[2023-06-08 09:31:58,355] [INFO] DFAST_QC pipeline started.
[2023-06-08 09:31:58,366] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 09:31:58,367] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d50a39c-4ad3-4eda-af51-16cfce655c58/dqc_reference
[2023-06-08 09:31:59,772] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 09:31:59,773] [INFO] Task started: Prodigal
[2023-06-08 09:31:59,773] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ee61ad5-c548-4577-87b1-6048fe9a057a/GCA_902616545.1_AG-892-C06_genomic.fna.gz | prodigal -d GCA_902616545.1_AG-892-C06_genomic.fna/cds.fna -a GCA_902616545.1_AG-892-C06_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 09:32:02,718] [INFO] Task succeeded: Prodigal
[2023-06-08 09:32:02,718] [INFO] Task started: HMMsearch
[2023-06-08 09:32:02,719] [INFO] Running command: hmmsearch --tblout GCA_902616545.1_AG-892-C06_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d50a39c-4ad3-4eda-af51-16cfce655c58/dqc_reference/reference_markers.hmm GCA_902616545.1_AG-892-C06_genomic.fna/protein.faa > /dev/null
[2023-06-08 09:32:02,937] [INFO] Task succeeded: HMMsearch
[2023-06-08 09:32:02,939] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg7ee61ad5-c548-4577-87b1-6048fe9a057a/GCA_902616545.1_AG-892-C06_genomic.fna.gz]
[2023-06-08 09:32:02,954] [INFO] Query marker FASTA was written to GCA_902616545.1_AG-892-C06_genomic.fna/markers.fasta
[2023-06-08 09:32:02,954] [INFO] Task started: Blastn
[2023-06-08 09:32:02,956] [INFO] Running command: blastn -query GCA_902616545.1_AG-892-C06_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d50a39c-4ad3-4eda-af51-16cfce655c58/dqc_reference/reference_markers.fasta -out GCA_902616545.1_AG-892-C06_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:32:03,439] [INFO] Task succeeded: Blastn
[2023-06-08 09:32:03,447] [INFO] Selected 6 target genomes.
[2023-06-08 09:32:03,448] [INFO] Target genome list was writen to GCA_902616545.1_AG-892-C06_genomic.fna/target_genomes.txt
[2023-06-08 09:32:03,452] [INFO] Task started: fastANI
[2023-06-08 09:32:03,453] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ee61ad5-c548-4577-87b1-6048fe9a057a/GCA_902616545.1_AG-892-C06_genomic.fna.gz --refList GCA_902616545.1_AG-892-C06_genomic.fna/target_genomes.txt --output GCA_902616545.1_AG-892-C06_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 09:32:06,036] [INFO] Task succeeded: fastANI
[2023-06-08 09:32:06,036] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d50a39c-4ad3-4eda-af51-16cfce655c58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 09:32:06,037] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d50a39c-4ad3-4eda-af51-16cfce655c58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 09:32:06,038] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 09:32:06,038] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 09:32:06,039] [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
--------------------------------------------------------------------------------
[2023-06-08 09:32:06,040] [INFO] DFAST Taxonomy check result was written to GCA_902616545.1_AG-892-C06_genomic.fna/tc_result.tsv
[2023-06-08 09:32:06,041] [INFO] ===== Taxonomy check completed =====
[2023-06-08 09:32:06,041] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 09:32:06,041] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d50a39c-4ad3-4eda-af51-16cfce655c58/dqc_reference/checkm_data
[2023-06-08 09:32:06,044] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 09:32:06,062] [INFO] Task started: CheckM
[2023-06-08 09:32:06,062] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902616545.1_AG-892-C06_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902616545.1_AG-892-C06_genomic.fna/checkm_input GCA_902616545.1_AG-892-C06_genomic.fna/checkm_result
[2023-06-08 09:32:23,313] [INFO] Task succeeded: CheckM
[2023-06-08 09:32:23,314] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 09:32:23,332] [INFO] ===== Completeness check finished =====
[2023-06-08 09:32:23,333] [INFO] ===== Start GTDB Search =====
[2023-06-08 09:32:23,333] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902616545.1_AG-892-C06_genomic.fna/markers.fasta)
[2023-06-08 09:32:23,334] [INFO] Task started: Blastn
[2023-06-08 09:32:23,334] [INFO] Running command: blastn -query GCA_902616545.1_AG-892-C06_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d50a39c-4ad3-4eda-af51-16cfce655c58/dqc_reference/reference_markers_gtdb.fasta -out GCA_902616545.1_AG-892-C06_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:32:23,763] [INFO] Task succeeded: Blastn
[2023-06-08 09:32:23,768] [INFO] Selected 13 target genomes.
[2023-06-08 09:32:23,768] [INFO] Target genome list was writen to GCA_902616545.1_AG-892-C06_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 09:32:23,794] [INFO] Task started: fastANI
[2023-06-08 09:32:23,794] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ee61ad5-c548-4577-87b1-6048fe9a057a/GCA_902616545.1_AG-892-C06_genomic.fna.gz --refList GCA_902616545.1_AG-892-C06_genomic.fna/target_genomes_gtdb.txt --output GCA_902616545.1_AG-892-C06_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 09:32:27,427] [INFO] Task succeeded: fastANI
[2023-06-08 09:32:27,443] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 09:32:27,444] [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_902620425.1	s__AG-337-I02 sp902620425	93.8297	306	337	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	95.06	95.06	0.88	0.88	2	-
GCA_902615845.1	s__AG-337-I02 sp902615845	93.6894	250	337	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_902621165.1	s__AG-337-I02 sp902621165	93.6312	260	337	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	99.54	99.54	0.84	0.84	2	-
GCA_902573325.1	s__AG-337-I02 sp902573325	93.5954	262	337	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_902588745.1	s__AG-337-I02 sp902588745	93.4748	268	337	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_902612825.1	s__AG-337-I02 sp902612825	93.4467	228	337	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_902580765.1	s__AG-337-I02 sp902580765	93.425	201	337	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	99.49	99.49	0.62	0.62	2	-
GCA_902615745.1	s__AG-337-I02 sp902615745	93.2407	281	337	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	99.85	99.85	0.90	0.90	2	-
GCA_902602885.1	s__AG-337-I02 sp902602885	93.11	212	337	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_902571865.1	s__AG-337-I02 sp902571865	92.9829	282	337	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_902595805.1	s__AG-337-I02 sp902595805	92.3916	231	337	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_902575375.1	s__AG-337-I02 sp902575375	92.283	164	337	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_902618015.1	s__AG-337-I02 sp902618015	92.2565	259	337	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	-
--------------------------------------------------------------------------------
[2023-06-08 09:32:27,445] [INFO] GTDB search result was written to GCA_902616545.1_AG-892-C06_genomic.fna/result_gtdb.tsv
[2023-06-08 09:32:27,446] [INFO] ===== GTDB Search completed =====
[2023-06-08 09:32:27,449] [INFO] DFAST_QC result json was written to GCA_902616545.1_AG-892-C06_genomic.fna/dqc_result.json
[2023-06-08 09:32:27,449] [INFO] DFAST_QC completed!
[2023-06-08 09:32:27,449] [INFO] Total running time: 0h0m29s