[2023-06-30 03:56:31,406] [INFO] DFAST_QC pipeline started.
[2023-06-30 03:56:31,410] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 03:56:31,411] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f90a5ff-2dc5-4d98-9ab9-c7c9a4447c52/dqc_reference
[2023-06-30 03:56:32,626] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 03:56:32,628] [INFO] Task started: Prodigal
[2023-06-30 03:56:32,628] [INFO] Running command: gunzip -c /var/lib/cwl/stg402f8b5d-5525-4f68-975c-9c01dc9a0b47/GCA_903882385.1_freshwater_MAG_---_MJ120924A_bin-588_genomic.fna.gz | prodigal -d GCA_903882385.1_freshwater_MAG_---_MJ120924A_bin-588_genomic.fna/cds.fna -a GCA_903882385.1_freshwater_MAG_---_MJ120924A_bin-588_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 03:56:38,956] [INFO] Task succeeded: Prodigal
[2023-06-30 03:56:38,957] [INFO] Task started: HMMsearch
[2023-06-30 03:56:38,957] [INFO] Running command: hmmsearch --tblout GCA_903882385.1_freshwater_MAG_---_MJ120924A_bin-588_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f90a5ff-2dc5-4d98-9ab9-c7c9a4447c52/dqc_reference/reference_markers.hmm GCA_903882385.1_freshwater_MAG_---_MJ120924A_bin-588_genomic.fna/protein.faa > /dev/null
[2023-06-30 03:56:39,196] [INFO] Task succeeded: HMMsearch
[2023-06-30 03:56:39,198] [INFO] Found 6/6 markers.
[2023-06-30 03:56:39,228] [INFO] Query marker FASTA was written to GCA_903882385.1_freshwater_MAG_---_MJ120924A_bin-588_genomic.fna/markers.fasta
[2023-06-30 03:56:39,229] [INFO] Task started: Blastn
[2023-06-30 03:56:39,229] [INFO] Running command: blastn -query GCA_903882385.1_freshwater_MAG_---_MJ120924A_bin-588_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f90a5ff-2dc5-4d98-9ab9-c7c9a4447c52/dqc_reference/reference_markers.fasta -out GCA_903882385.1_freshwater_MAG_---_MJ120924A_bin-588_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:56:39,956] [INFO] Task succeeded: Blastn
[2023-06-30 03:56:39,961] [INFO] Selected 29 target genomes.
[2023-06-30 03:56:39,962] [INFO] Target genome list was writen to GCA_903882385.1_freshwater_MAG_---_MJ120924A_bin-588_genomic.fna/target_genomes.txt
[2023-06-30 03:56:39,963] [INFO] Task started: fastANI
[2023-06-30 03:56:39,963] [INFO] Running command: fastANI --query /var/lib/cwl/stg402f8b5d-5525-4f68-975c-9c01dc9a0b47/GCA_903882385.1_freshwater_MAG_---_MJ120924A_bin-588_genomic.fna.gz --refList GCA_903882385.1_freshwater_MAG_---_MJ120924A_bin-588_genomic.fna/target_genomes.txt --output GCA_903882385.1_freshwater_MAG_---_MJ120924A_bin-588_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 03:56:56,615] [INFO] Task succeeded: fastANI
[2023-06-30 03:56:56,615] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f90a5ff-2dc5-4d98-9ab9-c7c9a4447c52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 03:56:56,616] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f90a5ff-2dc5-4d98-9ab9-c7c9a4447c52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 03:56:56,626] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 03:56:56,626] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 03:56:56,627] [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
Gallionella capsiferriformans	strain=ES-2	GCA_000145255.1	370405	370405	type	True	79.4557	284	711	95	below_threshold
Ferrigenium kumadai	strain=An22	GCA_018324385.1	1682490	1682490	type	True	77.0431	144	711	95	below_threshold
Ferriphaselus amnicola	strain=OYT1	GCA_000974685.2	1188319	1188319	type	True	76.5629	81	711	95	below_threshold
Sulfurimicrobium lacus	strain=skT11	GCA_011764585.1	2715678	2715678	type	True	76.1767	53	711	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 03:56:56,629] [INFO] DFAST Taxonomy check result was written to GCA_903882385.1_freshwater_MAG_---_MJ120924A_bin-588_genomic.fna/tc_result.tsv
[2023-06-30 03:56:56,630] [INFO] ===== Taxonomy check completed =====
[2023-06-30 03:56:56,630] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 03:56:56,630] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f90a5ff-2dc5-4d98-9ab9-c7c9a4447c52/dqc_reference/checkm_data
[2023-06-30 03:56:56,632] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 03:56:56,663] [INFO] Task started: CheckM
[2023-06-30 03:56:56,664] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903882385.1_freshwater_MAG_---_MJ120924A_bin-588_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903882385.1_freshwater_MAG_---_MJ120924A_bin-588_genomic.fna/checkm_input GCA_903882385.1_freshwater_MAG_---_MJ120924A_bin-588_genomic.fna/checkm_result
[2023-06-30 03:57:21,548] [INFO] Task succeeded: CheckM
[2023-06-30 03:57:21,550] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 03:57:21,573] [INFO] ===== Completeness check finished =====
[2023-06-30 03:57:21,573] [INFO] ===== Start GTDB Search =====
[2023-06-30 03:57:21,574] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903882385.1_freshwater_MAG_---_MJ120924A_bin-588_genomic.fna/markers.fasta)
[2023-06-30 03:57:21,574] [INFO] Task started: Blastn
[2023-06-30 03:57:21,574] [INFO] Running command: blastn -query GCA_903882385.1_freshwater_MAG_---_MJ120924A_bin-588_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f90a5ff-2dc5-4d98-9ab9-c7c9a4447c52/dqc_reference/reference_markers_gtdb.fasta -out GCA_903882385.1_freshwater_MAG_---_MJ120924A_bin-588_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:57:22,700] [INFO] Task succeeded: Blastn
[2023-06-30 03:57:22,705] [INFO] Selected 10 target genomes.
[2023-06-30 03:57:22,705] [INFO] Target genome list was writen to GCA_903882385.1_freshwater_MAG_---_MJ120924A_bin-588_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 03:57:22,710] [INFO] Task started: fastANI
[2023-06-30 03:57:22,710] [INFO] Running command: fastANI --query /var/lib/cwl/stg402f8b5d-5525-4f68-975c-9c01dc9a0b47/GCA_903882385.1_freshwater_MAG_---_MJ120924A_bin-588_genomic.fna.gz --refList GCA_903882385.1_freshwater_MAG_---_MJ120924A_bin-588_genomic.fna/target_genomes_gtdb.txt --output GCA_903882385.1_freshwater_MAG_---_MJ120924A_bin-588_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 03:57:27,502] [INFO] Task succeeded: fastANI
[2023-06-30 03:57:27,514] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 03:57:27,515] [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_903885165.1	s__Gallionella sp903885165	99.7918	636	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	99.76	99.35	0.93	0.83	60	conclusive
GCF_000145255.1	s__Gallionella capsiferriformans	79.4557	284	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001801025.1	s__Gallionella sp001801025	79.273	298	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	99.91	99.81	0.99	0.99	3	-
GCA_002381565.1	s__Gallionella sp002381565	78.6034	292	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	98.74	97.66	0.88	0.86	3	-
GCA_903915035.1	s__Gallionella sp903915035	78.4175	238	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	99.81	99.81	0.88	0.88	2	-
GCA_017880865.1	s__Gallionella sp017880865	77.307	181	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001801105.1	s__Gallionella sp001801105	77.0339	127	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002403995.1	s__Gallionella sp002403995	76.9664	145	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016183575.1	s__Gallionella sp016183575	76.8207	97	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235045.1	s__Sideroxydans sp016235045	76.7639	112	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 03:57:27,518] [INFO] GTDB search result was written to GCA_903882385.1_freshwater_MAG_---_MJ120924A_bin-588_genomic.fna/result_gtdb.tsv
[2023-06-30 03:57:27,519] [INFO] ===== GTDB Search completed =====
[2023-06-30 03:57:27,522] [INFO] DFAST_QC result json was written to GCA_903882385.1_freshwater_MAG_---_MJ120924A_bin-588_genomic.fna/dqc_result.json
[2023-06-30 03:57:27,522] [INFO] DFAST_QC completed!
[2023-06-30 03:57:27,522] [INFO] Total running time: 0h0m56s