[2023-06-05 13:58:13,564] [INFO] DFAST_QC pipeline started.
[2023-06-05 13:58:13,566] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 13:58:13,566] [INFO] DQC Reference Directory: /var/lib/cwl/stga774603d-c218-4ba0-b513-9fb3db8915d1/dqc_reference
[2023-06-05 13:58:14,725] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 13:58:14,726] [INFO] Task started: Prodigal
[2023-06-05 13:58:14,726] [INFO] Running command: gunzip -c /var/lib/cwl/stg04c7e7c4-ce1b-4406-9a32-9a3c5fefcf71/GCA_902522155.1_AG-895-A09_genomic.fna.gz | prodigal -d GCA_902522155.1_AG-895-A09_genomic.fna/cds.fna -a GCA_902522155.1_AG-895-A09_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 13:58:18,231] [INFO] Task succeeded: Prodigal
[2023-06-05 13:58:18,231] [INFO] Task started: HMMsearch
[2023-06-05 13:58:18,232] [INFO] Running command: hmmsearch --tblout GCA_902522155.1_AG-895-A09_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga774603d-c218-4ba0-b513-9fb3db8915d1/dqc_reference/reference_markers.hmm GCA_902522155.1_AG-895-A09_genomic.fna/protein.faa > /dev/null
[2023-06-05 13:58:18,375] [INFO] Task succeeded: HMMsearch
[2023-06-05 13:58:18,376] [INFO] Found 6/6 markers.
[2023-06-05 13:58:18,393] [INFO] Query marker FASTA was written to GCA_902522155.1_AG-895-A09_genomic.fna/markers.fasta
[2023-06-05 13:58:18,393] [INFO] Task started: Blastn
[2023-06-05 13:58:18,393] [INFO] Running command: blastn -query GCA_902522155.1_AG-895-A09_genomic.fna/markers.fasta -db /var/lib/cwl/stga774603d-c218-4ba0-b513-9fb3db8915d1/dqc_reference/reference_markers.fasta -out GCA_902522155.1_AG-895-A09_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 13:58:19,005] [INFO] Task succeeded: Blastn
[2023-06-05 13:58:19,010] [INFO] Selected 15 target genomes.
[2023-06-05 13:58:19,010] [INFO] Target genome list was writen to GCA_902522155.1_AG-895-A09_genomic.fna/target_genomes.txt
[2023-06-05 13:58:19,015] [INFO] Task started: fastANI
[2023-06-05 13:58:19,015] [INFO] Running command: fastANI --query /var/lib/cwl/stg04c7e7c4-ce1b-4406-9a32-9a3c5fefcf71/GCA_902522155.1_AG-895-A09_genomic.fna.gz --refList GCA_902522155.1_AG-895-A09_genomic.fna/target_genomes.txt --output GCA_902522155.1_AG-895-A09_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 13:58:27,053] [INFO] Task succeeded: fastANI
[2023-06-05 13:58:27,053] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga774603d-c218-4ba0-b513-9fb3db8915d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 13:58:27,054] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga774603d-c218-4ba0-b513-9fb3db8915d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 13:58:27,055] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 13:58:27,055] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 13:58:27,055] [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 13:58:27,057] [INFO] DFAST Taxonomy check result was written to GCA_902522155.1_AG-895-A09_genomic.fna/tc_result.tsv
[2023-06-05 13:58:27,058] [INFO] ===== Taxonomy check completed =====
[2023-06-05 13:58:27,058] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 13:58:27,058] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga774603d-c218-4ba0-b513-9fb3db8915d1/dqc_reference/checkm_data
[2023-06-05 13:58:27,061] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 13:58:27,077] [INFO] Task started: CheckM
[2023-06-05 13:58:27,077] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902522155.1_AG-895-A09_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902522155.1_AG-895-A09_genomic.fna/checkm_input GCA_902522155.1_AG-895-A09_genomic.fna/checkm_result
[2023-06-05 13:58:44,561] [INFO] Task succeeded: CheckM
[2023-06-05 13:58:44,562] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 13:58:44,582] [INFO] ===== Completeness check finished =====
[2023-06-05 13:58:44,582] [INFO] ===== Start GTDB Search =====
[2023-06-05 13:58:44,582] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902522155.1_AG-895-A09_genomic.fna/markers.fasta)
[2023-06-05 13:58:44,582] [INFO] Task started: Blastn
[2023-06-05 13:58:44,582] [INFO] Running command: blastn -query GCA_902522155.1_AG-895-A09_genomic.fna/markers.fasta -db /var/lib/cwl/stga774603d-c218-4ba0-b513-9fb3db8915d1/dqc_reference/reference_markers_gtdb.fasta -out GCA_902522155.1_AG-895-A09_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 13:58:45,362] [INFO] Task succeeded: Blastn
[2023-06-05 13:58:45,366] [INFO] Selected 24 target genomes.
[2023-06-05 13:58:45,366] [INFO] Target genome list was writen to GCA_902522155.1_AG-895-A09_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 13:58:45,394] [INFO] Task started: fastANI
[2023-06-05 13:58:45,394] [INFO] Running command: fastANI --query /var/lib/cwl/stg04c7e7c4-ce1b-4406-9a32-9a3c5fefcf71/GCA_902522155.1_AG-895-A09_genomic.fna.gz --refList GCA_902522155.1_AG-895-A09_genomic.fna/target_genomes_gtdb.txt --output GCA_902522155.1_AG-895-A09_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 13:58:50,706] [INFO] Task succeeded: fastANI
[2023-06-05 13:58:50,723] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 13:58:50,724] [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_902542505.1	s__HIMB59 sp902542505	94.9979	157	404	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	95.42	95.42	0.57	0.57	2	-
GCA_902546975.1	s__HIMB59 sp902546975	94.9391	324	404	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	96.15	95.57	0.84	0.81	5	-
GCA_902538085.1	s__HIMB59 sp902538085	94.8598	331	404	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	95.32	95.03	0.79	0.77	3	-
GCA_902599405.1	s__HIMB59 sp902599405	94.652	328	404	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	95.30	95.00	0.81	0.78	10	-
GCA_902613845.1	s__HIMB59 sp902613845	94.5926	334	404	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	95.34	95.19	0.82	0.79	7	-
GCA_902524245.1	s__HIMB59 sp902524245	94.5476	348	404	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	95.30	95.23	0.87	0.86	3	-
GCA_902518505.1	s__HIMB59 sp902518505	94.4026	299	404	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	96.57	95.11	0.80	0.80	4	-
GCA_902616855.1	s__HIMB59 sp902616855	94.3395	300	404	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	95.19	95.15	0.77	0.74	3	-
GCA_902574995.1	s__HIMB59 sp902574995	94.0905	308	404	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902613185.1	s__HIMB59 sp902613185	94.0162	341	404	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	99.61	99.58	0.93	0.92	5	-
GCA_902521485.1	s__HIMB59 sp902521485	93.9128	296	404	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	98.22	98.22	0.76	0.76	2	-
GCA_902621205.1	s__HIMB59 sp902621205	93.9006	309	404	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	99.28	98.69	0.88	0.86	4	-
GCA_902617515.1	s__HIMB59 sp902617515	93.6331	233	404	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902530745.1	s__HIMB59 sp902530745	93.6324	308	404	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	96.01	95.70	0.83	0.77	8	-
GCA_902591315.1	s__HIMB59 sp902591315	93.626	246	404	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	95.30	95.30	0.78	0.78	2	-
GCA_003216195.1	s__HIMB59 sp003216195	93.5935	287	404	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	96.67	95.48	0.82	0.73	7	-
GCA_902595525.1	s__HIMB59 sp902595525	93.1588	176	404	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902521795.1	s__HIMB59 sp902560595	83.3914	259	404	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	95.49	95.27	0.76	0.73	4	-
GCA_902527045.1	s__HIMB59 sp902527045	83.2958	267	404	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902601865.1	s__HIMB59 sp902601865	83.184	271	404	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000299115.1	s__HIMB59 sp000299115	78.2005	162	404	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 13:58:50,726] [INFO] GTDB search result was written to GCA_902522155.1_AG-895-A09_genomic.fna/result_gtdb.tsv
[2023-06-05 13:58:50,727] [INFO] ===== GTDB Search completed =====
[2023-06-05 13:58:50,731] [INFO] DFAST_QC result json was written to GCA_902522155.1_AG-895-A09_genomic.fna/dqc_result.json
[2023-06-05 13:58:50,731] [INFO] DFAST_QC completed!
[2023-06-05 13:58:50,731] [INFO] Total running time: 0h0m37s