[2023-06-29 14:27:00,229] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:27:00,232] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:27:00,233] [INFO] DQC Reference Directory: /var/lib/cwl/stge9d8965d-cf77-49cb-9f1f-676f24659963/dqc_reference
[2023-06-29 14:27:01,508] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:27:01,509] [INFO] Task started: Prodigal
[2023-06-29 14:27:01,509] [INFO] Running command: gunzip -c /var/lib/cwl/stg327df833-048b-41ca-9375-946bbe44fd5d/GCA_910580185.1_MGBC119771_genomic.fna.gz | prodigal -d GCA_910580185.1_MGBC119771_genomic.fna/cds.fna -a GCA_910580185.1_MGBC119771_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:27:03,554] [INFO] Task succeeded: Prodigal
[2023-06-29 14:27:03,555] [INFO] Task started: HMMsearch
[2023-06-29 14:27:03,555] [INFO] Running command: hmmsearch --tblout GCA_910580185.1_MGBC119771_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9d8965d-cf77-49cb-9f1f-676f24659963/dqc_reference/reference_markers.hmm GCA_910580185.1_MGBC119771_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:27:03,837] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:27:03,839] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg327df833-048b-41ca-9375-946bbe44fd5d/GCA_910580185.1_MGBC119771_genomic.fna.gz]
[2023-06-29 14:27:03,870] [INFO] Query marker FASTA was written to GCA_910580185.1_MGBC119771_genomic.fna/markers.fasta
[2023-06-29 14:27:03,871] [INFO] Task started: Blastn
[2023-06-29 14:27:03,871] [INFO] Running command: blastn -query GCA_910580185.1_MGBC119771_genomic.fna/markers.fasta -db /var/lib/cwl/stge9d8965d-cf77-49cb-9f1f-676f24659963/dqc_reference/reference_markers.fasta -out GCA_910580185.1_MGBC119771_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:27:04,526] [INFO] Task succeeded: Blastn
[2023-06-29 14:27:04,531] [INFO] Selected 28 target genomes.
[2023-06-29 14:27:04,531] [INFO] Target genome list was writen to GCA_910580185.1_MGBC119771_genomic.fna/target_genomes.txt
[2023-06-29 14:27:04,533] [INFO] Task started: fastANI
[2023-06-29 14:27:04,533] [INFO] Running command: fastANI --query /var/lib/cwl/stg327df833-048b-41ca-9375-946bbe44fd5d/GCA_910580185.1_MGBC119771_genomic.fna.gz --refList GCA_910580185.1_MGBC119771_genomic.fna/target_genomes.txt --output GCA_910580185.1_MGBC119771_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:27:17,255] [INFO] Task succeeded: fastANI
[2023-06-29 14:27:17,256] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge9d8965d-cf77-49cb-9f1f-676f24659963/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:27:17,256] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge9d8965d-cf77-49cb-9f1f-676f24659963/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:27:17,258] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:27:17,259] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 14:27:17,259] [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
--------------------------------------------------------------------------------
[2023-06-29 14:27:17,261] [INFO] DFAST Taxonomy check result was written to GCA_910580185.1_MGBC119771_genomic.fna/tc_result.tsv
[2023-06-29 14:27:17,262] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:27:17,262] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:27:17,262] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9d8965d-cf77-49cb-9f1f-676f24659963/dqc_reference/checkm_data
[2023-06-29 14:27:17,265] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:27:17,282] [INFO] Task started: CheckM
[2023-06-29 14:27:17,283] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_910580185.1_MGBC119771_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_910580185.1_MGBC119771_genomic.fna/checkm_input GCA_910580185.1_MGBC119771_genomic.fna/checkm_result
[2023-06-29 14:27:32,319] [INFO] Task succeeded: CheckM
[2023-06-29 14:27:32,320] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 14:27:32,340] [INFO] ===== Completeness check finished =====
[2023-06-29 14:27:32,341] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:27:32,341] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_910580185.1_MGBC119771_genomic.fna/markers.fasta)
[2023-06-29 14:27:32,341] [INFO] Task started: Blastn
[2023-06-29 14:27:32,342] [INFO] Running command: blastn -query GCA_910580185.1_MGBC119771_genomic.fna/markers.fasta -db /var/lib/cwl/stge9d8965d-cf77-49cb-9f1f-676f24659963/dqc_reference/reference_markers_gtdb.fasta -out GCA_910580185.1_MGBC119771_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:27:33,197] [INFO] Task succeeded: Blastn
[2023-06-29 14:27:33,201] [INFO] Selected 14 target genomes.
[2023-06-29 14:27:33,202] [INFO] Target genome list was writen to GCA_910580185.1_MGBC119771_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:27:33,227] [INFO] Task started: fastANI
[2023-06-29 14:27:33,227] [INFO] Running command: fastANI --query /var/lib/cwl/stg327df833-048b-41ca-9375-946bbe44fd5d/GCA_910580185.1_MGBC119771_genomic.fna.gz --refList GCA_910580185.1_MGBC119771_genomic.fna/target_genomes_gtdb.txt --output GCA_910580185.1_MGBC119771_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:27:36,922] [INFO] Task succeeded: fastANI
[2023-06-29 14:27:36,939] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 14:27:36,940] [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_910580185.1	s__Aphodocola sp910580185	99.9999	441	441	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Aphodocola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910580135.1	s__Aphodocola sp910580135	82.5999	234	441	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Aphodocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000434835.1	s__Aphodocola sp000434835	79.7378	186	441	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Aphodocola	95.0	96.23	96.23	0.83	0.83	2	-
GCA_900547225.1	s__Aphodocola sp900547225	79.4256	188	441	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Aphodocola	95.0	98.53	98.53	0.90	0.90	2	-
GCA_900771805.1	s__Aphodocola sp900771805	78.9727	156	441	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Aphodocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900772415.1	s__Aphodocola sp900772415	78.6483	160	441	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Aphodocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018714855.1	s__Aphodocola excrementigallinarum	78.5377	182	441	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Aphodocola	95.0	99.84	99.84	0.90	0.90	2	-
GCA_900766325.1	s__Aphodocola sp900766325	78.31	119	441	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Aphodocola	95.0	99.97	99.97	1.00	1.00	2	-
GCA_902795755.1	s__Aphodocola sp902795755	78.0505	105	441	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Aphodocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900759985.1	s__Aphodocola sp900759985	77.8323	87	441	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Aphodocola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 14:27:36,948] [INFO] GTDB search result was written to GCA_910580185.1_MGBC119771_genomic.fna/result_gtdb.tsv
[2023-06-29 14:27:36,949] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:27:36,954] [INFO] DFAST_QC result json was written to GCA_910580185.1_MGBC119771_genomic.fna/dqc_result.json
[2023-06-29 14:27:36,954] [INFO] DFAST_QC completed!
[2023-06-29 14:27:36,954] [INFO] Total running time: 0h0m37s