[2023-06-30 15:09:16,150] [INFO] DFAST_QC pipeline started.
[2023-06-30 15:09:16,152] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 15:09:16,152] [INFO] DQC Reference Directory: /var/lib/cwl/stg140abe5c-a42d-4c56-b0c9-bd5ed54d940f/dqc_reference
[2023-06-30 15:09:17,463] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 15:09:17,464] [INFO] Task started: Prodigal
[2023-06-30 15:09:17,464] [INFO] Running command: gunzip -c /var/lib/cwl/stga700688b-2fb9-4c36-b831-94ff253139b8/GCA_024694055.1_ASM2469405v1_genomic.fna.gz | prodigal -d GCA_024694055.1_ASM2469405v1_genomic.fna/cds.fna -a GCA_024694055.1_ASM2469405v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 15:09:23,018] [INFO] Task succeeded: Prodigal
[2023-06-30 15:09:23,018] [INFO] Task started: HMMsearch
[2023-06-30 15:09:23,018] [INFO] Running command: hmmsearch --tblout GCA_024694055.1_ASM2469405v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg140abe5c-a42d-4c56-b0c9-bd5ed54d940f/dqc_reference/reference_markers.hmm GCA_024694055.1_ASM2469405v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 15:09:23,270] [INFO] Task succeeded: HMMsearch
[2023-06-30 15:09:23,271] [INFO] Found 6/6 markers.
[2023-06-30 15:09:23,296] [INFO] Query marker FASTA was written to GCA_024694055.1_ASM2469405v1_genomic.fna/markers.fasta
[2023-06-30 15:09:23,296] [INFO] Task started: Blastn
[2023-06-30 15:09:23,296] [INFO] Running command: blastn -query GCA_024694055.1_ASM2469405v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg140abe5c-a42d-4c56-b0c9-bd5ed54d940f/dqc_reference/reference_markers.fasta -out GCA_024694055.1_ASM2469405v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 15:09:23,902] [INFO] Task succeeded: Blastn
[2023-06-30 15:09:23,906] [INFO] Selected 21 target genomes.
[2023-06-30 15:09:23,906] [INFO] Target genome list was writen to GCA_024694055.1_ASM2469405v1_genomic.fna/target_genomes.txt
[2023-06-30 15:09:23,911] [INFO] Task started: fastANI
[2023-06-30 15:09:23,911] [INFO] Running command: fastANI --query /var/lib/cwl/stga700688b-2fb9-4c36-b831-94ff253139b8/GCA_024694055.1_ASM2469405v1_genomic.fna.gz --refList GCA_024694055.1_ASM2469405v1_genomic.fna/target_genomes.txt --output GCA_024694055.1_ASM2469405v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 15:09:36,735] [INFO] Task succeeded: fastANI
[2023-06-30 15:09:36,736] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg140abe5c-a42d-4c56-b0c9-bd5ed54d940f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 15:09:36,736] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg140abe5c-a42d-4c56-b0c9-bd5ed54d940f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 15:09:36,739] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 15:09:36,739] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 15:09:36,739] [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
--------------------------------------------------------------------------------
[2023-06-30 15:09:36,741] [INFO] DFAST Taxonomy check result was written to GCA_024694055.1_ASM2469405v1_genomic.fna/tc_result.tsv
[2023-06-30 15:09:36,742] [INFO] ===== Taxonomy check completed =====
[2023-06-30 15:09:36,742] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 15:09:36,743] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg140abe5c-a42d-4c56-b0c9-bd5ed54d940f/dqc_reference/checkm_data
[2023-06-30 15:09:36,747] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 15:09:36,778] [INFO] Task started: CheckM
[2023-06-30 15:09:36,778] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024694055.1_ASM2469405v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024694055.1_ASM2469405v1_genomic.fna/checkm_input GCA_024694055.1_ASM2469405v1_genomic.fna/checkm_result
[2023-06-30 15:10:00,479] [INFO] Task succeeded: CheckM
[2023-06-30 15:10:00,481] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.32%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 15:10:00,503] [INFO] ===== Completeness check finished =====
[2023-06-30 15:10:00,503] [INFO] ===== Start GTDB Search =====
[2023-06-30 15:10:00,504] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024694055.1_ASM2469405v1_genomic.fna/markers.fasta)
[2023-06-30 15:10:00,504] [INFO] Task started: Blastn
[2023-06-30 15:10:00,504] [INFO] Running command: blastn -query GCA_024694055.1_ASM2469405v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg140abe5c-a42d-4c56-b0c9-bd5ed54d940f/dqc_reference/reference_markers_gtdb.fasta -out GCA_024694055.1_ASM2469405v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 15:10:01,383] [INFO] Task succeeded: Blastn
[2023-06-30 15:10:01,387] [INFO] Selected 18 target genomes.
[2023-06-30 15:10:01,387] [INFO] Target genome list was writen to GCA_024694055.1_ASM2469405v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 15:10:01,422] [INFO] Task started: fastANI
[2023-06-30 15:10:01,422] [INFO] Running command: fastANI --query /var/lib/cwl/stga700688b-2fb9-4c36-b831-94ff253139b8/GCA_024694055.1_ASM2469405v1_genomic.fna.gz --refList GCA_024694055.1_ASM2469405v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024694055.1_ASM2469405v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 15:10:08,576] [INFO] Task succeeded: fastANI
[2023-06-30 15:10:08,590] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 15:10:08,590] [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_017540355.1	s__UBA1712 sp017540355	78.5264	203	663	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1712	95.0	97.99	97.99	0.85	0.85	2	-
GCA_902778165.1	s__UBA1712 sp902778165	78.4944	224	663	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1712	95.0	97.58	97.58	0.88	0.88	2	-
GCA_905235845.1	s__UBA1712 sp905235845	78.0751	185	663	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1712	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902779505.1	s__UBA1712 sp902779505	77.5456	73	663	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1712	95.0	98.45	98.04	0.85	0.80	3	-
GCA_002393095.1	s__UBA1712 sp002393095	77.443	176	663	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1712	95.0	99.62	99.62	0.88	0.88	2	-
GCA_902789785.1	s__UBA1712 sp902789785	77.3857	65	663	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1712	95.0	97.67	97.20	0.85	0.79	3	-
GCA_016290615.1	s__UBA1712 sp016290615	77.0204	70	663	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1712	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018064425.1	s__UBA1712 sp018064425	76.8966	62	663	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1712	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 15:10:08,593] [INFO] GTDB search result was written to GCA_024694055.1_ASM2469405v1_genomic.fna/result_gtdb.tsv
[2023-06-30 15:10:08,593] [INFO] ===== GTDB Search completed =====
[2023-06-30 15:10:08,596] [INFO] DFAST_QC result json was written to GCA_024694055.1_ASM2469405v1_genomic.fna/dqc_result.json
[2023-06-30 15:10:08,596] [INFO] DFAST_QC completed!
[2023-06-30 15:10:08,596] [INFO] Total running time: 0h0m52s