[2023-06-16 21:33:15,987] [INFO] DFAST_QC pipeline started.
[2023-06-16 21:33:15,989] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 21:33:15,990] [INFO] DQC Reference Directory: /var/lib/cwl/stg9594505c-1aea-4c63-ad64-0e938376fca9/dqc_reference
[2023-06-16 21:33:17,167] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 21:33:17,168] [INFO] Task started: Prodigal
[2023-06-16 21:33:17,168] [INFO] Running command: gunzip -c /var/lib/cwl/stg53c4b81b-b7f4-4bf4-802c-9589f13aacca/GCA_905201515.1_SRR2912776-mag-bin.15_genomic.fna.gz | prodigal -d GCA_905201515.1_SRR2912776-mag-bin.15_genomic.fna/cds.fna -a GCA_905201515.1_SRR2912776-mag-bin.15_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 21:33:18,877] [INFO] Task succeeded: Prodigal
[2023-06-16 21:33:18,877] [INFO] Task started: HMMsearch
[2023-06-16 21:33:18,877] [INFO] Running command: hmmsearch --tblout GCA_905201515.1_SRR2912776-mag-bin.15_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9594505c-1aea-4c63-ad64-0e938376fca9/dqc_reference/reference_markers.hmm GCA_905201515.1_SRR2912776-mag-bin.15_genomic.fna/protein.faa > /dev/null
[2023-06-16 21:33:19,064] [INFO] Task succeeded: HMMsearch
[2023-06-16 21:33:19,065] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg53c4b81b-b7f4-4bf4-802c-9589f13aacca/GCA_905201515.1_SRR2912776-mag-bin.15_genomic.fna.gz]
[2023-06-16 21:33:19,083] [INFO] Query marker FASTA was written to GCA_905201515.1_SRR2912776-mag-bin.15_genomic.fna/markers.fasta
[2023-06-16 21:33:19,083] [INFO] Task started: Blastn
[2023-06-16 21:33:19,084] [INFO] Running command: blastn -query GCA_905201515.1_SRR2912776-mag-bin.15_genomic.fna/markers.fasta -db /var/lib/cwl/stg9594505c-1aea-4c63-ad64-0e938376fca9/dqc_reference/reference_markers.fasta -out GCA_905201515.1_SRR2912776-mag-bin.15_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 21:33:19,548] [INFO] Task succeeded: Blastn
[2023-06-16 21:33:19,551] [INFO] Selected 11 target genomes.
[2023-06-16 21:33:19,552] [INFO] Target genome list was writen to GCA_905201515.1_SRR2912776-mag-bin.15_genomic.fna/target_genomes.txt
[2023-06-16 21:33:19,556] [INFO] Task started: fastANI
[2023-06-16 21:33:19,556] [INFO] Running command: fastANI --query /var/lib/cwl/stg53c4b81b-b7f4-4bf4-802c-9589f13aacca/GCA_905201515.1_SRR2912776-mag-bin.15_genomic.fna.gz --refList GCA_905201515.1_SRR2912776-mag-bin.15_genomic.fna/target_genomes.txt --output GCA_905201515.1_SRR2912776-mag-bin.15_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 21:33:24,066] [INFO] Task succeeded: fastANI
[2023-06-16 21:33:24,066] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9594505c-1aea-4c63-ad64-0e938376fca9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 21:33:24,066] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9594505c-1aea-4c63-ad64-0e938376fca9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 21:33:24,068] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 21:33:24,068] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-16 21:33:24,068] [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
--------------------------------------------------------------------------------
[2023-06-16 21:33:24,070] [INFO] DFAST Taxonomy check result was written to GCA_905201515.1_SRR2912776-mag-bin.15_genomic.fna/tc_result.tsv
[2023-06-16 21:33:24,071] [INFO] ===== Taxonomy check completed =====
[2023-06-16 21:33:24,071] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 21:33:24,071] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9594505c-1aea-4c63-ad64-0e938376fca9/dqc_reference/checkm_data
[2023-06-16 21:33:24,074] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 21:33:24,090] [INFO] Task started: CheckM
[2023-06-16 21:33:24,090] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905201515.1_SRR2912776-mag-bin.15_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905201515.1_SRR2912776-mag-bin.15_genomic.fna/checkm_input GCA_905201515.1_SRR2912776-mag-bin.15_genomic.fna/checkm_result
[2023-06-16 21:33:37,198] [INFO] Task succeeded: CheckM
[2023-06-16 21:33:37,199] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.61%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 21:33:37,214] [INFO] ===== Completeness check finished =====
[2023-06-16 21:33:37,214] [INFO] ===== Start GTDB Search =====
[2023-06-16 21:33:37,215] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905201515.1_SRR2912776-mag-bin.15_genomic.fna/markers.fasta)
[2023-06-16 21:33:37,215] [INFO] Task started: Blastn
[2023-06-16 21:33:37,215] [INFO] Running command: blastn -query GCA_905201515.1_SRR2912776-mag-bin.15_genomic.fna/markers.fasta -db /var/lib/cwl/stg9594505c-1aea-4c63-ad64-0e938376fca9/dqc_reference/reference_markers_gtdb.fasta -out GCA_905201515.1_SRR2912776-mag-bin.15_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 21:33:37,646] [INFO] Task succeeded: Blastn
[2023-06-16 21:33:37,650] [INFO] Selected 15 target genomes.
[2023-06-16 21:33:37,650] [INFO] Target genome list was writen to GCA_905201515.1_SRR2912776-mag-bin.15_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 21:33:37,681] [INFO] Task started: fastANI
[2023-06-16 21:33:37,681] [INFO] Running command: fastANI --query /var/lib/cwl/stg53c4b81b-b7f4-4bf4-802c-9589f13aacca/GCA_905201515.1_SRR2912776-mag-bin.15_genomic.fna.gz --refList GCA_905201515.1_SRR2912776-mag-bin.15_genomic.fna/target_genomes_gtdb.txt --output GCA_905201515.1_SRR2912776-mag-bin.15_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 21:33:41,974] [INFO] Task succeeded: fastANI
[2023-06-16 21:33:41,982] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 21:33:41,982] [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_900557475.1	s__CAG-793 sp900557475	100.0	250	254	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-793	95.0	100.00	100.00	0.98	0.98	2	conclusive
GCA_000433915.1	s__CAG-793 sp000433915	78.0734	66	254	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-793	95.0	98.87	98.80	0.92	0.89	3	-
GCA_003507395.1	s__CAG-273 sp003507395	76.7537	53	254	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-273	95.0	99.04	98.89	0.89	0.87	5	-
GCA_904420285.1	s__CAG-273 sp904420285	76.7259	59	254	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-273	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003525075.1	s__CAG-269 sp003525075	76.5849	62	254	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	99.02	98.89	0.90	0.88	5	-
GCA_001915995.1	s__CAG-269 sp001915995	76.5786	66	254	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900753245.1	s__UMGS1663 sp900753245	76.5336	54	254	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__UMGS1663	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 21:33:41,986] [INFO] GTDB search result was written to GCA_905201515.1_SRR2912776-mag-bin.15_genomic.fna/result_gtdb.tsv
[2023-06-16 21:33:41,987] [INFO] ===== GTDB Search completed =====
[2023-06-16 21:33:41,989] [INFO] DFAST_QC result json was written to GCA_905201515.1_SRR2912776-mag-bin.15_genomic.fna/dqc_result.json
[2023-06-16 21:33:41,990] [INFO] DFAST_QC completed!
[2023-06-16 21:33:41,990] [INFO] Total running time: 0h0m26s