[2023-06-28 09:02:35,691] [INFO] DFAST_QC pipeline started.
[2023-06-28 09:02:35,695] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 09:02:35,695] [INFO] DQC Reference Directory: /var/lib/cwl/stg13a3df3c-6d83-4af8-b1b4-ba9a6b005f83/dqc_reference
[2023-06-28 09:02:36,917] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 09:02:36,918] [INFO] Task started: Prodigal
[2023-06-28 09:02:36,918] [INFO] Running command: gunzip -c /var/lib/cwl/stg8bbb2ddd-2ffb-43e6-a7a4-bff865852cc0/GCA_017633775.1_ASM1763377v1_genomic.fna.gz | prodigal -d GCA_017633775.1_ASM1763377v1_genomic.fna/cds.fna -a GCA_017633775.1_ASM1763377v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 09:02:38,524] [INFO] Task succeeded: Prodigal
[2023-06-28 09:02:38,525] [INFO] Task started: HMMsearch
[2023-06-28 09:02:38,525] [INFO] Running command: hmmsearch --tblout GCA_017633775.1_ASM1763377v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13a3df3c-6d83-4af8-b1b4-ba9a6b005f83/dqc_reference/reference_markers.hmm GCA_017633775.1_ASM1763377v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 09:02:38,796] [INFO] Task succeeded: HMMsearch
[2023-06-28 09:02:38,797] [INFO] Found 6/6 markers.
[2023-06-28 09:02:38,810] [INFO] Query marker FASTA was written to GCA_017633775.1_ASM1763377v1_genomic.fna/markers.fasta
[2023-06-28 09:02:38,810] [INFO] Task started: Blastn
[2023-06-28 09:02:38,810] [INFO] Running command: blastn -query GCA_017633775.1_ASM1763377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13a3df3c-6d83-4af8-b1b4-ba9a6b005f83/dqc_reference/reference_markers.fasta -out GCA_017633775.1_ASM1763377v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 09:02:39,402] [INFO] Task succeeded: Blastn
[2023-06-28 09:02:39,407] [INFO] Selected 23 target genomes.
[2023-06-28 09:02:39,408] [INFO] Target genome list was writen to GCA_017633775.1_ASM1763377v1_genomic.fna/target_genomes.txt
[2023-06-28 09:02:39,412] [INFO] Task started: fastANI
[2023-06-28 09:02:39,412] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bbb2ddd-2ffb-43e6-a7a4-bff865852cc0/GCA_017633775.1_ASM1763377v1_genomic.fna.gz --refList GCA_017633775.1_ASM1763377v1_genomic.fna/target_genomes.txt --output GCA_017633775.1_ASM1763377v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 09:02:51,652] [INFO] Task succeeded: fastANI
[2023-06-28 09:02:51,653] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13a3df3c-6d83-4af8-b1b4-ba9a6b005f83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 09:02:51,654] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13a3df3c-6d83-4af8-b1b4-ba9a6b005f83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 09:02:51,656] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 09:02:51,656] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 09:02:51,656] [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
--------------------------------------------------------------------------------
[2023-06-28 09:02:51,678] [INFO] DFAST Taxonomy check result was written to GCA_017633775.1_ASM1763377v1_genomic.fna/tc_result.tsv
[2023-06-28 09:02:51,679] [INFO] ===== Taxonomy check completed =====
[2023-06-28 09:02:51,680] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 09:02:51,680] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13a3df3c-6d83-4af8-b1b4-ba9a6b005f83/dqc_reference/checkm_data
[2023-06-28 09:02:51,685] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 09:02:51,697] [INFO] Task started: CheckM
[2023-06-28 09:02:51,697] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017633775.1_ASM1763377v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017633775.1_ASM1763377v1_genomic.fna/checkm_input GCA_017633775.1_ASM1763377v1_genomic.fna/checkm_result
[2023-06-28 09:03:04,318] [INFO] Task succeeded: CheckM
[2023-06-28 09:03:04,320] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.63%
Contamintation: 6.25%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 09:03:04,341] [INFO] ===== Completeness check finished =====
[2023-06-28 09:03:04,341] [INFO] ===== Start GTDB Search =====
[2023-06-28 09:03:04,342] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017633775.1_ASM1763377v1_genomic.fna/markers.fasta)
[2023-06-28 09:03:04,342] [INFO] Task started: Blastn
[2023-06-28 09:03:04,342] [INFO] Running command: blastn -query GCA_017633775.1_ASM1763377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13a3df3c-6d83-4af8-b1b4-ba9a6b005f83/dqc_reference/reference_markers_gtdb.fasta -out GCA_017633775.1_ASM1763377v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 09:03:05,150] [INFO] Task succeeded: Blastn
[2023-06-28 09:03:05,155] [INFO] Selected 10 target genomes.
[2023-06-28 09:03:05,155] [INFO] Target genome list was writen to GCA_017633775.1_ASM1763377v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 09:03:05,159] [INFO] Task started: fastANI
[2023-06-28 09:03:05,160] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bbb2ddd-2ffb-43e6-a7a4-bff865852cc0/GCA_017633775.1_ASM1763377v1_genomic.fna.gz --refList GCA_017633775.1_ASM1763377v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017633775.1_ASM1763377v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 09:03:08,863] [INFO] Task succeeded: fastANI
[2023-06-28 09:03:08,872] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 09:03:08,873] [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_017965665.1	s__RGIG1476 sp017965665	98.9675	170	180	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__RGIG1476	95.0	97.91	97.58	0.97	0.93	8	conclusive
GCA_017538865.1	s__RGIG1476 sp017538865	85.3898	136	180	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__RGIG1476	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017632535.1	s__RGIG1476 sp017632535	83.5014	153	180	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__RGIG1476	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017632855.1	s__RGIG1476 sp017632855	80.3808	120	180	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__RGIG1476	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017632945.1	s__RGIG1476 sp017632945	79.9963	104	180	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__RGIG1476	95.0	97.99	97.22	0.94	0.90	4	-
GCA_017413255.1	s__RGIG1476 sp017413255	79.9244	113	180	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__RGIG1476	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017537945.1	s__RGIG1476 sp017537945	79.7098	105	180	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__RGIG1476	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 09:03:08,875] [INFO] GTDB search result was written to GCA_017633775.1_ASM1763377v1_genomic.fna/result_gtdb.tsv
[2023-06-28 09:03:08,876] [INFO] ===== GTDB Search completed =====
[2023-06-28 09:03:08,878] [INFO] DFAST_QC result json was written to GCA_017633775.1_ASM1763377v1_genomic.fna/dqc_result.json
[2023-06-28 09:03:08,879] [INFO] DFAST_QC completed!
[2023-06-28 09:03:08,879] [INFO] Total running time: 0h0m33s