[2023-06-30 18:32:17,120] [INFO] DFAST_QC pipeline started.
[2023-06-30 18:32:17,122] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 18:32:17,122] [INFO] DQC Reference Directory: /var/lib/cwl/stg82c11910-1b9b-4802-be9d-93aa6f1dab05/dqc_reference
[2023-06-30 18:32:18,344] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 18:32:18,345] [INFO] Task started: Prodigal
[2023-06-30 18:32:18,346] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ed8e99f-4b12-45f3-9c0c-b31dc6e64394/GCA_024276295.1_ASM2427629v1_genomic.fna.gz | prodigal -d GCA_024276295.1_ASM2427629v1_genomic.fna/cds.fna -a GCA_024276295.1_ASM2427629v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 18:32:24,785] [INFO] Task succeeded: Prodigal
[2023-06-30 18:32:24,785] [INFO] Task started: HMMsearch
[2023-06-30 18:32:24,785] [INFO] Running command: hmmsearch --tblout GCA_024276295.1_ASM2427629v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg82c11910-1b9b-4802-be9d-93aa6f1dab05/dqc_reference/reference_markers.hmm GCA_024276295.1_ASM2427629v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 18:32:25,030] [INFO] Task succeeded: HMMsearch
[2023-06-30 18:32:25,032] [INFO] Found 6/6 markers.
[2023-06-30 18:32:25,064] [INFO] Query marker FASTA was written to GCA_024276295.1_ASM2427629v1_genomic.fna/markers.fasta
[2023-06-30 18:32:25,064] [INFO] Task started: Blastn
[2023-06-30 18:32:25,065] [INFO] Running command: blastn -query GCA_024276295.1_ASM2427629v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82c11910-1b9b-4802-be9d-93aa6f1dab05/dqc_reference/reference_markers.fasta -out GCA_024276295.1_ASM2427629v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 18:32:25,795] [INFO] Task succeeded: Blastn
[2023-06-30 18:32:25,799] [INFO] Selected 30 target genomes.
[2023-06-30 18:32:25,800] [INFO] Target genome list was writen to GCA_024276295.1_ASM2427629v1_genomic.fna/target_genomes.txt
[2023-06-30 18:32:25,803] [INFO] Task started: fastANI
[2023-06-30 18:32:25,803] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ed8e99f-4b12-45f3-9c0c-b31dc6e64394/GCA_024276295.1_ASM2427629v1_genomic.fna.gz --refList GCA_024276295.1_ASM2427629v1_genomic.fna/target_genomes.txt --output GCA_024276295.1_ASM2427629v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 18:32:48,474] [INFO] Task succeeded: fastANI
[2023-06-30 18:32:48,475] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg82c11910-1b9b-4802-be9d-93aa6f1dab05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 18:32:48,476] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg82c11910-1b9b-4802-be9d-93aa6f1dab05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 18:32:48,494] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 18:32:48,495] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 18:32:48,495] [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
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	75.5744	84	758	95	below_threshold
Halomonas zincidurans	strain=B6	GCA_000731955.1	1178777	1178777	type	True	75.2388	51	758	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	75.1845	140	758	95	below_threshold
Corallococcus praedator	strain=CA031B	GCA_003612125.1	2316724	2316724	type	True	75.1246	65	758	95	below_threshold
Corallococcus terminator	strain=CA054A	GCA_003611635.1	2316733	2316733	type	True	75.1189	72	758	95	below_threshold
Corallococcus sicarius	strain=CA040B	GCA_003611735.1	2316726	2316726	type	True	75.1102	89	758	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	75.0942	71	758	95	below_threshold
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	75.051	109	758	95	below_threshold
Corallococcus llansteffanensis	strain=CA051B	GCA_003612055.1	2316731	2316731	type	True	75.0463	84	758	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	75.0139	164	758	95	below_threshold
Paracoccus tibetensis	strain=CGMCC 1.8925	GCA_900102505.1	336292	336292	type	True	75.0083	70	758	95	below_threshold
Frankia saprophytica	strain=CN3	GCA_000235425.3	298655	298655	type	True	74.8813	174	758	95	below_threshold
Zoogloea ramigera	strain=NBRC 15342	GCA_006539865.1	350	350	type	True	74.8806	61	758	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	74.8713	77	758	95	below_threshold
Frankia asymbiotica	strain=NRRL B-16386	GCA_001983105.1	1834516	1834516	type	True	74.8344	167	758	95	below_threshold
Demequina maris	strain=NBRC 109392	GCA_000971155.1	1638982	1638982	type	True	74.8197	83	758	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 18:32:48,497] [INFO] DFAST Taxonomy check result was written to GCA_024276295.1_ASM2427629v1_genomic.fna/tc_result.tsv
[2023-06-30 18:32:48,498] [INFO] ===== Taxonomy check completed =====
[2023-06-30 18:32:48,499] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 18:32:48,499] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg82c11910-1b9b-4802-be9d-93aa6f1dab05/dqc_reference/checkm_data
[2023-06-30 18:32:48,501] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 18:32:48,538] [INFO] Task started: CheckM
[2023-06-30 18:32:48,538] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024276295.1_ASM2427629v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024276295.1_ASM2427629v1_genomic.fna/checkm_input GCA_024276295.1_ASM2427629v1_genomic.fna/checkm_result
[2023-06-30 18:33:13,085] [INFO] Task succeeded: CheckM
[2023-06-30 18:33:13,088] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 18:33:13,115] [INFO] ===== Completeness check finished =====
[2023-06-30 18:33:13,116] [INFO] ===== Start GTDB Search =====
[2023-06-30 18:33:13,116] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024276295.1_ASM2427629v1_genomic.fna/markers.fasta)
[2023-06-30 18:33:13,116] [INFO] Task started: Blastn
[2023-06-30 18:33:13,116] [INFO] Running command: blastn -query GCA_024276295.1_ASM2427629v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82c11910-1b9b-4802-be9d-93aa6f1dab05/dqc_reference/reference_markers_gtdb.fasta -out GCA_024276295.1_ASM2427629v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 18:33:14,303] [INFO] Task succeeded: Blastn
[2023-06-30 18:33:14,309] [INFO] Selected 20 target genomes.
[2023-06-30 18:33:14,309] [INFO] Target genome list was writen to GCA_024276295.1_ASM2427629v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 18:33:14,320] [INFO] Task started: fastANI
[2023-06-30 18:33:14,321] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ed8e99f-4b12-45f3-9c0c-b31dc6e64394/GCA_024276295.1_ASM2427629v1_genomic.fna.gz --refList GCA_024276295.1_ASM2427629v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024276295.1_ASM2427629v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 18:33:27,099] [INFO] Task succeeded: fastANI
[2023-06-30 18:33:27,116] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 18:33:27,116] [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_003695625.1	s__J065 sp003695625	82.6166	533	758	d__Bacteria;p__Acidobacteriota;c__Mor1;o__J045;f__J045;g__J065	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017994815.1	s__JAGOJY01 sp017994815	77.0956	282	758	d__Bacteria;p__Acidobacteriota;c__Mor1;o__J045;f__J045;g__JAGOJY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003696075.1	s__J045 sp003696075	76.476	187	758	d__Bacteria;p__Acidobacteriota;c__Mor1;o__J045;f__J045;g__J045	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002279285.1	s__RBG-13-68-16 sp002279285	75.9535	78	758	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Thermoanaerobaculales;f__Thermoanaerobaculaceae;g__RBG-13-68-16	95.0	98.89	98.89	0.79	0.79	2	-
GCA_018606725.1	s__JAGYID01 sp018606725	75.6441	110	758	d__Bacteria;p__Acidobacteriota;c__Mor1;o__Gp22-AA2;f__Gp22-AA2;g__JAGYID01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003133645.1	s__RBG-13-68-16 sp003133645	75.6426	79	758	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Thermoanaerobaculales;f__Thermoanaerobaculaceae;g__RBG-13-68-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003388555.1	s__QQVD01 sp003388555	75.4219	154	758	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__QQVD01	95.0	99.97	99.97	0.99	0.99	2	-
GCA_016867695.1	s__VGIY01 sp016867695	75.3025	67	758	d__Bacteria;p__Eisenbacteria;c__RBG-16-71-46;o__CAIMUX01;f__WJJG01;g__VGIY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015489145.1	s__S143-5 sp015489145	75.1769	113	758	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__S143-5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217215.1	s__Rivibacter subsaxonicus	75.1745	98	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016583645.1	s__Rhodovibrio sodomensis	75.0567	108	758	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Rhodovibrionaceae;g__Rhodovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240325.1	s__Rubrivivax sp018240325	74.9144	115	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001293525.1	s__Ideonella_A sakaiensis	74.9111	155	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241785.1	s__Amaricoccus sp003241785	74.8995	124	758	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003220475.1	s__AR12 sp003220475	74.8896	99	758	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__AR12	95.0	98.70	98.70	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-06-30 18:33:27,119] [INFO] GTDB search result was written to GCA_024276295.1_ASM2427629v1_genomic.fna/result_gtdb.tsv
[2023-06-30 18:33:27,119] [INFO] ===== GTDB Search completed =====
[2023-06-30 18:33:27,123] [INFO] DFAST_QC result json was written to GCA_024276295.1_ASM2427629v1_genomic.fna/dqc_result.json
[2023-06-30 18:33:27,124] [INFO] DFAST_QC completed!
[2023-06-30 18:33:27,124] [INFO] Total running time: 0h1m10s