[2023-06-13 14:46:19,277] [INFO] DFAST_QC pipeline started.
[2023-06-13 14:46:19,280] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 14:46:19,280] [INFO] DQC Reference Directory: /var/lib/cwl/stgeeb795e3-c45a-4e05-b04d-11039b24a8bd/dqc_reference
[2023-06-13 14:46:20,495] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 14:46:20,496] [INFO] Task started: Prodigal
[2023-06-13 14:46:20,496] [INFO] Running command: gunzip -c /var/lib/cwl/stg1765066c-5357-4d87-831c-3a60a249665d/GCA_938016545.1_ERR414241_bin.44_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938016545.1_ERR414241_bin.44_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938016545.1_ERR414241_bin.44_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 14:46:34,390] [INFO] Task succeeded: Prodigal
[2023-06-13 14:46:34,390] [INFO] Task started: HMMsearch
[2023-06-13 14:46:34,391] [INFO] Running command: hmmsearch --tblout GCA_938016545.1_ERR414241_bin.44_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeeb795e3-c45a-4e05-b04d-11039b24a8bd/dqc_reference/reference_markers.hmm GCA_938016545.1_ERR414241_bin.44_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 14:46:34,712] [INFO] Task succeeded: HMMsearch
[2023-06-13 14:46:34,714] [INFO] Found 6/6 markers.
[2023-06-13 14:46:34,764] [INFO] Query marker FASTA was written to GCA_938016545.1_ERR414241_bin.44_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 14:46:34,764] [INFO] Task started: Blastn
[2023-06-13 14:46:34,765] [INFO] Running command: blastn -query GCA_938016545.1_ERR414241_bin.44_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgeeb795e3-c45a-4e05-b04d-11039b24a8bd/dqc_reference/reference_markers.fasta -out GCA_938016545.1_ERR414241_bin.44_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:46:35,604] [INFO] Task succeeded: Blastn
[2023-06-13 14:46:35,609] [INFO] Selected 12 target genomes.
[2023-06-13 14:46:35,609] [INFO] Target genome list was writen to GCA_938016545.1_ERR414241_bin.44_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 14:46:35,612] [INFO] Task started: fastANI
[2023-06-13 14:46:35,613] [INFO] Running command: fastANI --query /var/lib/cwl/stg1765066c-5357-4d87-831c-3a60a249665d/GCA_938016545.1_ERR414241_bin.44_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938016545.1_ERR414241_bin.44_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938016545.1_ERR414241_bin.44_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 14:46:50,258] [INFO] Task succeeded: fastANI
[2023-06-13 14:46:50,258] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeeb795e3-c45a-4e05-b04d-11039b24a8bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 14:46:50,259] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeeb795e3-c45a-4e05-b04d-11039b24a8bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 14:46:50,274] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2023-06-13 14:46:50,274] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-06-13 14:46:50,275] [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
Klebsiella grimontii	strain=06D021	GCA_900200035.1	2058152	2058152	type	True	99.2047	1721	1863	95	inconclusive
Klebsiella pasteurii		GCA_902158725.1	2587529	2587529	type	True	96.0296	1642	1863	95	inconclusive
Klebsiella michiganensis	strain=CCUG 66515	GCA_009173485.1	1134687	1134687	type	True	93.816	1638	1863	95	below_threshold
Klebsiella michiganensis	strain=DSM 25444	GCA_002925905.1	1134687	1134687	type	True	93.7327	1645	1863	95	below_threshold
Klebsiella oxytoca	strain=NBRC 105695	GCA_001598695.1	571	571	type	True	91.6123	1557	1863	95	below_threshold
Klebsiella spallanzanii		GCA_902158555.1	2587528	2587528	type	True	89.2393	1495	1863	95	below_threshold
Klebsiella pneumoniae	strain=PartO-Kpneumoniae-RM8376	GCA_022869665.1	573	573	type	True	84.3391	1257	1863	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	81.8651	914	1863	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	81.8062	864	1863	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.6239	942	1863	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.4336	893	1863	95	below_threshold
Leminorella grimontii	strain=JCM 5902	GCA_024343555.1	82981	82981	type	True	77.4623	265	1863	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 14:46:50,276] [INFO] DFAST Taxonomy check result was written to GCA_938016545.1_ERR414241_bin.44_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 14:46:50,277] [INFO] ===== Taxonomy check completed =====
[2023-06-13 14:46:50,278] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 14:46:50,278] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeeb795e3-c45a-4e05-b04d-11039b24a8bd/dqc_reference/checkm_data
[2023-06-13 14:46:50,281] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 14:46:50,337] [INFO] Task started: CheckM
[2023-06-13 14:46:50,337] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938016545.1_ERR414241_bin.44_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938016545.1_ERR414241_bin.44_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938016545.1_ERR414241_bin.44_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 14:47:33,190] [INFO] Task succeeded: CheckM
[2023-06-13 14:47:33,192] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 14:47:33,219] [INFO] ===== Completeness check finished =====
[2023-06-13 14:47:33,219] [INFO] ===== Start GTDB Search =====
[2023-06-13 14:47:33,220] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938016545.1_ERR414241_bin.44_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 14:47:33,220] [INFO] Task started: Blastn
[2023-06-13 14:47:33,220] [INFO] Running command: blastn -query GCA_938016545.1_ERR414241_bin.44_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgeeb795e3-c45a-4e05-b04d-11039b24a8bd/dqc_reference/reference_markers_gtdb.fasta -out GCA_938016545.1_ERR414241_bin.44_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:47:34,383] [INFO] Task succeeded: Blastn
[2023-06-13 14:47:34,400] [INFO] Selected 10 target genomes.
[2023-06-13 14:47:34,400] [INFO] Target genome list was writen to GCA_938016545.1_ERR414241_bin.44_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 14:47:34,405] [INFO] Task started: fastANI
[2023-06-13 14:47:34,405] [INFO] Running command: fastANI --query /var/lib/cwl/stg1765066c-5357-4d87-831c-3a60a249665d/GCA_938016545.1_ERR414241_bin.44_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938016545.1_ERR414241_bin.44_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938016545.1_ERR414241_bin.44_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 14:47:47,420] [INFO] Task succeeded: fastANI
[2023-06-13 14:47:47,433] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 14:47:47,433] [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
GCF_900200035.1	s__Klebsiella grimontii	99.2047	1721	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.56	95.68	0.89	0.83	175	conclusive
GCF_002925905.1	s__Klebsiella michiganensis	93.7323	1644	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.53	97.41	0.90	0.83	291	-
GCF_001598695.1	s__Klebsiella oxytoca	91.6123	1557	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	99.31	98.97	0.94	0.89	181	-
GCF_009707385.1	s__Klebsiella oxytoca_C	90.3323	1444	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902158555.1	s__Klebsiella spallanzanii	89.2424	1494	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.75	98.01	0.91	0.88	4	-
GCF_003261575.2	s__Klebsiella huaxiensis	88.2459	1481	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	96.95	95.21	0.89	0.84	9	-
GCF_005860775.1	s__Klebsiella indica	86.4474	1232	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	99.34	99.34	0.92	0.92	2	-
GCF_004342285.1	s__Klebsiella sp004342285	84.7922	1196	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000735435.1	s__Klebsiella planticola	84.5762	1287	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.7194	99.21	98.49	0.93	0.89	44	-
GCF_000439085.1	s__Leminorella grimontii	77.4324	273	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leminorella	95.0	99.99	99.98	1.00	0.99	4	-
--------------------------------------------------------------------------------
[2023-06-13 14:47:47,435] [INFO] GTDB search result was written to GCA_938016545.1_ERR414241_bin.44_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 14:47:47,436] [INFO] ===== GTDB Search completed =====
[2023-06-13 14:47:47,441] [INFO] DFAST_QC result json was written to GCA_938016545.1_ERR414241_bin.44_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 14:47:47,441] [INFO] DFAST_QC completed!
[2023-06-13 14:47:47,441] [INFO] Total running time: 0h1m28s