[2023-06-29 18:37:32,197] [INFO] DFAST_QC pipeline started.
[2023-06-29 18:37:32,208] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 18:37:32,209] [INFO] DQC Reference Directory: /var/lib/cwl/stg6fb282cd-66c7-4dde-a896-c6e489d79160/dqc_reference
[2023-06-29 18:37:34,387] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 18:37:34,388] [INFO] Task started: Prodigal
[2023-06-29 18:37:34,388] [INFO] Running command: gunzip -c /var/lib/cwl/stg08d1328d-6e4c-4050-a911-b6a0267621b4/GCA_910588025.1_MGBC163973_genomic.fna.gz | prodigal -d GCA_910588025.1_MGBC163973_genomic.fna/cds.fna -a GCA_910588025.1_MGBC163973_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 18:37:36,581] [INFO] Task succeeded: Prodigal
[2023-06-29 18:37:36,581] [INFO] Task started: HMMsearch
[2023-06-29 18:37:36,581] [INFO] Running command: hmmsearch --tblout GCA_910588025.1_MGBC163973_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6fb282cd-66c7-4dde-a896-c6e489d79160/dqc_reference/reference_markers.hmm GCA_910588025.1_MGBC163973_genomic.fna/protein.faa > /dev/null
[2023-06-29 18:37:36,805] [INFO] Task succeeded: HMMsearch
[2023-06-29 18:37:36,806] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg08d1328d-6e4c-4050-a911-b6a0267621b4/GCA_910588025.1_MGBC163973_genomic.fna.gz]
[2023-06-29 18:37:36,825] [INFO] Query marker FASTA was written to GCA_910588025.1_MGBC163973_genomic.fna/markers.fasta
[2023-06-29 18:37:36,825] [INFO] Task started: Blastn
[2023-06-29 18:37:36,825] [INFO] Running command: blastn -query GCA_910588025.1_MGBC163973_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fb282cd-66c7-4dde-a896-c6e489d79160/dqc_reference/reference_markers.fasta -out GCA_910588025.1_MGBC163973_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 18:37:39,355] [INFO] Task succeeded: Blastn
[2023-06-29 18:37:39,360] [INFO] Selected 25 target genomes.
[2023-06-29 18:37:39,360] [INFO] Target genome list was writen to GCA_910588025.1_MGBC163973_genomic.fna/target_genomes.txt
[2023-06-29 18:37:39,371] [INFO] Task started: fastANI
[2023-06-29 18:37:39,372] [INFO] Running command: fastANI --query /var/lib/cwl/stg08d1328d-6e4c-4050-a911-b6a0267621b4/GCA_910588025.1_MGBC163973_genomic.fna.gz --refList GCA_910588025.1_MGBC163973_genomic.fna/target_genomes.txt --output GCA_910588025.1_MGBC163973_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 18:37:50,207] [INFO] Task succeeded: fastANI
[2023-06-29 18:37:50,208] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6fb282cd-66c7-4dde-a896-c6e489d79160/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 18:37:50,209] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6fb282cd-66c7-4dde-a896-c6e489d79160/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 18:37:50,211] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 18:37:50,211] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 18:37:50,211] [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 18:37:50,214] [INFO] DFAST Taxonomy check result was written to GCA_910588025.1_MGBC163973_genomic.fna/tc_result.tsv
[2023-06-29 18:37:50,214] [INFO] ===== Taxonomy check completed =====
[2023-06-29 18:37:50,215] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 18:37:50,215] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6fb282cd-66c7-4dde-a896-c6e489d79160/dqc_reference/checkm_data
[2023-06-29 18:37:50,219] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 18:37:50,239] [INFO] Task started: CheckM
[2023-06-29 18:37:50,239] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_910588025.1_MGBC163973_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_910588025.1_MGBC163973_genomic.fna/checkm_input GCA_910588025.1_MGBC163973_genomic.fna/checkm_result
[2023-06-29 18:38:04,988] [INFO] Task succeeded: CheckM
[2023-06-29 18:38:04,990] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 18:38:05,013] [INFO] ===== Completeness check finished =====
[2023-06-29 18:38:05,014] [INFO] ===== Start GTDB Search =====
[2023-06-29 18:38:05,014] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_910588025.1_MGBC163973_genomic.fna/markers.fasta)
[2023-06-29 18:38:05,015] [INFO] Task started: Blastn
[2023-06-29 18:38:05,015] [INFO] Running command: blastn -query GCA_910588025.1_MGBC163973_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fb282cd-66c7-4dde-a896-c6e489d79160/dqc_reference/reference_markers_gtdb.fasta -out GCA_910588025.1_MGBC163973_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 18:38:05,823] [INFO] Task succeeded: Blastn
[2023-06-29 18:38:05,828] [INFO] Selected 16 target genomes.
[2023-06-29 18:38:05,829] [INFO] Target genome list was writen to GCA_910588025.1_MGBC163973_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 18:38:05,836] [INFO] Task started: fastANI
[2023-06-29 18:38:05,836] [INFO] Running command: fastANI --query /var/lib/cwl/stg08d1328d-6e4c-4050-a911-b6a0267621b4/GCA_910588025.1_MGBC163973_genomic.fna.gz --refList GCA_910588025.1_MGBC163973_genomic.fna/target_genomes_gtdb.txt --output GCA_910588025.1_MGBC163973_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 18:38:09,974] [INFO] Task succeeded: fastANI
[2023-06-29 18:38:09,989] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 18:38:09,989] [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_910588025.1	s__MGBC162267 sp910588025	100.0	433	433	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__MGBC162267	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910587775.1	s__MGBC162267 sp910587775	84.5971	285	433	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__MGBC162267	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585915.1	s__MGBC162267 sp910585915	79.2439	170	433	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__MGBC162267	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587325.1	s__MGBC108787 sp910587325	77.9926	69	433	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__MGBC108787	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018712835.1	s__Ventrenecus stercoripullorum	76.913	52	433	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Ventrenecus	95.0	99.90	99.90	0.85	0.85	2	-
GCA_905205665.1	s__Ventrenecus sp905205665	76.8017	57	433	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Ventrenecus	95.0	97.62	97.62	0.88	0.88	2	-
GCA_016297695.1	s__RUG14121 sp016297695	76.4819	66	433	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG14121	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902795845.1	s__RUG14121 sp902795845	76.0702	56	433	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG14121	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 18:38:09,991] [INFO] GTDB search result was written to GCA_910588025.1_MGBC163973_genomic.fna/result_gtdb.tsv
[2023-06-29 18:38:09,991] [INFO] ===== GTDB Search completed =====
[2023-06-29 18:38:09,995] [INFO] DFAST_QC result json was written to GCA_910588025.1_MGBC163973_genomic.fna/dqc_result.json
[2023-06-29 18:38:09,995] [INFO] DFAST_QC completed!
[2023-06-29 18:38:09,995] [INFO] Total running time: 0h0m38s