[2023-06-28 00:33:37,381] [INFO] DFAST_QC pipeline started.
[2023-06-28 00:33:37,386] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 00:33:37,387] [INFO] DQC Reference Directory: /var/lib/cwl/stg6974b88b-d20b-4cfa-a41c-8d6fa244e57d/dqc_reference
[2023-06-28 00:33:38,692] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 00:33:38,693] [INFO] Task started: Prodigal
[2023-06-28 00:33:38,693] [INFO] Running command: gunzip -c /var/lib/cwl/stg03349f89-c1bd-447f-a605-6a64f00d546c/GCA_017652425.1_ASM1765242v1_genomic.fna.gz | prodigal -d GCA_017652425.1_ASM1765242v1_genomic.fna/cds.fna -a GCA_017652425.1_ASM1765242v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 00:33:42,658] [INFO] Task succeeded: Prodigal
[2023-06-28 00:33:42,658] [INFO] Task started: HMMsearch
[2023-06-28 00:33:42,659] [INFO] Running command: hmmsearch --tblout GCA_017652425.1_ASM1765242v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6974b88b-d20b-4cfa-a41c-8d6fa244e57d/dqc_reference/reference_markers.hmm GCA_017652425.1_ASM1765242v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 00:33:42,890] [INFO] Task succeeded: HMMsearch
[2023-06-28 00:33:42,892] [INFO] Found 6/6 markers.
[2023-06-28 00:33:42,921] [INFO] Query marker FASTA was written to GCA_017652425.1_ASM1765242v1_genomic.fna/markers.fasta
[2023-06-28 00:33:42,922] [INFO] Task started: Blastn
[2023-06-28 00:33:42,922] [INFO] Running command: blastn -query GCA_017652425.1_ASM1765242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6974b88b-d20b-4cfa-a41c-8d6fa244e57d/dqc_reference/reference_markers.fasta -out GCA_017652425.1_ASM1765242v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:33:43,518] [INFO] Task succeeded: Blastn
[2023-06-28 00:33:43,523] [INFO] Selected 42 target genomes.
[2023-06-28 00:33:43,523] [INFO] Target genome list was writen to GCA_017652425.1_ASM1765242v1_genomic.fna/target_genomes.txt
[2023-06-28 00:33:43,529] [INFO] Task started: fastANI
[2023-06-28 00:33:43,529] [INFO] Running command: fastANI --query /var/lib/cwl/stg03349f89-c1bd-447f-a605-6a64f00d546c/GCA_017652425.1_ASM1765242v1_genomic.fna.gz --refList GCA_017652425.1_ASM1765242v1_genomic.fna/target_genomes.txt --output GCA_017652425.1_ASM1765242v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 00:34:11,704] [INFO] Task succeeded: fastANI
[2023-06-28 00:34:11,705] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6974b88b-d20b-4cfa-a41c-8d6fa244e57d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 00:34:11,705] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6974b88b-d20b-4cfa-a41c-8d6fa244e57d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 00:34:11,707] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 00:34:11,707] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 00:34:11,707] [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 00:34:11,710] [INFO] DFAST Taxonomy check result was written to GCA_017652425.1_ASM1765242v1_genomic.fna/tc_result.tsv
[2023-06-28 00:34:11,710] [INFO] ===== Taxonomy check completed =====
[2023-06-28 00:34:11,711] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 00:34:11,711] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6974b88b-d20b-4cfa-a41c-8d6fa244e57d/dqc_reference/checkm_data
[2023-06-28 00:34:11,715] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 00:34:11,740] [INFO] Task started: CheckM
[2023-06-28 00:34:11,741] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017652425.1_ASM1765242v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017652425.1_ASM1765242v1_genomic.fna/checkm_input GCA_017652425.1_ASM1765242v1_genomic.fna/checkm_result
[2023-06-28 00:34:30,493] [INFO] Task succeeded: CheckM
[2023-06-28 00:34:30,495] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.37%
Contamintation: 8.33%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-28 00:34:30,524] [INFO] ===== Completeness check finished =====
[2023-06-28 00:34:30,524] [INFO] ===== Start GTDB Search =====
[2023-06-28 00:34:30,524] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017652425.1_ASM1765242v1_genomic.fna/markers.fasta)
[2023-06-28 00:34:30,525] [INFO] Task started: Blastn
[2023-06-28 00:34:30,525] [INFO] Running command: blastn -query GCA_017652425.1_ASM1765242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6974b88b-d20b-4cfa-a41c-8d6fa244e57d/dqc_reference/reference_markers_gtdb.fasta -out GCA_017652425.1_ASM1765242v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:34:31,350] [INFO] Task succeeded: Blastn
[2023-06-28 00:34:31,354] [INFO] Selected 13 target genomes.
[2023-06-28 00:34:31,354] [INFO] Target genome list was writen to GCA_017652425.1_ASM1765242v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 00:34:31,431] [INFO] Task started: fastANI
[2023-06-28 00:34:31,432] [INFO] Running command: fastANI --query /var/lib/cwl/stg03349f89-c1bd-447f-a605-6a64f00d546c/GCA_017652425.1_ASM1765242v1_genomic.fna.gz --refList GCA_017652425.1_ASM1765242v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017652425.1_ASM1765242v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 00:34:35,824] [INFO] Task succeeded: fastANI
[2023-06-28 00:34:35,836] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 00:34:35,836] [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_904502175.1	s__RUG420 sp904502175	97.4749	180	270	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__RUG420	95.0	100.00	100.00	0.98	0.98	2	conclusive
GCA_900317985.1	s__RUG420 sp900317985	84.4626	203	270	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__RUG420	95.0	99.01	98.76	0.89	0.86	49	-
GCA_017433225.1	s__RUG420 sp017433225	84.4251	210	270	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__RUG420	95.0	96.27	96.19	0.87	0.81	5	-
GCA_017461005.1	s__RUG420 sp017461005	83.9673	204	270	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__RUG420	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900317085.1	s__RUG420 sp900317085	83.9437	194	270	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__RUG420	95.0	98.92	97.74	0.88	0.83	42	-
GCA_017614275.1	s__RUG420 sp017614275	82.9298	129	270	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__RUG420	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017476565.1	s__RUG420 sp017476565	81.6566	143	270	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__RUG420	95.0	98.44	98.44	0.71	0.71	2	-
--------------------------------------------------------------------------------
[2023-06-28 00:34:35,838] [INFO] GTDB search result was written to GCA_017652425.1_ASM1765242v1_genomic.fna/result_gtdb.tsv
[2023-06-28 00:34:35,839] [INFO] ===== GTDB Search completed =====
[2023-06-28 00:34:35,842] [INFO] DFAST_QC result json was written to GCA_017652425.1_ASM1765242v1_genomic.fna/dqc_result.json
[2023-06-28 00:34:35,842] [INFO] DFAST_QC completed!
[2023-06-28 00:34:35,842] [INFO] Total running time: 0h0m58s