[2023-06-12 22:40:34,161] [INFO] DFAST_QC pipeline started.
[2023-06-12 22:40:34,167] [INFO] DFAST_QC version: 0.5.7
[2023-06-12 22:40:34,167] [INFO] DQC Reference Directory: /var/lib/cwl/stg37da4a26-b240-4b7f-abf5-bfece107e1a2/dqc_reference
[2023-06-12 22:40:35,743] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-12 22:40:35,743] [INFO] Task started: Prodigal
[2023-06-12 22:40:35,744] [INFO] Running command: gunzip -c /var/lib/cwl/stge8ba4080-783c-42e2-8d20-f29ea1b95523/GCA_022866045.1_ASM2286604v1_genomic.fna.gz | prodigal -d GCA_022866045.1_ASM2286604v1_genomic.fna/cds.fna -a GCA_022866045.1_ASM2286604v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-12 22:40:42,937] [INFO] Task succeeded: Prodigal
[2023-06-12 22:40:42,938] [INFO] Task started: HMMsearch
[2023-06-12 22:40:42,938] [INFO] Running command: hmmsearch --tblout GCA_022866045.1_ASM2286604v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg37da4a26-b240-4b7f-abf5-bfece107e1a2/dqc_reference/reference_markers.hmm GCA_022866045.1_ASM2286604v1_genomic.fna/protein.faa > /dev/null
[2023-06-12 22:40:43,215] [INFO] Task succeeded: HMMsearch
[2023-06-12 22:40:43,217] [INFO] Found 6/6 markers.
[2023-06-12 22:40:43,251] [INFO] Query marker FASTA was written to GCA_022866045.1_ASM2286604v1_genomic.fna/markers.fasta
[2023-06-12 22:40:43,251] [INFO] Task started: Blastn
[2023-06-12 22:40:43,251] [INFO] Running command: blastn -query GCA_022866045.1_ASM2286604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37da4a26-b240-4b7f-abf5-bfece107e1a2/dqc_reference/reference_markers.fasta -out GCA_022866045.1_ASM2286604v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 22:40:43,883] [INFO] Task succeeded: Blastn
[2023-06-12 22:40:43,887] [INFO] Selected 25 target genomes.
[2023-06-12 22:40:43,888] [INFO] Target genome list was writen to GCA_022866045.1_ASM2286604v1_genomic.fna/target_genomes.txt
[2023-06-12 22:40:43,893] [INFO] Task started: fastANI
[2023-06-12 22:40:43,893] [INFO] Running command: fastANI --query /var/lib/cwl/stge8ba4080-783c-42e2-8d20-f29ea1b95523/GCA_022866045.1_ASM2286604v1_genomic.fna.gz --refList GCA_022866045.1_ASM2286604v1_genomic.fna/target_genomes.txt --output GCA_022866045.1_ASM2286604v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-12 22:40:59,175] [INFO] Task succeeded: fastANI
[2023-06-12 22:40:59,175] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg37da4a26-b240-4b7f-abf5-bfece107e1a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-12 22:40:59,176] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg37da4a26-b240-4b7f-abf5-bfece107e1a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-12 22:40:59,177] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-12 22:40:59,177] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-12 22:40:59,177] [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
--------------------------------------------------------------------------------
[2023-06-12 22:40:59,179] [INFO] DFAST Taxonomy check result was written to GCA_022866045.1_ASM2286604v1_genomic.fna/tc_result.tsv
[2023-06-12 22:40:59,180] [INFO] ===== Taxonomy check completed =====
[2023-06-12 22:40:59,180] [INFO] ===== Start completeness check using CheckM =====
[2023-06-12 22:40:59,180] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg37da4a26-b240-4b7f-abf5-bfece107e1a2/dqc_reference/checkm_data
[2023-06-12 22:40:59,183] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-12 22:40:59,222] [INFO] Task started: CheckM
[2023-06-12 22:40:59,222] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022866045.1_ASM2286604v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022866045.1_ASM2286604v1_genomic.fna/checkm_input GCA_022866045.1_ASM2286604v1_genomic.fna/checkm_result
[2023-06-12 22:41:26,096] [INFO] Task succeeded: CheckM
[2023-06-12 22:41:26,097] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-12 22:41:26,120] [INFO] ===== Completeness check finished =====
[2023-06-12 22:41:26,120] [INFO] ===== Start GTDB Search =====
[2023-06-12 22:41:26,121] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022866045.1_ASM2286604v1_genomic.fna/markers.fasta)
[2023-06-12 22:41:26,121] [INFO] Task started: Blastn
[2023-06-12 22:41:26,121] [INFO] Running command: blastn -query GCA_022866045.1_ASM2286604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37da4a26-b240-4b7f-abf5-bfece107e1a2/dqc_reference/reference_markers_gtdb.fasta -out GCA_022866045.1_ASM2286604v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 22:41:27,008] [INFO] Task succeeded: Blastn
[2023-06-12 22:41:27,017] [INFO] Selected 18 target genomes.
[2023-06-12 22:41:27,018] [INFO] Target genome list was writen to GCA_022866045.1_ASM2286604v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-12 22:41:27,063] [INFO] Task started: fastANI
[2023-06-12 22:41:27,063] [INFO] Running command: fastANI --query /var/lib/cwl/stge8ba4080-783c-42e2-8d20-f29ea1b95523/GCA_022866045.1_ASM2286604v1_genomic.fna.gz --refList GCA_022866045.1_ASM2286604v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022866045.1_ASM2286604v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-12 22:41:34,861] [INFO] Task succeeded: fastANI
[2023-06-12 22:41:34,879] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-12 22:41:34,880] [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_017883285.1	s__FEN-413 sp017883285	77.9444	319	906	d__Bacteria;p__Acidobacteriota;c__Aminicenantia;o__Aminicenantales;f__UBA4085;g__FEN-413	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003141555.1	s__FEN-413 sp003141555	77.6534	294	906	d__Bacteria;p__Acidobacteriota;c__Aminicenantia;o__Aminicenantales;f__UBA4085;g__FEN-413	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014894455.1	s__RBG-16-66-30 sp014894455	76.9133	150	906	d__Bacteria;p__Acidobacteriota;c__Aminicenantia;o__Aminicenantales;f__RBG-16-66-30;g__RBG-16-66-30	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016867585.1	s__JAAZPG01 sp016867585	76.8568	168	906	d__Bacteria;p__Acidobacteriota;c__Aminicenantia;o__Aminicenantales;f__UBA4085;g__JAAZPG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001775755.1	s__RBG-16-66-30 sp001775755	76.8385	152	906	d__Bacteria;p__Acidobacteriota;c__Aminicenantia;o__Aminicenantales;f__RBG-16-66-30;g__RBG-16-66-30	95.0	99.12	99.12	0.81	0.81	2	-
GCA_017886205.1	s__UBA8522 sp017886205	76.8276	135	906	d__Bacteria;p__Acidobacteriota;c__Aminicenantia;o__Aminicenantales;f__UBA8522;g__UBA8522	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001775715.1	s__RBG-16-66-30 sp001775715	76.8068	122	906	d__Bacteria;p__Acidobacteriota;c__Aminicenantia;o__Aminicenantales;f__RBG-16-66-30;g__RBG-16-66-30	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016867635.1	s__RBG-16-66-30 sp016867635	76.6839	125	906	d__Bacteria;p__Acidobacteriota;c__Aminicenantia;o__Aminicenantales;f__RBG-16-66-30;g__RBG-16-66-30	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001773855.1	s__RBG-16-66-30 sp001773855	76.6634	95	906	d__Bacteria;p__Acidobacteriota;c__Aminicenantia;o__Aminicenantales;f__RBG-16-66-30;g__RBG-16-66-30	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016933355.1	s__JAFGBC01 sp016933355	76.6611	92	906	d__Bacteria;p__Acidobacteriota;c__Aminicenantia;o__Aminicenantales;f__JAFGBC01;g__JAFGBC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012797375.1	s__JAAZPG01 sp012797375	76.505	66	906	d__Bacteria;p__Acidobacteriota;c__Aminicenantia;o__Aminicenantales;f__UBA4085;g__JAAZPG01	95.0	99.06	99.06	0.91	0.91	2	-
GCA_011048485.1	s__RBG-16-66-30 sp011048485	76.4731	83	906	d__Bacteria;p__Acidobacteriota;c__Aminicenantia;o__Aminicenantales;f__RBG-16-66-30;g__RBG-16-66-30	95.0	97.98	97.98	0.65	0.65	2	-
GCA_003524335.1	s__UBA8522 sp003524335	76.4431	92	906	d__Bacteria;p__Acidobacteriota;c__Aminicenantia;o__Aminicenantales;f__UBA8522;g__UBA8522	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-12 22:41:34,881] [INFO] GTDB search result was written to GCA_022866045.1_ASM2286604v1_genomic.fna/result_gtdb.tsv
[2023-06-12 22:41:34,882] [INFO] ===== GTDB Search completed =====
[2023-06-12 22:41:34,885] [INFO] DFAST_QC result json was written to GCA_022866045.1_ASM2286604v1_genomic.fna/dqc_result.json
[2023-06-12 22:41:34,885] [INFO] DFAST_QC completed!
[2023-06-12 22:41:34,885] [INFO] Total running time: 0h1m1s