[2023-06-13 01:40:01,519] [INFO] DFAST_QC pipeline started.
[2023-06-13 01:40:01,530] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 01:40:01,531] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e909d4b-75ed-4b32-a660-ff86a518ccf0/dqc_reference
[2023-06-13 01:40:03,677] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 01:40:03,678] [INFO] Task started: Prodigal
[2023-06-13 01:40:03,678] [INFO] Running command: gunzip -c /var/lib/cwl/stg91232837-faea-4fce-868c-0159eefd895d/GCA_947488975.1_ZE-17mar17-28_genomic.fna.gz | prodigal -d GCA_947488975.1_ZE-17mar17-28_genomic.fna/cds.fna -a GCA_947488975.1_ZE-17mar17-28_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 01:40:10,804] [INFO] Task succeeded: Prodigal
[2023-06-13 01:40:10,804] [INFO] Task started: HMMsearch
[2023-06-13 01:40:10,805] [INFO] Running command: hmmsearch --tblout GCA_947488975.1_ZE-17mar17-28_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e909d4b-75ed-4b32-a660-ff86a518ccf0/dqc_reference/reference_markers.hmm GCA_947488975.1_ZE-17mar17-28_genomic.fna/protein.faa > /dev/null
[2023-06-13 01:40:11,101] [INFO] Task succeeded: HMMsearch
[2023-06-13 01:40:11,102] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg91232837-faea-4fce-868c-0159eefd895d/GCA_947488975.1_ZE-17mar17-28_genomic.fna.gz]
[2023-06-13 01:40:11,140] [INFO] Query marker FASTA was written to GCA_947488975.1_ZE-17mar17-28_genomic.fna/markers.fasta
[2023-06-13 01:40:11,141] [INFO] Task started: Blastn
[2023-06-13 01:40:11,141] [INFO] Running command: blastn -query GCA_947488975.1_ZE-17mar17-28_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e909d4b-75ed-4b32-a660-ff86a518ccf0/dqc_reference/reference_markers.fasta -out GCA_947488975.1_ZE-17mar17-28_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 01:40:11,775] [INFO] Task succeeded: Blastn
[2023-06-13 01:40:11,780] [INFO] Selected 25 target genomes.
[2023-06-13 01:40:11,781] [INFO] Target genome list was writen to GCA_947488975.1_ZE-17mar17-28_genomic.fna/target_genomes.txt
[2023-06-13 01:40:11,789] [INFO] Task started: fastANI
[2023-06-13 01:40:11,790] [INFO] Running command: fastANI --query /var/lib/cwl/stg91232837-faea-4fce-868c-0159eefd895d/GCA_947488975.1_ZE-17mar17-28_genomic.fna.gz --refList GCA_947488975.1_ZE-17mar17-28_genomic.fna/target_genomes.txt --output GCA_947488975.1_ZE-17mar17-28_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 01:40:33,352] [INFO] Task succeeded: fastANI
[2023-06-13 01:40:33,352] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e909d4b-75ed-4b32-a660-ff86a518ccf0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 01:40:33,353] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e909d4b-75ed-4b32-a660-ff86a518ccf0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 01:40:33,371] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 01:40:33,371] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 01:40:33,371] [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
Herminiimonas fonticola	strain=S-94	GCA_003293745.1	303380	303380	type	True	77.174	81	736	95	below_threshold
Herminiimonas fonticola	strain=DSM 18555	GCA_004361795.1	303380	303380	type	True	77.174	81	736	95	below_threshold
Noviherbaspirillum aerium	strain=122213-3	GCA_008929045.1	2588497	2588497	type	True	77.0499	116	736	95	below_threshold
Herbaspirillum camelliae	strain=WT00C	GCA_001929405.1	1892903	1892903	type	True	77.0276	114	736	95	below_threshold
Herbaspirillum rhizosphaerae	strain=UMS-37	GCA_001189965.1	346179	346179	type	True	77.0235	114	736	95	below_threshold
Oxalicibacterium solurbis	strain=CCM 7664	GCA_014635845.1	69280	69280	type	True	76.9657	103	736	95	below_threshold
Herbaspirillum autotrophicum	strain=IAM 14942	GCA_001189915.1	180195	180195	type	True	76.849	118	736	95	below_threshold
Noviherbaspirillum cavernae	strain=K2R10-39	GCA_003590875.1	2320862	2320862	type	True	76.8483	115	736	95	below_threshold
Collimonas fungivorans	strain=Ter6	GCA_001584145.1	158899	158899	type	True	76.755	98	736	95	below_threshold
Noviherbaspirillum malthae	strain=CC-AFH3	GCA_015352985.1	1260987	1260987	type	True	76.7266	129	736	95	below_threshold
Collimonas arenae	strain=Ter10	GCA_001584165.1	279058	279058	type	True	76.7204	93	736	95	below_threshold
Collimonas pratensis	strain=Ter91	GCA_001584185.1	279113	279113	type	True	76.6953	106	736	95	below_threshold
Noviherbaspirillum aridicola	strain=NCCP-691	GCA_019656455.1	2849687	2849687	type	True	76.6586	120	736	95	below_threshold
Collimonas silvisoli	strain=RXD178	GCA_018305005.1	2825884	2825884	type	True	76.6403	103	736	95	below_threshold
Massilia soli	strain=R798	GCA_016809835.2	2792854	2792854	type	True	76.6322	89	736	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	76.6092	78	736	95	below_threshold
Herbaspirillum robiniae	strain=HZ10	GCA_002213415.1	2014887	2014887	type	True	76.6066	107	736	95	below_threshold
Collimonas humicola	strain=RLT1W51	GCA_018304945.1	2825886	2825886	type	True	76.5924	114	736	95	below_threshold
Massilia rubra	strain=CCM 8692	GCA_011682065.1	2607910	2607910	type	True	76.5531	113	736	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	76.5483	87	736	95	below_threshold
Massilia psychrophila	strain=CGMCC 1.15196	GCA_014641415.1	1603353	1603353	type	True	76.4131	115	736	95	below_threshold
Janthinobacterium tructae	strain=SNU WT3	GCA_006517255.1	2590869	2590869	type	True	76.1869	94	736	95	below_threshold
Massilia forsythiae	strain=GN2-R2	GCA_012849555.1	2728020	2728020	type	True	76.108	75	736	95	below_threshold
Massilia alkalitolerans	strain=DSM 17462	GCA_000427785.1	286638	286638	type	True	76.0695	83	736	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 01:40:33,375] [INFO] DFAST Taxonomy check result was written to GCA_947488975.1_ZE-17mar17-28_genomic.fna/tc_result.tsv
[2023-06-13 01:40:33,379] [INFO] ===== Taxonomy check completed =====
[2023-06-13 01:40:33,379] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 01:40:33,380] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e909d4b-75ed-4b32-a660-ff86a518ccf0/dqc_reference/checkm_data
[2023-06-13 01:40:33,381] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 01:40:33,422] [INFO] Task started: CheckM
[2023-06-13 01:40:33,423] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947488975.1_ZE-17mar17-28_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947488975.1_ZE-17mar17-28_genomic.fna/checkm_input GCA_947488975.1_ZE-17mar17-28_genomic.fna/checkm_result
[2023-06-13 01:41:00,236] [INFO] Task succeeded: CheckM
[2023-06-13 01:41:00,238] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 01:41:00,265] [INFO] ===== Completeness check finished =====
[2023-06-13 01:41:00,265] [INFO] ===== Start GTDB Search =====
[2023-06-13 01:41:00,266] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947488975.1_ZE-17mar17-28_genomic.fna/markers.fasta)
[2023-06-13 01:41:00,266] [INFO] Task started: Blastn
[2023-06-13 01:41:00,266] [INFO] Running command: blastn -query GCA_947488975.1_ZE-17mar17-28_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e909d4b-75ed-4b32-a660-ff86a518ccf0/dqc_reference/reference_markers_gtdb.fasta -out GCA_947488975.1_ZE-17mar17-28_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 01:41:01,157] [INFO] Task succeeded: Blastn
[2023-06-13 01:41:01,162] [INFO] Selected 25 target genomes.
[2023-06-13 01:41:01,163] [INFO] Target genome list was writen to GCA_947488975.1_ZE-17mar17-28_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 01:41:01,175] [INFO] Task started: fastANI
[2023-06-13 01:41:01,176] [INFO] Running command: fastANI --query /var/lib/cwl/stg91232837-faea-4fce-868c-0159eefd895d/GCA_947488975.1_ZE-17mar17-28_genomic.fna.gz --refList GCA_947488975.1_ZE-17mar17-28_genomic.fna/target_genomes_gtdb.txt --output GCA_947488975.1_ZE-17mar17-28_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 01:41:18,002] [INFO] Task succeeded: fastANI
[2023-06-13 01:41:18,021] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 01:41:18,022] [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_903904635.1	s__SYFN01 sp903904635	77.8791	176	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SYFN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903872555.1	s__SYFN01 sp903872555	77.779	136	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SYFN01	95.0	98.62	98.25	0.82	0.81	3	-
GCA_903846425.1	s__SYFN01 sp903846425	77.2349	73	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SYFN01	95.0	98.24	98.19	0.76	0.73	3	-
GCF_003293745.1	s__Herminiimonas fonticola	77.174	81	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008831265.1	s__Lacisediminimonas profundi	77.0751	107	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lacisediminimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001189965.1	s__Herbaspirillum rhizosphaerae	77.0235	114	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015767275.1	s__Herbaspirillum sp013426985	76.9881	102	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001189915.1	s__Herbaspirillum autotrophicum	76.849	118	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014377845.1	s__CAILRJ01 sp014377845	76.8093	96	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAILRJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004134995.1	s__Herbaspirillum sp004134995	76.765	115	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019232795.1	s__PKWO01 sp019232795	76.7401	80	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__PKWO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002257565.1	s__Herbaspirillum sp002257565	76.7167	105	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000786695.1	s__Collimonas arenae_A	76.7061	87	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001584185.1	s__Collimonas pratensis	76.6953	106	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	98.16	98.11	0.88	0.88	3	-
GCA_016467405.1	s__Lacisediminimonas sp016467405	76.6939	108	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lacisediminimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018305005.1	s__Collimonas sp018305005	76.6612	102	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903836575.1	s__CAILRJ01 sp903836575	76.6412	90	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAILRJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241865.1	s__Paucimonas sp018241865	76.6148	83	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018304945.1	s__Collimonas sp018304945	76.5924	114	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	98.22	98.22	0.87	0.87	2	-
GCA_004570315.1	s__Noviherbaspirillum sp004570315	76.5611	93	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009937955.1	s__Undibacterium sp009937955	76.5557	64	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002564105.1	s__Collimonas sp002564105	76.4535	109	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200725.1	s__Janthinobacterium sp014200725	76.3866	88	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_002797895.1	s__Janthinobacterium sp002797895	76.1948	89	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0	99.02	99.02	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-06-13 01:41:18,024] [INFO] GTDB search result was written to GCA_947488975.1_ZE-17mar17-28_genomic.fna/result_gtdb.tsv
[2023-06-13 01:41:18,025] [INFO] ===== GTDB Search completed =====
[2023-06-13 01:41:18,031] [INFO] DFAST_QC result json was written to GCA_947488975.1_ZE-17mar17-28_genomic.fna/dqc_result.json
[2023-06-13 01:41:18,031] [INFO] DFAST_QC completed!
[2023-06-13 01:41:18,031] [INFO] Total running time: 0h1m17s