[2023-06-13 17:33:02,463] [INFO] DFAST_QC pipeline started.
[2023-06-13 17:33:02,465] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 17:33:02,465] [INFO] DQC Reference Directory: /var/lib/cwl/stgc938f551-7aef-4799-9dd6-82211542b9cb/dqc_reference
[2023-06-13 17:33:03,749] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 17:33:03,750] [INFO] Task started: Prodigal
[2023-06-13 17:33:03,750] [INFO] Running command: gunzip -c /var/lib/cwl/stgc59e3f30-4bec-4ea1-ba2f-36c749d9d33d/GCA_022563325.1_ASM2256332v1_genomic.fna.gz | prodigal -d GCA_022563325.1_ASM2256332v1_genomic.fna/cds.fna -a GCA_022563325.1_ASM2256332v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 17:33:06,747] [INFO] Task succeeded: Prodigal
[2023-06-13 17:33:06,747] [INFO] Task started: HMMsearch
[2023-06-13 17:33:06,747] [INFO] Running command: hmmsearch --tblout GCA_022563325.1_ASM2256332v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc938f551-7aef-4799-9dd6-82211542b9cb/dqc_reference/reference_markers.hmm GCA_022563325.1_ASM2256332v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 17:33:06,967] [INFO] Task succeeded: HMMsearch
[2023-06-13 17:33:06,968] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc59e3f30-4bec-4ea1-ba2f-36c749d9d33d/GCA_022563325.1_ASM2256332v1_genomic.fna.gz]
[2023-06-13 17:33:06,986] [INFO] Query marker FASTA was written to GCA_022563325.1_ASM2256332v1_genomic.fna/markers.fasta
[2023-06-13 17:33:06,986] [INFO] Task started: Blastn
[2023-06-13 17:33:06,986] [INFO] Running command: blastn -query GCA_022563325.1_ASM2256332v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc938f551-7aef-4799-9dd6-82211542b9cb/dqc_reference/reference_markers.fasta -out GCA_022563325.1_ASM2256332v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:33:07,553] [INFO] Task succeeded: Blastn
[2023-06-13 17:33:07,556] [INFO] Selected 23 target genomes.
[2023-06-13 17:33:07,556] [INFO] Target genome list was writen to GCA_022563325.1_ASM2256332v1_genomic.fna/target_genomes.txt
[2023-06-13 17:33:07,561] [INFO] Task started: fastANI
[2023-06-13 17:33:07,561] [INFO] Running command: fastANI --query /var/lib/cwl/stgc59e3f30-4bec-4ea1-ba2f-36c749d9d33d/GCA_022563325.1_ASM2256332v1_genomic.fna.gz --refList GCA_022563325.1_ASM2256332v1_genomic.fna/target_genomes.txt --output GCA_022563325.1_ASM2256332v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 17:33:22,936] [INFO] Task succeeded: fastANI
[2023-06-13 17:33:22,936] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc938f551-7aef-4799-9dd6-82211542b9cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 17:33:22,936] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc938f551-7aef-4799-9dd6-82211542b9cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 17:33:22,938] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 17:33:22,938] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 17:33:22,938] [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 17:33:22,940] [INFO] DFAST Taxonomy check result was written to GCA_022563325.1_ASM2256332v1_genomic.fna/tc_result.tsv
[2023-06-13 17:33:22,940] [INFO] ===== Taxonomy check completed =====
[2023-06-13 17:33:22,940] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 17:33:22,941] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc938f551-7aef-4799-9dd6-82211542b9cb/dqc_reference/checkm_data
[2023-06-13 17:33:22,943] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 17:33:22,968] [INFO] Task started: CheckM
[2023-06-13 17:33:22,969] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022563325.1_ASM2256332v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022563325.1_ASM2256332v1_genomic.fna/checkm_input GCA_022563325.1_ASM2256332v1_genomic.fna/checkm_result
[2023-06-13 17:33:38,378] [INFO] Task succeeded: CheckM
[2023-06-13 17:33:38,379] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.62%
Contamintation: 5.15%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-13 17:33:38,403] [INFO] ===== Completeness check finished =====
[2023-06-13 17:33:38,403] [INFO] ===== Start GTDB Search =====
[2023-06-13 17:33:38,404] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022563325.1_ASM2256332v1_genomic.fna/markers.fasta)
[2023-06-13 17:33:38,404] [INFO] Task started: Blastn
[2023-06-13 17:33:38,404] [INFO] Running command: blastn -query GCA_022563325.1_ASM2256332v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc938f551-7aef-4799-9dd6-82211542b9cb/dqc_reference/reference_markers_gtdb.fasta -out GCA_022563325.1_ASM2256332v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:33:39,296] [INFO] Task succeeded: Blastn
[2023-06-13 17:33:39,300] [INFO] Selected 26 target genomes.
[2023-06-13 17:33:39,300] [INFO] Target genome list was writen to GCA_022563325.1_ASM2256332v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 17:33:39,310] [INFO] Task started: fastANI
[2023-06-13 17:33:39,310] [INFO] Running command: fastANI --query /var/lib/cwl/stgc59e3f30-4bec-4ea1-ba2f-36c749d9d33d/GCA_022563325.1_ASM2256332v1_genomic.fna.gz --refList GCA_022563325.1_ASM2256332v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022563325.1_ASM2256332v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 17:33:50,619] [INFO] Task succeeded: fastANI
[2023-06-13 17:33:50,624] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 17:33:50,624] [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_001796995.1	s__RBG-16-68-14 sp001796995	79.6929	199	354	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_003228685.1	s__SZUA-185 sp003228685	77.6238	122	354	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_016178045.1	s__JACOUE01 sp016178045	76.9346	64	354	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SM23-28-2;f__RBG-16-64-32;g__JACOUE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011047455.1	s__HRBIN24 sp011047455	76.8241	50	354	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SM23-28-2;f__HRbin24;g__HRBIN24	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015478665.1	s__JADMII01 sp015478665	76.3298	70	354	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__DSTF01;f__JACRBR01;g__JADMII01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011057325.1	s__DSGV01 sp011057325	76.1446	60	354	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__DSGV01;f__DSGV01;g__DSGV01	95.0	99.93	99.92	0.96	0.94	3	-
--------------------------------------------------------------------------------
[2023-06-13 17:33:50,626] [INFO] GTDB search result was written to GCA_022563325.1_ASM2256332v1_genomic.fna/result_gtdb.tsv
[2023-06-13 17:33:50,627] [INFO] ===== GTDB Search completed =====
[2023-06-13 17:33:50,629] [INFO] DFAST_QC result json was written to GCA_022563325.1_ASM2256332v1_genomic.fna/dqc_result.json
[2023-06-13 17:33:50,629] [INFO] DFAST_QC completed!
[2023-06-13 17:33:50,629] [INFO] Total running time: 0h0m48s