[2023-06-17 09:12:58,309] [INFO] DFAST_QC pipeline started.
[2023-06-17 09:12:58,311] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 09:12:58,311] [INFO] DQC Reference Directory: /var/lib/cwl/stga9f99413-76cc-4b38-b003-52eec7e1e9bf/dqc_reference
[2023-06-17 09:12:59,685] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 09:12:59,686] [INFO] Task started: Prodigal
[2023-06-17 09:12:59,686] [INFO] Running command: gunzip -c /var/lib/cwl/stg118bb571-5f30-4d82-82b8-8331d6c2da8a/GCA_003161045.1_20110600_S1D_genomic.fna.gz | prodigal -d GCA_003161045.1_20110600_S1D_genomic.fna/cds.fna -a GCA_003161045.1_20110600_S1D_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 09:13:06,608] [INFO] Task succeeded: Prodigal
[2023-06-17 09:13:06,609] [INFO] Task started: HMMsearch
[2023-06-17 09:13:06,609] [INFO] Running command: hmmsearch --tblout GCA_003161045.1_20110600_S1D_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga9f99413-76cc-4b38-b003-52eec7e1e9bf/dqc_reference/reference_markers.hmm GCA_003161045.1_20110600_S1D_genomic.fna/protein.faa > /dev/null
[2023-06-17 09:13:06,805] [INFO] Task succeeded: HMMsearch
[2023-06-17 09:13:06,807] [INFO] Found 6/6 markers.
[2023-06-17 09:13:06,831] [INFO] Query marker FASTA was written to GCA_003161045.1_20110600_S1D_genomic.fna/markers.fasta
[2023-06-17 09:13:06,831] [INFO] Task started: Blastn
[2023-06-17 09:13:06,831] [INFO] Running command: blastn -query GCA_003161045.1_20110600_S1D_genomic.fna/markers.fasta -db /var/lib/cwl/stga9f99413-76cc-4b38-b003-52eec7e1e9bf/dqc_reference/reference_markers.fasta -out GCA_003161045.1_20110600_S1D_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 09:13:07,485] [INFO] Task succeeded: Blastn
[2023-06-17 09:13:07,488] [INFO] Selected 21 target genomes.
[2023-06-17 09:13:07,488] [INFO] Target genome list was writen to GCA_003161045.1_20110600_S1D_genomic.fna/target_genomes.txt
[2023-06-17 09:13:07,490] [INFO] Task started: fastANI
[2023-06-17 09:13:07,490] [INFO] Running command: fastANI --query /var/lib/cwl/stg118bb571-5f30-4d82-82b8-8331d6c2da8a/GCA_003161045.1_20110600_S1D_genomic.fna.gz --refList GCA_003161045.1_20110600_S1D_genomic.fna/target_genomes.txt --output GCA_003161045.1_20110600_S1D_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 09:13:24,476] [INFO] Task succeeded: fastANI
[2023-06-17 09:13:24,476] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga9f99413-76cc-4b38-b003-52eec7e1e9bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 09:13:24,477] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga9f99413-76cc-4b38-b003-52eec7e1e9bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 09:13:24,488] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 09:13:24,488] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 09:13:24,488] [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
Occallatibacter riparius	strain=DSM 25168	GCA_025264625.1	1002689	1002689	type	True	76.9259	209	828	95	below_threshold
Terracidiphilus gabretensis	strain=S55	GCA_001449115.1	1577687	1577687	type	True	76.8078	157	828	95	below_threshold
Silvibacterium dinghuense	strain=CGMCC 1.13007	GCA_014640355.1	1560006	1560006	type	True	76.8011	135	828	95	below_threshold
Silvibacterium dinghuense	strain=DHOF10	GCA_004123295.1	1560006	1560006	type	True	76.7859	135	828	95	below_threshold
Paracidobacterium acidisoli	strain=4G-K13	GCA_003428625.2	2303751	2303751	type	True	76.7655	126	828	95	below_threshold
Silvibacterium bohemicum	strain=DSM 103733	GCA_014201455.1	1577686	1577686	type	True	76.5044	129	828	95	below_threshold
Silvibacterium bohemicum	strain=S15	GCA_001006305.1	1577686	1577686	type	True	76.5037	131	828	95	below_threshold
Acidipila rosea	strain=DSM 103428	GCA_004339725.1	768535	768535	type	True	76.4743	89	828	95	below_threshold
Granulicella rosea	strain=DSM 18704	GCA_900188085.1	474952	474952	type	True	76.427	119	828	95	below_threshold
Bryocella elongata	strain=DSM 22489	GCA_900108185.1	863522	863522	type	True	76.2061	82	828	95	below_threshold
Edaphobacter lichenicola	strain=DSM 104462	GCA_025264645.1	2051959	2051959	suspected-type	True	75.9749	56	828	95	below_threshold
Myxococcus fulvus	strain=DSM 16525	GCA_900111765.1	33	33	type	True	74.9235	52	828	95	below_threshold
Myxococcus fulvus	strain=NBRC 100333	GCA_007991095.1	33	33	type	True	74.9235	52	828	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 09:13:24,493] [INFO] DFAST Taxonomy check result was written to GCA_003161045.1_20110600_S1D_genomic.fna/tc_result.tsv
[2023-06-17 09:13:24,494] [INFO] ===== Taxonomy check completed =====
[2023-06-17 09:13:24,494] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 09:13:24,494] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga9f99413-76cc-4b38-b003-52eec7e1e9bf/dqc_reference/checkm_data
[2023-06-17 09:13:24,495] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 09:13:24,541] [INFO] Task started: CheckM
[2023-06-17 09:13:24,542] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003161045.1_20110600_S1D_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003161045.1_20110600_S1D_genomic.fna/checkm_input GCA_003161045.1_20110600_S1D_genomic.fna/checkm_result
[2023-06-17 09:13:49,002] [INFO] Task succeeded: CheckM
[2023-06-17 09:13:49,003] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.61%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 09:13:49,017] [INFO] ===== Completeness check finished =====
[2023-06-17 09:13:49,018] [INFO] ===== Start GTDB Search =====
[2023-06-17 09:13:49,018] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003161045.1_20110600_S1D_genomic.fna/markers.fasta)
[2023-06-17 09:13:49,018] [INFO] Task started: Blastn
[2023-06-17 09:13:49,018] [INFO] Running command: blastn -query GCA_003161045.1_20110600_S1D_genomic.fna/markers.fasta -db /var/lib/cwl/stga9f99413-76cc-4b38-b003-52eec7e1e9bf/dqc_reference/reference_markers_gtdb.fasta -out GCA_003161045.1_20110600_S1D_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 09:13:49,991] [INFO] Task succeeded: Blastn
[2023-06-17 09:13:49,994] [INFO] Selected 14 target genomes.
[2023-06-17 09:13:49,994] [INFO] Target genome list was writen to GCA_003161045.1_20110600_S1D_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 09:13:49,996] [INFO] Task started: fastANI
[2023-06-17 09:13:49,996] [INFO] Running command: fastANI --query /var/lib/cwl/stg118bb571-5f30-4d82-82b8-8331d6c2da8a/GCA_003161045.1_20110600_S1D_genomic.fna.gz --refList GCA_003161045.1_20110600_S1D_genomic.fna/target_genomes_gtdb.txt --output GCA_003161045.1_20110600_S1D_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 09:14:00,634] [INFO] Task succeeded: fastANI
[2023-06-17 09:14:00,646] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 09:14:00,646] [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_003161045.1	s__Terracidiphilus sp003161045	100.0	818	828	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.61	99.39	0.87	0.83	8	conclusive
GCA_003134855.1	s__Terracidiphilus sp003134855	81.0762	527	828	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003167305.1	s__Terracidiphilus sp003167305	80.9224	393	828	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003159355.1	s__Terracidiphilus sp003159355	80.6438	474	828	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.48	99.30	0.83	0.80	7	-
GCA_003170825.1	s__Terracidiphilus sp003170825	80.5254	502	828	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.88	99.70	0.95	0.95	8	-
GCA_003142015.1	s__Terracidiphilus sp003142015	80.5046	482	828	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.69	99.69	0.91	0.91	2	-
GCA_003156235.1	s__Terracidiphilus sp003156235	80.1457	430	828	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903849645.1	s__Terracidiphilus sp903849645	78.9185	402	828	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.99	99.99	0.99	0.99	2	-
GCA_003138365.1	s__Terracidiphilus sp003138365	78.8589	412	828	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.60	99.22	0.93	0.83	18	-
GCA_903911925.1	s__Terracidiphilus sp903911925	78.1312	350	828	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003162495.1	s__Terracidiphilus sp003162495	78.0304	244	828	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003165075.1	s__Terracidiphilus sp003165075	77.9431	343	828	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003133425.1	s__Terracidiphilus sp003133425	77.6243	324	828	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.36	99.32	0.83	0.80	3	-
GCA_003151985.1	s__Terracidiphilus sp003151985	77.4757	287	828	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	98.76	98.76	0.71	0.71	2	-
--------------------------------------------------------------------------------
[2023-06-17 09:14:00,649] [INFO] GTDB search result was written to GCA_003161045.1_20110600_S1D_genomic.fna/result_gtdb.tsv
[2023-06-17 09:14:00,651] [INFO] ===== GTDB Search completed =====
[2023-06-17 09:14:00,654] [INFO] DFAST_QC result json was written to GCA_003161045.1_20110600_S1D_genomic.fna/dqc_result.json
[2023-06-17 09:14:00,654] [INFO] DFAST_QC completed!
[2023-06-17 09:14:00,654] [INFO] Total running time: 0h1m2s