[2023-06-13 09:12:09,989] [INFO] DFAST_QC pipeline started.
[2023-06-13 09:12:09,992] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 09:12:09,993] [INFO] DQC Reference Directory: /var/lib/cwl/stga073a428-ef6a-412a-a822-b9dbd9c099ed/dqc_reference
[2023-06-13 09:12:11,275] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 09:12:11,276] [INFO] Task started: Prodigal
[2023-06-13 09:12:11,276] [INFO] Running command: gunzip -c /var/lib/cwl/stg9af631da-fcc6-44d8-8b60-130e3b60f93f/GCA_022449655.1_ASM2244965v1_genomic.fna.gz | prodigal -d GCA_022449655.1_ASM2244965v1_genomic.fna/cds.fna -a GCA_022449655.1_ASM2244965v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 09:12:14,418] [INFO] Task succeeded: Prodigal
[2023-06-13 09:12:14,418] [INFO] Task started: HMMsearch
[2023-06-13 09:12:14,418] [INFO] Running command: hmmsearch --tblout GCA_022449655.1_ASM2244965v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga073a428-ef6a-412a-a822-b9dbd9c099ed/dqc_reference/reference_markers.hmm GCA_022449655.1_ASM2244965v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 09:12:14,609] [INFO] Task succeeded: HMMsearch
[2023-06-13 09:12:14,611] [INFO] Found 6/6 markers.
[2023-06-13 09:12:14,632] [INFO] Query marker FASTA was written to GCA_022449655.1_ASM2244965v1_genomic.fna/markers.fasta
[2023-06-13 09:12:14,632] [INFO] Task started: Blastn
[2023-06-13 09:12:14,632] [INFO] Running command: blastn -query GCA_022449655.1_ASM2244965v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga073a428-ef6a-412a-a822-b9dbd9c099ed/dqc_reference/reference_markers.fasta -out GCA_022449655.1_ASM2244965v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 09:12:15,234] [INFO] Task succeeded: Blastn
[2023-06-13 09:12:15,238] [INFO] Selected 20 target genomes.
[2023-06-13 09:12:15,239] [INFO] Target genome list was writen to GCA_022449655.1_ASM2244965v1_genomic.fna/target_genomes.txt
[2023-06-13 09:12:15,242] [INFO] Task started: fastANI
[2023-06-13 09:12:15,242] [INFO] Running command: fastANI --query /var/lib/cwl/stg9af631da-fcc6-44d8-8b60-130e3b60f93f/GCA_022449655.1_ASM2244965v1_genomic.fna.gz --refList GCA_022449655.1_ASM2244965v1_genomic.fna/target_genomes.txt --output GCA_022449655.1_ASM2244965v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 09:12:23,931] [INFO] Task succeeded: fastANI
[2023-06-13 09:12:23,931] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga073a428-ef6a-412a-a822-b9dbd9c099ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 09:12:23,932] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga073a428-ef6a-412a-a822-b9dbd9c099ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 09:12:23,934] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 09:12:23,934] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 09:12:23,934] [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 09:12:23,937] [INFO] DFAST Taxonomy check result was written to GCA_022449655.1_ASM2244965v1_genomic.fna/tc_result.tsv
[2023-06-13 09:12:23,938] [INFO] ===== Taxonomy check completed =====
[2023-06-13 09:12:23,938] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 09:12:23,938] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga073a428-ef6a-412a-a822-b9dbd9c099ed/dqc_reference/checkm_data
[2023-06-13 09:12:23,941] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 09:12:23,964] [INFO] Task started: CheckM
[2023-06-13 09:12:23,964] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022449655.1_ASM2244965v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022449655.1_ASM2244965v1_genomic.fna/checkm_input GCA_022449655.1_ASM2244965v1_genomic.fna/checkm_result
[2023-06-13 09:12:42,588] [INFO] Task succeeded: CheckM
[2023-06-13 09:12:42,590] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.94%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 09:12:42,621] [INFO] ===== Completeness check finished =====
[2023-06-13 09:12:42,621] [INFO] ===== Start GTDB Search =====
[2023-06-13 09:12:42,621] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022449655.1_ASM2244965v1_genomic.fna/markers.fasta)
[2023-06-13 09:12:42,621] [INFO] Task started: Blastn
[2023-06-13 09:12:42,622] [INFO] Running command: blastn -query GCA_022449655.1_ASM2244965v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga073a428-ef6a-412a-a822-b9dbd9c099ed/dqc_reference/reference_markers_gtdb.fasta -out GCA_022449655.1_ASM2244965v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 09:12:43,554] [INFO] Task succeeded: Blastn
[2023-06-13 09:12:43,561] [INFO] Selected 24 target genomes.
[2023-06-13 09:12:43,561] [INFO] Target genome list was writen to GCA_022449655.1_ASM2244965v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 09:12:43,572] [INFO] Task started: fastANI
[2023-06-13 09:12:43,573] [INFO] Running command: fastANI --query /var/lib/cwl/stg9af631da-fcc6-44d8-8b60-130e3b60f93f/GCA_022449655.1_ASM2244965v1_genomic.fna.gz --refList GCA_022449655.1_ASM2244965v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022449655.1_ASM2244965v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 09:12:49,140] [INFO] Task succeeded: fastANI
[2023-06-13 09:12:49,153] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 09:12:49,153] [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_002938255.1	s__MarineAlpha5-Bin3 sp002938255	99.4036	236	528	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__MarineAlpha5-Bin3	95.0	98.64	97.83	0.78	0.73	3	conclusive
GCA_902607435.1	s__CACLJX01 sp902607435	79.6812	150	528	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__CACLJX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902596065.1	s__MarineAlpha5-Bin3 sp902596065	76.6663	91	528	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__MarineAlpha5-Bin3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902522015.1	s__AG-337-I02 sp902522015	76.4709	52	528	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902518985.1	s__AG-337-I02 sp902518985	76.1831	73	528	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902619045.1	s__AG-337-I02 sp902619045	76.1415	52	528	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902591485.1	s__AG-337-I02 sp902591485	76.1209	79	528	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	97.00	97.00	0.77	0.77	2	-
GCA_002938195.1	s__MarineAlpha5-Bin7 sp002938195	76.1172	90	528	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__MarineAlpha5-Bin7	95.0	99.81	99.67	0.81	0.76	3	-
GCA_902623255.1	s__AG-337-I02 sp902623255	76.0267	77	528	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902577905.1	s__AG-337-I02 sp902577905	76.018	78	528	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902595425.1	s__AG-337-I02 sp902595425	75.986	84	528	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902630465.1	s__AG-337-I02 sp902630465	75.8931	50	528	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902601455.1	s__AG-337-I02 sp902601455	75.8347	85	528	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002937855.1	s__MarineAlpha5-Bin12 sp002937855	75.7102	69	528	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__MarineAlpha5-Bin12	95.0	99.77	99.77	0.93	0.93	2	-
GCA_902577945.1	s__AG-337-I02 sp902577945	75.4681	61	528	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 09:12:49,156] [INFO] GTDB search result was written to GCA_022449655.1_ASM2244965v1_genomic.fna/result_gtdb.tsv
[2023-06-13 09:12:49,157] [INFO] ===== GTDB Search completed =====
[2023-06-13 09:12:49,161] [INFO] DFAST_QC result json was written to GCA_022449655.1_ASM2244965v1_genomic.fna/dqc_result.json
[2023-06-13 09:12:49,161] [INFO] DFAST_QC completed!
[2023-06-13 09:12:49,161] [INFO] Total running time: 0h0m39s