[2023-06-28 13:41:05,794] [INFO] DFAST_QC pipeline started.
[2023-06-28 13:41:05,796] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 13:41:05,796] [INFO] DQC Reference Directory: /var/lib/cwl/stgaeda4957-245d-46b3-9842-97214bb8b580/dqc_reference
[2023-06-28 13:41:06,903] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 13:41:06,903] [INFO] Task started: Prodigal
[2023-06-28 13:41:06,904] [INFO] Running command: gunzip -c /var/lib/cwl/stg9cbd67d3-cfa4-4941-a01c-1e8d2f70f562/GCA_020845895.1_ASM2084589v1_genomic.fna.gz | prodigal -d GCA_020845895.1_ASM2084589v1_genomic.fna/cds.fna -a GCA_020845895.1_ASM2084589v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 13:41:19,046] [INFO] Task succeeded: Prodigal
[2023-06-28 13:41:19,046] [INFO] Task started: HMMsearch
[2023-06-28 13:41:19,046] [INFO] Running command: hmmsearch --tblout GCA_020845895.1_ASM2084589v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaeda4957-245d-46b3-9842-97214bb8b580/dqc_reference/reference_markers.hmm GCA_020845895.1_ASM2084589v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 13:41:19,288] [INFO] Task succeeded: HMMsearch
[2023-06-28 13:41:19,289] [INFO] Found 6/6 markers.
[2023-06-28 13:41:19,326] [INFO] Query marker FASTA was written to GCA_020845895.1_ASM2084589v1_genomic.fna/markers.fasta
[2023-06-28 13:41:19,326] [INFO] Task started: Blastn
[2023-06-28 13:41:19,327] [INFO] Running command: blastn -query GCA_020845895.1_ASM2084589v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaeda4957-245d-46b3-9842-97214bb8b580/dqc_reference/reference_markers.fasta -out GCA_020845895.1_ASM2084589v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:41:19,934] [INFO] Task succeeded: Blastn
[2023-06-28 13:41:19,937] [INFO] Selected 35 target genomes.
[2023-06-28 13:41:19,937] [INFO] Target genome list was writen to GCA_020845895.1_ASM2084589v1_genomic.fna/target_genomes.txt
[2023-06-28 13:41:19,946] [INFO] Task started: fastANI
[2023-06-28 13:41:19,947] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cbd67d3-cfa4-4941-a01c-1e8d2f70f562/GCA_020845895.1_ASM2084589v1_genomic.fna.gz --refList GCA_020845895.1_ASM2084589v1_genomic.fna/target_genomes.txt --output GCA_020845895.1_ASM2084589v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 13:41:47,136] [INFO] Task succeeded: fastANI
[2023-06-28 13:41:47,136] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaeda4957-245d-46b3-9842-97214bb8b580/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 13:41:47,137] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaeda4957-245d-46b3-9842-97214bb8b580/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 13:41:47,147] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 13:41:47,147] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 13:41:47,147] [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
Geomonas silvestris	strain=Red330	GCA_014193515.1	2740184	2740184	type	True	75.2979	51	1571	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	75.2556	70	1571	95	below_threshold
Pseudoxanthomonas jiangsuensis	strain=DSM 22398	GCA_010093185.1	619688	619688	type	True	75.2252	62	1571	95	below_threshold
Sulfurifustis variabilis	strain=skN76	GCA_002355415.1	1675686	1675686	type	True	75.1197	52	1571	95	below_threshold
Pseudomonas carbonaria	strain=CIP 111764	GCA_904061905.1	2762745	2762745	type	True	75.1094	52	1571	95	below_threshold
Thauera aromatica	strain=K172	GCA_003030465.1	59405	59405	type	True	75.0928	59	1571	95	below_threshold
Paracoccus aeridis	strain=JC501	GCA_004923205.2	1966466	1966466	type	True	74.9423	53	1571	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	74.9377	73	1571	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	74.9371	86	1571	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	74.9141	87	1571	95	below_threshold
Salinarimonas ramus	strain=CGMCC 1.9161	GCA_014645695.1	690164	690164	type	True	74.8814	116	1571	95	below_threshold
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	74.8778	90	1571	95	below_threshold
Bradyrhizobium agreste	strain=CNPSo 4010	GCA_016031625.1	2751811	2751811	type	True	74.873	76	1571	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	74.8582	81	1571	95	below_threshold
Propylenella binzhouense	strain=L72	GCA_009866965.1	2555902	2555902	type	True	74.8424	85	1571	95	below_threshold
Bradyrhizobium yuanmingense	strain=CCBAU 10071	GCA_900094575.1	108015	108015	type	True	74.8116	77	1571	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 13:41:47,149] [INFO] DFAST Taxonomy check result was written to GCA_020845895.1_ASM2084589v1_genomic.fna/tc_result.tsv
[2023-06-28 13:41:47,149] [INFO] ===== Taxonomy check completed =====
[2023-06-28 13:41:47,149] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 13:41:47,149] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaeda4957-245d-46b3-9842-97214bb8b580/dqc_reference/checkm_data
[2023-06-28 13:41:47,150] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 13:41:47,195] [INFO] Task started: CheckM
[2023-06-28 13:41:47,195] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020845895.1_ASM2084589v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020845895.1_ASM2084589v1_genomic.fna/checkm_input GCA_020845895.1_ASM2084589v1_genomic.fna/checkm_result
[2023-06-28 13:42:31,301] [INFO] Task succeeded: CheckM
[2023-06-28 13:42:31,302] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 13:42:31,318] [INFO] ===== Completeness check finished =====
[2023-06-28 13:42:31,318] [INFO] ===== Start GTDB Search =====
[2023-06-28 13:42:31,320] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020845895.1_ASM2084589v1_genomic.fna/markers.fasta)
[2023-06-28 13:42:31,320] [INFO] Task started: Blastn
[2023-06-28 13:42:31,320] [INFO] Running command: blastn -query GCA_020845895.1_ASM2084589v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaeda4957-245d-46b3-9842-97214bb8b580/dqc_reference/reference_markers_gtdb.fasta -out GCA_020845895.1_ASM2084589v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:42:32,259] [INFO] Task succeeded: Blastn
[2023-06-28 13:42:32,262] [INFO] Selected 32 target genomes.
[2023-06-28 13:42:32,262] [INFO] Target genome list was writen to GCA_020845895.1_ASM2084589v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 13:42:32,314] [INFO] Task started: fastANI
[2023-06-28 13:42:32,314] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cbd67d3-cfa4-4941-a01c-1e8d2f70f562/GCA_020845895.1_ASM2084589v1_genomic.fna.gz --refList GCA_020845895.1_ASM2084589v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020845895.1_ASM2084589v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 13:42:56,511] [INFO] Task succeeded: fastANI
[2023-06-28 13:42:56,521] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 13:42:56,521] [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_012517325.1	s__JAAYVF01 sp012517325	75.638	155	1571	d__Bacteria;p__FEN-1099;c__FEN-1099;o__FEN-1099;f__FEN-1099;g__JAAYVF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093185.1	s__Pseudoxanthomonas jiangsuensis	75.2572	63	1571	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017997455.1	s__JAGOEZ01 sp017997455	75.1709	50	1571	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__JAGOEZ01	95.0	98.60	98.27	0.77	0.77	3	-
GCA_011368045.1	s__JAAZNF01 sp011368045	75.1478	50	1571	d__Bacteria;p__Myxococcota;c__B64-G9;o__B64-G9;f__B64-G9;g__JAAZNF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016879935.1	s__JAEUJQ01 sp016879935	75.1134	128	1571	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__JAEUJQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000310225.1	s__Thauera phenylacetica	74.9377	73	1571	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794545.1	s__JABFXX01 sp016794545	74.9251	173	1571	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__JABFXX01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016031625.1	s__Bradyrhizobium agreste	74.8753	75	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004571025.1	s__Bradyrhizobium niftali	74.8724	91	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.00	95.49	0.80	0.80	3	-
GCA_003576805.1	s__PR03 sp003576805	74.8693	204	1571	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__PR03;g__PR03	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016708825.1	s__FEB-7 sp016708825	74.8411	59	1571	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__FEB-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003170275.1	s__PALSA-1104 sp003170275	74.8144	153	1571	d__Bacteria;p__Myxococcota;c__Polyangia;o__Palsa-1104;f__Palsa-1104;g__PALSA-1104	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004123905.1	s__Bradyrhizobium betae_A	74.7992	73	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009692555.1	s__SHYY01 sp009692555	74.7273	98	1571	d__Bacteria;p__Myxococcota;c__Polyangia;o__Palsa-1104;f__Palsa-1104;g__SHYY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016195115.1	s__JACQAI01 sp016195115	74.6951	91	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Elsterales;f__Elsteraceae;g__JACQAI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005883675.1	s__SCGC-AG-212-J23 sp005883675	74.6749	69	1571	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__SCGC-AG-212-J23	95.0	98.58	98.58	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-06-28 13:42:56,526] [INFO] GTDB search result was written to GCA_020845895.1_ASM2084589v1_genomic.fna/result_gtdb.tsv
[2023-06-28 13:42:56,527] [INFO] ===== GTDB Search completed =====
[2023-06-28 13:42:56,530] [INFO] DFAST_QC result json was written to GCA_020845895.1_ASM2084589v1_genomic.fna/dqc_result.json
[2023-06-28 13:42:56,530] [INFO] DFAST_QC completed!
[2023-06-28 13:42:56,530] [INFO] Total running time: 0h1m51s