[2023-06-19 13:54:28,882] [INFO] DFAST_QC pipeline started.
[2023-06-19 13:54:28,887] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 13:54:28,887] [INFO] DQC Reference Directory: /var/lib/cwl/stg51abf701-cf27-4ec3-a2b7-2b9ac5be3126/dqc_reference
[2023-06-19 13:54:30,244] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 13:54:30,245] [INFO] Task started: Prodigal
[2023-06-19 13:54:30,245] [INFO] Running command: gunzip -c /var/lib/cwl/stgcfe76a28-e2ee-4cd8-820f-a62df9a6f1ce/GCA_013694635.1_ASM1369463v1_genomic.fna.gz | prodigal -d GCA_013694635.1_ASM1369463v1_genomic.fna/cds.fna -a GCA_013694635.1_ASM1369463v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 13:54:38,794] [INFO] Task succeeded: Prodigal
[2023-06-19 13:54:38,795] [INFO] Task started: HMMsearch
[2023-06-19 13:54:38,795] [INFO] Running command: hmmsearch --tblout GCA_013694635.1_ASM1369463v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg51abf701-cf27-4ec3-a2b7-2b9ac5be3126/dqc_reference/reference_markers.hmm GCA_013694635.1_ASM1369463v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 13:54:39,146] [INFO] Task succeeded: HMMsearch
[2023-06-19 13:54:39,148] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgcfe76a28-e2ee-4cd8-820f-a62df9a6f1ce/GCA_013694635.1_ASM1369463v1_genomic.fna.gz]
[2023-06-19 13:54:39,183] [INFO] Query marker FASTA was written to GCA_013694635.1_ASM1369463v1_genomic.fna/markers.fasta
[2023-06-19 13:54:39,184] [INFO] Task started: Blastn
[2023-06-19 13:54:39,184] [INFO] Running command: blastn -query GCA_013694635.1_ASM1369463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51abf701-cf27-4ec3-a2b7-2b9ac5be3126/dqc_reference/reference_markers.fasta -out GCA_013694635.1_ASM1369463v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:54:39,889] [INFO] Task succeeded: Blastn
[2023-06-19 13:54:39,894] [INFO] Selected 19 target genomes.
[2023-06-19 13:54:39,894] [INFO] Target genome list was writen to GCA_013694635.1_ASM1369463v1_genomic.fna/target_genomes.txt
[2023-06-19 13:54:39,899] [INFO] Task started: fastANI
[2023-06-19 13:54:39,899] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfe76a28-e2ee-4cd8-820f-a62df9a6f1ce/GCA_013694635.1_ASM1369463v1_genomic.fna.gz --refList GCA_013694635.1_ASM1369463v1_genomic.fna/target_genomes.txt --output GCA_013694635.1_ASM1369463v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 13:54:58,820] [INFO] Task succeeded: fastANI
[2023-06-19 13:54:58,821] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg51abf701-cf27-4ec3-a2b7-2b9ac5be3126/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 13:54:58,821] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg51abf701-cf27-4ec3-a2b7-2b9ac5be3126/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 13:54:58,827] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 13:54:58,827] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 13:54:58,827] [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
Luteitalea pratensis	strain=DSM 100886; HEG_-6_39	GCA_001618865.1	1855912	1855912	type	True	76.5618	120	796	95	below_threshold
Sandaracinus amylolyticus	strain=DSM 53668	GCA_000737325.2	927083	927083	type	True	74.9585	100	796	95	below_threshold
Patulibacter americanus	strain=DSM 16676	GCA_000420025.1	588672	588672	type	True	74.7765	52	796	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 13:54:58,829] [INFO] DFAST Taxonomy check result was written to GCA_013694635.1_ASM1369463v1_genomic.fna/tc_result.tsv
[2023-06-19 13:54:58,830] [INFO] ===== Taxonomy check completed =====
[2023-06-19 13:54:58,830] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 13:54:58,830] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg51abf701-cf27-4ec3-a2b7-2b9ac5be3126/dqc_reference/checkm_data
[2023-06-19 13:54:58,832] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 13:54:58,874] [INFO] Task started: CheckM
[2023-06-19 13:54:58,874] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013694635.1_ASM1369463v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013694635.1_ASM1369463v1_genomic.fna/checkm_input GCA_013694635.1_ASM1369463v1_genomic.fna/checkm_result
[2023-06-19 13:55:29,578] [INFO] Task succeeded: CheckM
[2023-06-19 13:55:29,579] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.44%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 13:55:29,604] [INFO] ===== Completeness check finished =====
[2023-06-19 13:55:29,605] [INFO] ===== Start GTDB Search =====
[2023-06-19 13:55:29,605] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013694635.1_ASM1369463v1_genomic.fna/markers.fasta)
[2023-06-19 13:55:29,605] [INFO] Task started: Blastn
[2023-06-19 13:55:29,606] [INFO] Running command: blastn -query GCA_013694635.1_ASM1369463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51abf701-cf27-4ec3-a2b7-2b9ac5be3126/dqc_reference/reference_markers_gtdb.fasta -out GCA_013694635.1_ASM1369463v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:55:30,674] [INFO] Task succeeded: Blastn
[2023-06-19 13:55:30,679] [INFO] Selected 15 target genomes.
[2023-06-19 13:55:30,679] [INFO] Target genome list was writen to GCA_013694635.1_ASM1369463v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 13:55:30,688] [INFO] Task started: fastANI
[2023-06-19 13:55:30,688] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfe76a28-e2ee-4cd8-820f-a62df9a6f1ce/GCA_013694635.1_ASM1369463v1_genomic.fna.gz --refList GCA_013694635.1_ASM1369463v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013694635.1_ASM1369463v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 13:55:41,986] [INFO] Task succeeded: fastANI
[2023-06-19 13:55:42,000] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 13:55:42,001] [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_013694635.1	s__JACDCA01 sp013694635	100.0	787	796	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__JACDCA01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013813355.1	s__JACCRT01 sp013813355	78.386	86	796	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__JACCRT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001767455.1	s__2-12-FULL-66-21 sp001767455	78.2762	245	796	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__2-12-FULL-66-21	95.0	99.91	99.91	0.96	0.96	2	-
GCA_013817065.1	s__JACDCA01 sp013817065	78.2446	222	796	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__JACDCA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013694845.1	s__JACDCA01 sp013694845	77.8474	257	796	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__JACDCA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003223835.1	s__Gp6-AA38 sp003223835	77.7614	218	796	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__Gp6-AA38	95.0	98.48	98.48	0.89	0.89	2	-
GCA_003222675.1	s__QHWT01 sp003222675	77.7391	206	796	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__QHWT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013697225.1	s__JACCXG01 sp013697225	77.6831	120	796	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__JACCXG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362195.1	s__QHWT01 sp013362195	77.2535	167	796	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__QHWT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003222535.1	s__Gp6-AA45 sp003222535	76.8332	142	796	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA45	95.0	99.30	99.28	0.90	0.90	3	-
GCA_012271165.1	s__JAAXGX01 sp012271165	76.6056	50	796	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__JAAXGX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 13:55:42,003] [INFO] GTDB search result was written to GCA_013694635.1_ASM1369463v1_genomic.fna/result_gtdb.tsv
[2023-06-19 13:55:42,003] [INFO] ===== GTDB Search completed =====
[2023-06-19 13:55:42,007] [INFO] DFAST_QC result json was written to GCA_013694635.1_ASM1369463v1_genomic.fna/dqc_result.json
[2023-06-19 13:55:42,007] [INFO] DFAST_QC completed!
[2023-06-19 13:55:42,007] [INFO] Total running time: 0h1m13s