[2023-06-27 11:42:27,438] [INFO] DFAST_QC pipeline started.
[2023-06-27 11:42:27,444] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 11:42:27,444] [INFO] DQC Reference Directory: /var/lib/cwl/stg08b4b7ef-74e9-4201-a52e-9795ca7d2706/dqc_reference
[2023-06-27 11:42:28,623] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 11:42:28,624] [INFO] Task started: Prodigal
[2023-06-27 11:42:28,624] [INFO] Running command: gunzip -c /var/lib/cwl/stgb69812a1-0b44-43bf-bdff-e998419cbc26/GCA_002431815.1_ASM243181v1_genomic.fna.gz | prodigal -d GCA_002431815.1_ASM243181v1_genomic.fna/cds.fna -a GCA_002431815.1_ASM243181v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 11:42:33,506] [INFO] Task succeeded: Prodigal
[2023-06-27 11:42:33,506] [INFO] Task started: HMMsearch
[2023-06-27 11:42:33,506] [INFO] Running command: hmmsearch --tblout GCA_002431815.1_ASM243181v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg08b4b7ef-74e9-4201-a52e-9795ca7d2706/dqc_reference/reference_markers.hmm GCA_002431815.1_ASM243181v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 11:42:33,667] [INFO] Task succeeded: HMMsearch
[2023-06-27 11:42:33,668] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgb69812a1-0b44-43bf-bdff-e998419cbc26/GCA_002431815.1_ASM243181v1_genomic.fna.gz]
[2023-06-27 11:42:33,701] [INFO] Query marker FASTA was written to GCA_002431815.1_ASM243181v1_genomic.fna/markers.fasta
[2023-06-27 11:42:33,702] [INFO] Task started: Blastn
[2023-06-27 11:42:33,702] [INFO] Running command: blastn -query GCA_002431815.1_ASM243181v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08b4b7ef-74e9-4201-a52e-9795ca7d2706/dqc_reference/reference_markers.fasta -out GCA_002431815.1_ASM243181v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:42:34,220] [INFO] Task succeeded: Blastn
[2023-06-27 11:42:34,223] [INFO] Selected 15 target genomes.
[2023-06-27 11:42:34,223] [INFO] Target genome list was writen to GCA_002431815.1_ASM243181v1_genomic.fna/target_genomes.txt
[2023-06-27 11:42:34,226] [INFO] Task started: fastANI
[2023-06-27 11:42:34,226] [INFO] Running command: fastANI --query /var/lib/cwl/stgb69812a1-0b44-43bf-bdff-e998419cbc26/GCA_002431815.1_ASM243181v1_genomic.fna.gz --refList GCA_002431815.1_ASM243181v1_genomic.fna/target_genomes.txt --output GCA_002431815.1_ASM243181v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 11:42:43,073] [INFO] Task succeeded: fastANI
[2023-06-27 11:42:43,073] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg08b4b7ef-74e9-4201-a52e-9795ca7d2706/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 11:42:43,073] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg08b4b7ef-74e9-4201-a52e-9795ca7d2706/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 11:42:43,076] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 11:42:43,076] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 11:42:43,076] [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
--------------------------------------------------------------------------------
[2023-06-27 11:42:43,086] [INFO] DFAST Taxonomy check result was written to GCA_002431815.1_ASM243181v1_genomic.fna/tc_result.tsv
[2023-06-27 11:42:43,087] [INFO] ===== Taxonomy check completed =====
[2023-06-27 11:42:43,087] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 11:42:43,087] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg08b4b7ef-74e9-4201-a52e-9795ca7d2706/dqc_reference/checkm_data
[2023-06-27 11:42:43,090] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 11:42:43,121] [INFO] Task started: CheckM
[2023-06-27 11:42:43,122] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002431815.1_ASM243181v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002431815.1_ASM243181v1_genomic.fna/checkm_input GCA_002431815.1_ASM243181v1_genomic.fna/checkm_result
[2023-06-27 11:43:03,196] [INFO] Task succeeded: CheckM
[2023-06-27 11:43:03,197] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 49.25%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 11:43:03,215] [INFO] ===== Completeness check finished =====
[2023-06-27 11:43:03,215] [INFO] ===== Start GTDB Search =====
[2023-06-27 11:43:03,215] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002431815.1_ASM243181v1_genomic.fna/markers.fasta)
[2023-06-27 11:43:03,216] [INFO] Task started: Blastn
[2023-06-27 11:43:03,216] [INFO] Running command: blastn -query GCA_002431815.1_ASM243181v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08b4b7ef-74e9-4201-a52e-9795ca7d2706/dqc_reference/reference_markers_gtdb.fasta -out GCA_002431815.1_ASM243181v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:43:03,799] [INFO] Task succeeded: Blastn
[2023-06-27 11:43:03,802] [INFO] Selected 7 target genomes.
[2023-06-27 11:43:03,802] [INFO] Target genome list was writen to GCA_002431815.1_ASM243181v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 11:43:03,839] [INFO] Task started: fastANI
[2023-06-27 11:43:03,839] [INFO] Running command: fastANI --query /var/lib/cwl/stgb69812a1-0b44-43bf-bdff-e998419cbc26/GCA_002431815.1_ASM243181v1_genomic.fna.gz --refList GCA_002431815.1_ASM243181v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002431815.1_ASM243181v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 11:43:06,846] [INFO] Task succeeded: fastANI
[2023-06-27 11:43:06,853] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 11:43:06,854] [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_002404605.1	s__UBA738 sp002404605	99.7329	500	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA738	95.0	99.68	99.62	0.91	0.89	3	conclusive
GCA_003522945.1	s__UBA738 sp003522945	91.3287	341	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA738	95.0	97.42	97.25	0.82	0.69	7	-
GCA_004557735.1	s__UBA738 sp004557735	89.5562	436	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA738	95.0	96.30	95.55	0.89	0.83	10	-
GCA_900763675.1	s__UBA738 sp900763675	86.0564	389	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA738	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017411265.1	s__UBA738 sp017411265	78.2105	131	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA738	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017541825.1	s__UBA738 sp017541825	77.8787	142	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA738	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017455685.1	s__UBA738 sp017455685	77.6199	104	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA738	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 11:43:06,856] [INFO] GTDB search result was written to GCA_002431815.1_ASM243181v1_genomic.fna/result_gtdb.tsv
[2023-06-27 11:43:06,856] [INFO] ===== GTDB Search completed =====
[2023-06-27 11:43:06,859] [INFO] DFAST_QC result json was written to GCA_002431815.1_ASM243181v1_genomic.fna/dqc_result.json
[2023-06-27 11:43:06,860] [INFO] DFAST_QC completed!
[2023-06-27 11:43:06,860] [INFO] Total running time: 0h0m39s