[2023-07-01 00:46:30,263] [INFO] DFAST_QC pipeline started.
[2023-07-01 00:46:30,265] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 00:46:30,265] [INFO] DQC Reference Directory: /var/lib/cwl/stg15376c36-0d62-4ccc-b1fb-4c64fc9b2d85/dqc_reference
[2023-07-01 00:46:31,532] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 00:46:31,533] [INFO] Task started: Prodigal
[2023-07-01 00:46:31,533] [INFO] Running command: gunzip -c /var/lib/cwl/stgd3732fed-898a-499b-bedb-5eef8886747b/GCA_025360495.1_ASM2536049v1_genomic.fna.gz | prodigal -d GCA_025360495.1_ASM2536049v1_genomic.fna/cds.fna -a GCA_025360495.1_ASM2536049v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 00:47:10,352] [INFO] Task succeeded: Prodigal
[2023-07-01 00:47:10,352] [INFO] Task started: HMMsearch
[2023-07-01 00:47:10,352] [INFO] Running command: hmmsearch --tblout GCA_025360495.1_ASM2536049v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15376c36-0d62-4ccc-b1fb-4c64fc9b2d85/dqc_reference/reference_markers.hmm GCA_025360495.1_ASM2536049v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 00:47:10,636] [INFO] Task succeeded: HMMsearch
[2023-07-01 00:47:10,637] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgd3732fed-898a-499b-bedb-5eef8886747b/GCA_025360495.1_ASM2536049v1_genomic.fna.gz]
[2023-07-01 00:47:10,681] [INFO] Query marker FASTA was written to GCA_025360495.1_ASM2536049v1_genomic.fna/markers.fasta
[2023-07-01 00:47:10,681] [INFO] Task started: Blastn
[2023-07-01 00:47:10,682] [INFO] Running command: blastn -query GCA_025360495.1_ASM2536049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15376c36-0d62-4ccc-b1fb-4c64fc9b2d85/dqc_reference/reference_markers.fasta -out GCA_025360495.1_ASM2536049v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 00:47:11,195] [INFO] Task succeeded: Blastn
[2023-07-01 00:47:11,200] [INFO] Selected 17 target genomes.
[2023-07-01 00:47:11,200] [INFO] Target genome list was writen to GCA_025360495.1_ASM2536049v1_genomic.fna/target_genomes.txt
[2023-07-01 00:47:11,219] [INFO] Task started: fastANI
[2023-07-01 00:47:11,219] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3732fed-898a-499b-bedb-5eef8886747b/GCA_025360495.1_ASM2536049v1_genomic.fna.gz --refList GCA_025360495.1_ASM2536049v1_genomic.fna/target_genomes.txt --output GCA_025360495.1_ASM2536049v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 00:47:25,232] [INFO] Task succeeded: fastANI
[2023-07-01 00:47:25,233] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15376c36-0d62-4ccc-b1fb-4c64fc9b2d85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 00:47:25,233] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15376c36-0d62-4ccc-b1fb-4c64fc9b2d85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 00:47:25,244] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 00:47:25,245] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 00:47:25,245] [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
Chthoniobacter flavus	strain=DSM 22515	GCA_004341915.1	191863	191863	type	True	75.4269	65	1697	95	below_threshold
Chthoniobacter flavus	strain=Ellin428	GCA_000173075.1	191863	191863	type	True	75.3777	67	1697	95	below_threshold
Nonomuraea rubra	strain=DSM 43768	GCA_014207985.1	46180	46180	type	True	74.7267	91	1697	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	74.62	88	1697	95	below_threshold
Nonomuraea fuscirosea	strain=CGMCC 4.7104	GCA_003001935.1	1291556	1291556	type	True	74.6003	98	1697	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	74.5998	85	1697	95	below_threshold
Nonomuraea deserti	strain=KC310	GCA_004348685.1	1848322	1848322	type	True	74.5645	79	1697	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 00:47:25,247] [INFO] DFAST Taxonomy check result was written to GCA_025360495.1_ASM2536049v1_genomic.fna/tc_result.tsv
[2023-07-01 00:47:25,247] [INFO] ===== Taxonomy check completed =====
[2023-07-01 00:47:25,247] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 00:47:25,248] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15376c36-0d62-4ccc-b1fb-4c64fc9b2d85/dqc_reference/checkm_data
[2023-07-01 00:47:25,248] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 00:47:25,307] [INFO] Task started: CheckM
[2023-07-01 00:47:25,307] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025360495.1_ASM2536049v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025360495.1_ASM2536049v1_genomic.fna/checkm_input GCA_025360495.1_ASM2536049v1_genomic.fna/checkm_result
[2023-07-01 00:49:18,563] [INFO] Task succeeded: CheckM
[2023-07-01 00:49:18,565] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 00:49:18,586] [INFO] ===== Completeness check finished =====
[2023-07-01 00:49:18,587] [INFO] ===== Start GTDB Search =====
[2023-07-01 00:49:18,587] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025360495.1_ASM2536049v1_genomic.fna/markers.fasta)
[2023-07-01 00:49:18,587] [INFO] Task started: Blastn
[2023-07-01 00:49:18,588] [INFO] Running command: blastn -query GCA_025360495.1_ASM2536049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15376c36-0d62-4ccc-b1fb-4c64fc9b2d85/dqc_reference/reference_markers_gtdb.fasta -out GCA_025360495.1_ASM2536049v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 00:49:19,082] [INFO] Task succeeded: Blastn
[2023-07-01 00:49:19,086] [INFO] Selected 18 target genomes.
[2023-07-01 00:49:19,087] [INFO] Target genome list was writen to GCA_025360495.1_ASM2536049v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 00:49:19,096] [INFO] Task started: fastANI
[2023-07-01 00:49:19,096] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3732fed-898a-499b-bedb-5eef8886747b/GCA_025360495.1_ASM2536049v1_genomic.fna.gz --refList GCA_025360495.1_ASM2536049v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025360495.1_ASM2536049v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 00:49:31,091] [INFO] Task succeeded: fastANI
[2023-07-01 00:49:31,106] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-07-01 00:49:31,106] [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_008933025.1	s__UBA6176 sp008933025	77.8212	379	1697	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__UBA6176	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903842505.1	s__UBA6176 sp903842505	76.9509	230	1697	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__UBA6176	95.0	99.72	99.54	0.92	0.90	4	-
GCA_903916195.1	s__CAIVQB01 sp903916195	76.746	216	1697	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__CAIVQB01	95.0	99.38	98.88	0.92	0.89	6	-
GCA_903907995.1	s__CAIVQB01 sp903907995	76.7069	198	1697	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__CAIVQB01	95.0	99.97	99.94	0.97	0.95	6	-
GCA_903922605.1	s__CAIVQB01 sp903922605	76.6204	202	1697	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__CAIVQB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002422905.1	s__UBA6176 sp002422905	76.5547	217	1697	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__UBA6176	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871615.1	s__SXXZ01 sp016871615	76.5169	165	1697	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__SXXZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903907925.1	s__CAIVQB01 sp903907925	76.4739	176	1697	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__CAIVQB01	95.0	99.94	99.94	0.98	0.98	2	-
GCA_903910585.1	s__CAIWAH01 sp903910585	76.2317	183	1697	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__CAIWAH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903930165.1	s__SXXZ01 sp903930165	76.1911	117	1697	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__SXXZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903844265.1	s__CAIMTB01 sp903844265	76.1655	104	1697	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__CAIMTB01;g__CAIMTB01	95.0	99.52	99.41	0.88	0.83	6	-
GCA_017302195.1	s__UBA9464 sp017302195	76.0662	118	1697	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__UBA9464	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 00:49:31,108] [INFO] GTDB search result was written to GCA_025360495.1_ASM2536049v1_genomic.fna/result_gtdb.tsv
[2023-07-01 00:49:31,109] [INFO] ===== GTDB Search completed =====
[2023-07-01 00:49:31,112] [INFO] DFAST_QC result json was written to GCA_025360495.1_ASM2536049v1_genomic.fna/dqc_result.json
[2023-07-01 00:49:31,112] [INFO] DFAST_QC completed!
[2023-07-01 00:49:31,113] [INFO] Total running time: 0h3m1s