_bin.268_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 12:31:25,279] [INFO] Task succeeded: Blastn
[2023-06-05 12:31:25,282] [INFO] Selected 14 target genomes.
[2023-06-05 12:31:25,283] [INFO] Target genome list was writen to GCA_934591745.1_ERR7738223_bin.268_genomic.fna/target_genomes.txt
[2023-06-05 12:31:25,284] [INFO] Task started: fastANI
[2023-06-05 12:31:25,284] [INFO] Running command: fastANI --query /var/lib/cwl/stg1edba66a-60c1-4415-9d70-aaab0517128e/GCA_934591745.1_ERR7738223_bin.268_genomic.fna.gz --refList GCA_934591745.1_ERR7738223_bin.268_genomic.fna/target_genomes.txt --output GCA_934591745.1_ERR7738223_bin.268_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 12:31:31,435] [INFO] Task succeeded: fastANI
[2023-06-05 12:31:31,435] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06b27e53-314e-4033-8c44-135a3e71f558/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 12:31:31,436] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06b27e53-314e-4033-8c44-135a3e71f558/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 12:31:31,448] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 12:31:31,449] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 12:31:31,449] [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
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	81.6755	241	481	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	80.249	211	481	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	78.9682	169	481	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	78.2915	92	481	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	78.2668	141	481	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	77.7505	89	481	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	77.4227	78	481	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	77.4026	107	481	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	77.06	50	481	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_003425665.1	2211183	2211183	type	True	76.787	57	481	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 12:31:31,453] [INFO] DFAST Taxonomy check result was written to GCA_934591745.1_ERR7738223_bin.268_genomic.fna/tc_result.tsv
[2023-06-05 12:31:31,453] [INFO] ===== Taxonomy check completed =====
[2023-06-05 12:31:31,454] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 12:31:31,454] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06b27e53-314e-4033-8c44-135a3e71f558/dqc_reference/checkm_data
[2023-06-05 12:31:31,455] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 12:31:31,478] [INFO] Task started: CheckM
[2023-06-05 12:31:31,478] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934591745.1_ERR7738223_bin.268_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934591745.1_ERR7738223_bin.268_genomic.fna/checkm_input GCA_934591745.1_ERR7738223_bin.268_genomic.fna/checkm_result
[2023-06-05 12:31:51,073] [INFO] Task succeeded: CheckM
[2023-06-05 12:31:51,074] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 12:31:51,091] [INFO] ===== Completeness check finished =====
[2023-06-05 12:31:51,092] [INFO] ===== Start GTDB Search =====
[2023-06-05 12:31:51,092] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934591745.1_ERR7738223_bin.268_genomic.fna/markers.fasta)
[2023-06-05 12:31:51,092] [INFO] Task started: Blastn
[2023-06-05 12:31:51,093] [INFO] Running command: blastn -query GCA_934591745.1_ERR7738223_bin.268_genomic.fna/markers.fasta -db /var/lib/cwl/stg06b27e53-314e-4033-8c44-135a3e71f558/dqc_reference/reference_markers_gtdb.fasta -out GCA_934591745.1_ERR7738223_bin.268_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 12:31:52,284] [INFO] Task succeeded: Blastn
[2023-06-05 12:31:52,290] [INFO] Selected 10 target genomes.
[2023-06-05 12:31:52,290] [INFO] Target genome list was writen to GCA_934591745.1_ERR7738223_bin.268_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 12:31:52,291] [INFO] Task started: fastANI
[2023-06-05 12:31:52,292] [INFO] Running command: fastANI --query /var/lib/cwl/stg1edba66a-60c1-4415-9d70-aaab0517128e/GCA_934591745.1_ERR7738223_bin.268_genomic.fna.gz --refList GCA_934591745.1_ERR7738223_bin.268_genomic.fna/target_genomes_gtdb.txt --output GCA_934591745.1_ERR7738223_bin.268_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 12:31:56,164] [INFO] Task succeeded: fastANI
[2023-06-05 12:31:56,178] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 12:31:56,178] [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_900551355.1	s__CAG-83 sp900551355	93.5644	286	481	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.94	98.90	0.93	0.92	3	-
GCA_900550585.1	s__CAG-83 sp900550585	93.1679	355	481	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	99.85	99.85	0.92	0.92	2	-
GCA_900547745.1	s__CAG-83 sp900547745	91.1706	341	481	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	99.22	99.21	0.93	0.91	3	-
GCA_900545495.1	s__CAG-83 sp900545495	89.7771	329	481	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.95	95.34	0.89	0.84	5	-
GCA_900545585.1	s__CAG-83 sp900545585	88.1172	338	481	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.41	98.11	0.88	0.81	5	-
GCA_003487665.1	s__CAG-83 sp003487665	84.673	282	481	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.43	97.11	0.80	0.74	11	-
GCA_900554275.1	s__CAG-83 sp900554275	84.2647	266	481	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.46	96.91	0.80	0.75	4	-
GCA_900556015.1	s__CAG-83 sp900556015	83.5392	179	481	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.42	97.27	0.78	0.77	3	-
GCA_000435555.1	s__CAG-83 sp000435555	83.3372	256	481	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.91	97.56	0.88	0.73	17	-
GCA_900551995.1	s__CAG-83 sp900551995	83.3197	278	481	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.79	97.61	0.85	0.83	3	-
--------------------------------------------------------------------------------
[2023-06-05 12:31:56,181] [INFO] GTDB search result was written to GCA_934591745.1_ERR7738223_bin.268_genomic.fna/result_gtdb.tsv
[2023-06-05 12:31:56,182] [INFO] ===== GTDB Search completed =====
[2023-06-05 12:31:56,187] [INFO] DFAST_QC result json was written to GCA_934591745.1_ERR7738223_bin.268_genomic.fna/dqc_result.json
[2023-06-05 12:31:56,188] [INFO] DFAST_QC completed!
[2023-06-05 12:31:56,188] [INFO] Total running time: 0h0m38s