[2023-06-17 08:52:27,301] [INFO] DFAST_QC pipeline started.
[2023-06-17 08:52:27,325] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 08:52:27,326] [INFO] DQC Reference Directory: /var/lib/cwl/stgb1a1cf0c-9f92-4a18-acf9-cb55ab604708/dqc_reference
[2023-06-17 08:52:28,590] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 08:52:28,591] [INFO] Task started: Prodigal
[2023-06-17 08:52:28,591] [INFO] Running command: gunzip -c /var/lib/cwl/stg72691169-a400-4187-8653-973212c3a686/GCA_003167455.1_20110700_P2D_genomic.fna.gz | prodigal -d GCA_003167455.1_20110700_P2D_genomic.fna/cds.fna -a GCA_003167455.1_20110700_P2D_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 08:52:34,701] [INFO] Task succeeded: Prodigal
[2023-06-17 08:52:34,701] [INFO] Task started: HMMsearch
[2023-06-17 08:52:34,701] [INFO] Running command: hmmsearch --tblout GCA_003167455.1_20110700_P2D_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb1a1cf0c-9f92-4a18-acf9-cb55ab604708/dqc_reference/reference_markers.hmm GCA_003167455.1_20110700_P2D_genomic.fna/protein.faa > /dev/null
[2023-06-17 08:52:34,955] [INFO] Task succeeded: HMMsearch
[2023-06-17 08:52:34,957] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg72691169-a400-4187-8653-973212c3a686/GCA_003167455.1_20110700_P2D_genomic.fna.gz]
[2023-06-17 08:52:34,990] [INFO] Query marker FASTA was written to GCA_003167455.1_20110700_P2D_genomic.fna/markers.fasta
[2023-06-17 08:52:34,990] [INFO] Task started: Blastn
[2023-06-17 08:52:34,991] [INFO] Running command: blastn -query GCA_003167455.1_20110700_P2D_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1a1cf0c-9f92-4a18-acf9-cb55ab604708/dqc_reference/reference_markers.fasta -out GCA_003167455.1_20110700_P2D_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 08:52:35,488] [INFO] Task succeeded: Blastn
[2023-06-17 08:52:35,514] [INFO] Selected 15 target genomes.
[2023-06-17 08:52:35,514] [INFO] Target genome list was writen to GCA_003167455.1_20110700_P2D_genomic.fna/target_genomes.txt
[2023-06-17 08:52:35,517] [INFO] Task started: fastANI
[2023-06-17 08:52:35,518] [INFO] Running command: fastANI --query /var/lib/cwl/stg72691169-a400-4187-8653-973212c3a686/GCA_003167455.1_20110700_P2D_genomic.fna.gz --refList GCA_003167455.1_20110700_P2D_genomic.fna/target_genomes.txt --output GCA_003167455.1_20110700_P2D_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 08:52:45,378] [INFO] Task succeeded: fastANI
[2023-06-17 08:52:45,379] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb1a1cf0c-9f92-4a18-acf9-cb55ab604708/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 08:52:45,380] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb1a1cf0c-9f92-4a18-acf9-cb55ab604708/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 08:52:45,382] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 08:52:45,383] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 08:52:45,383] [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
--------------------------------------------------------------------------------
[2023-06-17 08:52:45,385] [INFO] DFAST Taxonomy check result was written to GCA_003167455.1_20110700_P2D_genomic.fna/tc_result.tsv
[2023-06-17 08:52:45,386] [INFO] ===== Taxonomy check completed =====
[2023-06-17 08:52:45,387] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 08:52:45,387] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb1a1cf0c-9f92-4a18-acf9-cb55ab604708/dqc_reference/checkm_data
[2023-06-17 08:52:45,391] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 08:52:45,424] [INFO] Task started: CheckM
[2023-06-17 08:52:45,425] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003167455.1_20110700_P2D_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003167455.1_20110700_P2D_genomic.fna/checkm_input GCA_003167455.1_20110700_P2D_genomic.fna/checkm_result
[2023-06-17 08:53:09,034] [INFO] Task succeeded: CheckM
[2023-06-17 08:53:09,036] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 08:53:09,062] [INFO] ===== Completeness check finished =====
[2023-06-17 08:53:09,063] [INFO] ===== Start GTDB Search =====
[2023-06-17 08:53:09,063] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003167455.1_20110700_P2D_genomic.fna/markers.fasta)
[2023-06-17 08:53:09,064] [INFO] Task started: Blastn
[2023-06-17 08:53:09,064] [INFO] Running command: blastn -query GCA_003167455.1_20110700_P2D_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1a1cf0c-9f92-4a18-acf9-cb55ab604708/dqc_reference/reference_markers_gtdb.fasta -out GCA_003167455.1_20110700_P2D_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 08:53:09,585] [INFO] Task succeeded: Blastn
[2023-06-17 08:53:09,591] [INFO] Selected 12 target genomes.
[2023-06-17 08:53:09,591] [INFO] Target genome list was writen to GCA_003167455.1_20110700_P2D_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 08:53:09,596] [INFO] Task started: fastANI
[2023-06-17 08:53:09,596] [INFO] Running command: fastANI --query /var/lib/cwl/stg72691169-a400-4187-8653-973212c3a686/GCA_003167455.1_20110700_P2D_genomic.fna.gz --refList GCA_003167455.1_20110700_P2D_genomic.fna/target_genomes_gtdb.txt --output GCA_003167455.1_20110700_P2D_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 08:53:16,754] [INFO] Task succeeded: fastANI
[2023-06-17 08:53:16,769] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 08:53:16,770] [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_003134695.1	s__Zemynaea palustris	99.6741	700	743	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Zemynaea	95.0	99.68	99.42	0.94	0.92	6	conclusive
GCA_002413145.1	s__Zemynaea sp002413145	80.4993	372	743	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Zemynaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003136895.1	s__Erabacter solicola	77.9258	261	743	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Erabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014304965.1	s__Cryoxeromicrobium davisii	77.1338	175	743	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Cryoxeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003136655.1	s__Hesperobacter lustricola	77.0774	217	743	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Hesperobacter	95.0	99.53	99.53	0.92	0.92	2	-
GCA_903970385.1	s__Palsa-1515 sp903970385	76.8222	202	743	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Palsa-1515	95.0	97.40	97.40	0.78	0.78	2	-
GCA_003156715.1	s__Tityobacter terrigena	76.7732	158	743	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Tityobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003161435.1	s__Elarobacter pasteuri	76.5753	153	743	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Elarobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003158195.1	s__Palsibacter borealis	76.4914	189	743	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Palsibacter	95.0	99.15	99.15	0.89	0.89	2	-
GCA_003168375.1	s__Elarobacter winogradskyi	76.4785	201	743	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Elarobacter	95.0	99.98	99.85	1.00	0.97	12	-
GCA_013036095.1	s__Rubrimentiphilum sp013036095	76.4731	74	743	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Rubrimentiphilum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 08:53:16,772] [INFO] GTDB search result was written to GCA_003167455.1_20110700_P2D_genomic.fna/result_gtdb.tsv
[2023-06-17 08:53:16,772] [INFO] ===== GTDB Search completed =====
[2023-06-17 08:53:16,775] [INFO] DFAST_QC result json was written to GCA_003167455.1_20110700_P2D_genomic.fna/dqc_result.json
[2023-06-17 08:53:16,775] [INFO] DFAST_QC completed!
[2023-06-17 08:53:16,775] [INFO] Total running time: 0h0m49s