[2023-06-13 04:46:15,268] [INFO] DFAST_QC pipeline started.
[2023-06-13 04:46:15,272] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 04:46:15,272] [INFO] DQC Reference Directory: /var/lib/cwl/stgf29fedaa-b658-46d5-8289-22f356b2affa/dqc_reference
[2023-06-13 04:46:16,484] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 04:46:16,484] [INFO] Task started: Prodigal
[2023-06-13 04:46:16,485] [INFO] Running command: gunzip -c /var/lib/cwl/stg47e14255-b84b-4714-b598-493e7a0ad58d/GCA_022564735.1_ASM2256473v1_genomic.fna.gz | prodigal -d GCA_022564735.1_ASM2256473v1_genomic.fna/cds.fna -a GCA_022564735.1_ASM2256473v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 04:46:23,530] [INFO] Task succeeded: Prodigal
[2023-06-13 04:46:23,531] [INFO] Task started: HMMsearch
[2023-06-13 04:46:23,531] [INFO] Running command: hmmsearch --tblout GCA_022564735.1_ASM2256473v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf29fedaa-b658-46d5-8289-22f356b2affa/dqc_reference/reference_markers.hmm GCA_022564735.1_ASM2256473v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 04:46:23,780] [INFO] Task succeeded: HMMsearch
[2023-06-13 04:46:23,782] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg47e14255-b84b-4714-b598-493e7a0ad58d/GCA_022564735.1_ASM2256473v1_genomic.fna.gz]
[2023-06-13 04:46:23,843] [INFO] Query marker FASTA was written to GCA_022564735.1_ASM2256473v1_genomic.fna/markers.fasta
[2023-06-13 04:46:23,844] [INFO] Task started: Blastn
[2023-06-13 04:46:23,844] [INFO] Running command: blastn -query GCA_022564735.1_ASM2256473v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf29fedaa-b658-46d5-8289-22f356b2affa/dqc_reference/reference_markers.fasta -out GCA_022564735.1_ASM2256473v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 04:46:24,453] [INFO] Task succeeded: Blastn
[2023-06-13 04:46:24,458] [INFO] Selected 25 target genomes.
[2023-06-13 04:46:24,459] [INFO] Target genome list was writen to GCA_022564735.1_ASM2256473v1_genomic.fna/target_genomes.txt
[2023-06-13 04:46:24,464] [INFO] Task started: fastANI
[2023-06-13 04:46:24,464] [INFO] Running command: fastANI --query /var/lib/cwl/stg47e14255-b84b-4714-b598-493e7a0ad58d/GCA_022564735.1_ASM2256473v1_genomic.fna.gz --refList GCA_022564735.1_ASM2256473v1_genomic.fna/target_genomes.txt --output GCA_022564735.1_ASM2256473v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 04:46:41,266] [INFO] Task succeeded: fastANI
[2023-06-13 04:46:41,267] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf29fedaa-b658-46d5-8289-22f356b2affa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 04:46:41,267] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf29fedaa-b658-46d5-8289-22f356b2affa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 04:46:41,269] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 04:46:41,269] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 04:46:41,269] [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
--------------------------------------------------------------------------------
[2023-06-13 04:46:41,271] [INFO] DFAST Taxonomy check result was written to GCA_022564735.1_ASM2256473v1_genomic.fna/tc_result.tsv
[2023-06-13 04:46:41,272] [INFO] ===== Taxonomy check completed =====
[2023-06-13 04:46:41,272] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 04:46:41,272] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf29fedaa-b658-46d5-8289-22f356b2affa/dqc_reference/checkm_data
[2023-06-13 04:46:41,276] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 04:46:41,311] [INFO] Task started: CheckM
[2023-06-13 04:46:41,311] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022564735.1_ASM2256473v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022564735.1_ASM2256473v1_genomic.fna/checkm_input GCA_022564735.1_ASM2256473v1_genomic.fna/checkm_result
[2023-06-13 04:47:07,753] [INFO] Task succeeded: CheckM
[2023-06-13 04:47:07,754] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.93%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 04:47:07,781] [INFO] ===== Completeness check finished =====
[2023-06-13 04:47:07,782] [INFO] ===== Start GTDB Search =====
[2023-06-13 04:47:07,782] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022564735.1_ASM2256473v1_genomic.fna/markers.fasta)
[2023-06-13 04:47:07,782] [INFO] Task started: Blastn
[2023-06-13 04:47:07,783] [INFO] Running command: blastn -query GCA_022564735.1_ASM2256473v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf29fedaa-b658-46d5-8289-22f356b2affa/dqc_reference/reference_markers_gtdb.fasta -out GCA_022564735.1_ASM2256473v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 04:47:08,636] [INFO] Task succeeded: Blastn
[2023-06-13 04:47:08,641] [INFO] Selected 21 target genomes.
[2023-06-13 04:47:08,641] [INFO] Target genome list was writen to GCA_022564735.1_ASM2256473v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 04:47:08,679] [INFO] Task started: fastANI
[2023-06-13 04:47:08,679] [INFO] Running command: fastANI --query /var/lib/cwl/stg47e14255-b84b-4714-b598-493e7a0ad58d/GCA_022564735.1_ASM2256473v1_genomic.fna.gz --refList GCA_022564735.1_ASM2256473v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022564735.1_ASM2256473v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 04:47:17,678] [INFO] Task succeeded: fastANI
[2023-06-13 04:47:17,683] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 04:47:17,683] [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_003228685.1	s__SZUA-185 sp003228685	86.8387	666	852	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__DSTF01;f__RBG-16-68-14;g__SZUA-185	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001796995.1	s__RBG-16-68-14 sp001796995	77.6763	166	852	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__DSTF01;f__RBG-16-68-14;g__RBG-16-68-14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015478665.1	s__JADMII01 sp015478665	76.0583	98	852	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__DSTF01;f__JACRBR01;g__JADMII01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016866055.1	s__VGNK01 sp016866055	75.8181	59	852	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__VGNK01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 04:47:17,685] [INFO] GTDB search result was written to GCA_022564735.1_ASM2256473v1_genomic.fna/result_gtdb.tsv
[2023-06-13 04:47:17,686] [INFO] ===== GTDB Search completed =====
[2023-06-13 04:47:17,688] [INFO] DFAST_QC result json was written to GCA_022564735.1_ASM2256473v1_genomic.fna/dqc_result.json
[2023-06-13 04:47:17,689] [INFO] DFAST_QC completed!
[2023-06-13 04:47:17,689] [INFO] Total running time: 0h1m2s