[2023-06-05 10:23:33,443] [INFO] DFAST_QC pipeline started.
[2023-06-05 10:23:33,445] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 10:23:33,445] [INFO] DQC Reference Directory: /var/lib/cwl/stge2bc2d3f-2288-4bcc-afa2-861874543fc2/dqc_reference
[2023-06-05 10:23:34,733] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 10:23:34,734] [INFO] Task started: Prodigal
[2023-06-05 10:23:34,734] [INFO] Running command: gunzip -c /var/lib/cwl/stgf4fc3623-585f-458e-b8c3-aa9a3838bd99/GCA_902525495.1_AG-895-O08_genomic.fna.gz | prodigal -d GCA_902525495.1_AG-895-O08_genomic.fna/cds.fna -a GCA_902525495.1_AG-895-O08_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 10:23:37,351] [INFO] Task succeeded: Prodigal
[2023-06-05 10:23:37,351] [INFO] Task started: HMMsearch
[2023-06-05 10:23:37,351] [INFO] Running command: hmmsearch --tblout GCA_902525495.1_AG-895-O08_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2bc2d3f-2288-4bcc-afa2-861874543fc2/dqc_reference/reference_markers.hmm GCA_902525495.1_AG-895-O08_genomic.fna/protein.faa > /dev/null
[2023-06-05 10:23:37,494] [INFO] Task succeeded: HMMsearch
[2023-06-05 10:23:37,497] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgf4fc3623-585f-458e-b8c3-aa9a3838bd99/GCA_902525495.1_AG-895-O08_genomic.fna.gz]
[2023-06-05 10:23:37,511] [INFO] Query marker FASTA was written to GCA_902525495.1_AG-895-O08_genomic.fna/markers.fasta
[2023-06-05 10:23:37,511] [INFO] Task started: Blastn
[2023-06-05 10:23:37,511] [INFO] Running command: blastn -query GCA_902525495.1_AG-895-O08_genomic.fna/markers.fasta -db /var/lib/cwl/stge2bc2d3f-2288-4bcc-afa2-861874543fc2/dqc_reference/reference_markers.fasta -out GCA_902525495.1_AG-895-O08_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:23:38,027] [INFO] Task succeeded: Blastn
[2023-06-05 10:23:38,031] [INFO] Selected 12 target genomes.
[2023-06-05 10:23:38,031] [INFO] Target genome list was writen to GCA_902525495.1_AG-895-O08_genomic.fna/target_genomes.txt
[2023-06-05 10:23:38,035] [INFO] Task started: fastANI
[2023-06-05 10:23:38,035] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4fc3623-585f-458e-b8c3-aa9a3838bd99/GCA_902525495.1_AG-895-O08_genomic.fna.gz --refList GCA_902525495.1_AG-895-O08_genomic.fna/target_genomes.txt --output GCA_902525495.1_AG-895-O08_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 10:23:42,643] [INFO] Task succeeded: fastANI
[2023-06-05 10:23:42,643] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2bc2d3f-2288-4bcc-afa2-861874543fc2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 10:23:42,643] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2bc2d3f-2288-4bcc-afa2-861874543fc2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 10:23:42,645] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 10:23:42,645] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 10:23:42,645] [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
--------------------------------------------------------------------------------
[2023-06-05 10:23:42,647] [INFO] DFAST Taxonomy check result was written to GCA_902525495.1_AG-895-O08_genomic.fna/tc_result.tsv
[2023-06-05 10:23:42,648] [INFO] ===== Taxonomy check completed =====
[2023-06-05 10:23:42,648] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 10:23:42,648] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2bc2d3f-2288-4bcc-afa2-861874543fc2/dqc_reference/checkm_data
[2023-06-05 10:23:42,651] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 10:23:42,664] [INFO] Task started: CheckM
[2023-06-05 10:23:42,664] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902525495.1_AG-895-O08_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902525495.1_AG-895-O08_genomic.fna/checkm_input GCA_902525495.1_AG-895-O08_genomic.fna/checkm_result
[2023-06-05 10:23:57,781] [INFO] Task succeeded: CheckM
[2023-06-05 10:23:57,782] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 10:23:57,806] [INFO] ===== Completeness check finished =====
[2023-06-05 10:23:57,806] [INFO] ===== Start GTDB Search =====
[2023-06-05 10:23:57,806] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902525495.1_AG-895-O08_genomic.fna/markers.fasta)
[2023-06-05 10:23:57,807] [INFO] Task started: Blastn
[2023-06-05 10:23:57,807] [INFO] Running command: blastn -query GCA_902525495.1_AG-895-O08_genomic.fna/markers.fasta -db /var/lib/cwl/stge2bc2d3f-2288-4bcc-afa2-861874543fc2/dqc_reference/reference_markers_gtdb.fasta -out GCA_902525495.1_AG-895-O08_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:23:58,332] [INFO] Task succeeded: Blastn
[2023-06-05 10:23:58,336] [INFO] Selected 17 target genomes.
[2023-06-05 10:23:58,336] [INFO] Target genome list was writen to GCA_902525495.1_AG-895-O08_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 10:23:58,344] [INFO] Task started: fastANI
[2023-06-05 10:23:58,344] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4fc3623-585f-458e-b8c3-aa9a3838bd99/GCA_902525495.1_AG-895-O08_genomic.fna.gz --refList GCA_902525495.1_AG-895-O08_genomic.fna/target_genomes_gtdb.txt --output GCA_902525495.1_AG-895-O08_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 10:24:02,340] [INFO] Task succeeded: fastANI
[2023-06-05 10:24:02,356] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 10:24:02,356] [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_902613275.1	s__AG-337-I02 sp902613275	98.7107	140	296	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	conclusive
GCA_902614375.1	s__AG-337-I02 sp902614375	92.9002	221	296	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_902522015.1	s__AG-337-I02 sp902522015	92.6296	157	296	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_902590695.1	s__AG-337-I02 sp902590695	92.5427	227	296	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_902522865.1	s__AG-337-I02 sp902522865	92.1679	221	296	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_902623255.1	s__AG-337-I02 sp902623255	92.078	206	296	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_902615845.1	s__AG-337-I02 sp902615845	91.8858	211	296	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_902616075.1	s__AG-337-I02 sp902616075	91.8556	171	296	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	99.45	99.29	0.64	0.59	3	-
GCA_902538155.1	s__AG-337-I02 sp902538155	91.6504	158	296	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_902515745.1	s__AG-337-I02 sp902515745	91.5456	241	296	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_902575815.1	s__AG-337-I02 sp902575815	91.082	164	296	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_902615625.1	s__AG-337-I02 sp902615625	90.9027	177	296	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	90.8549	209	296	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_902521315.1	s__AG-337-I02 sp902521315	90.6713	231	296	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_902540265.1	s__AG-337-I02 sp902540265	90.4602	197	296	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_902553005.1	s__AG-337-I02 sp902553005	90.2242	156	296	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_902625365.1	s__AG-337-I02 sp902625365	89.5887	152	296	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	-
--------------------------------------------------------------------------------
[2023-06-05 10:24:02,358] [INFO] GTDB search result was written to GCA_902525495.1_AG-895-O08_genomic.fna/result_gtdb.tsv
[2023-06-05 10:24:02,359] [INFO] ===== GTDB Search completed =====
[2023-06-05 10:24:02,363] [INFO] DFAST_QC result json was written to GCA_902525495.1_AG-895-O08_genomic.fna/dqc_result.json
[2023-06-05 10:24:02,363] [INFO] DFAST_QC completed!
[2023-06-05 10:24:02,363] [INFO] Total running time: 0h0m29s