[2023-06-05 02:12:29,350] [INFO] DFAST_QC pipeline started.
[2023-06-05 02:12:29,352] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 02:12:29,353] [INFO] DQC Reference Directory: /var/lib/cwl/stge63a49fc-4e21-445a-b87d-bfe14da6bce4/dqc_reference
[2023-06-05 02:12:30,925] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 02:12:30,926] [INFO] Task started: Prodigal
[2023-06-05 02:12:30,926] [INFO] Running command: gunzip -c /var/lib/cwl/stg322d65ce-f760-45bd-9a1e-7b9702b0d71e/GCA_934087265.1_ERR7737966_bin.113_genomic.fna.gz | prodigal -d GCA_934087265.1_ERR7737966_bin.113_genomic.fna/cds.fna -a GCA_934087265.1_ERR7737966_bin.113_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 02:12:32,808] [INFO] Task succeeded: Prodigal
[2023-06-05 02:12:32,809] [INFO] Task started: HMMsearch
[2023-06-05 02:12:32,809] [INFO] Running command: hmmsearch --tblout GCA_934087265.1_ERR7737966_bin.113_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge63a49fc-4e21-445a-b87d-bfe14da6bce4/dqc_reference/reference_markers.hmm GCA_934087265.1_ERR7737966_bin.113_genomic.fna/protein.faa > /dev/null
[2023-06-05 02:12:33,048] [INFO] Task succeeded: HMMsearch
[2023-06-05 02:12:33,049] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg322d65ce-f760-45bd-9a1e-7b9702b0d71e/GCA_934087265.1_ERR7737966_bin.113_genomic.fna.gz]
[2023-06-05 02:12:33,068] [INFO] Query marker FASTA was written to GCA_934087265.1_ERR7737966_bin.113_genomic.fna/markers.fasta
[2023-06-05 02:12:33,069] [INFO] Task started: Blastn
[2023-06-05 02:12:33,069] [INFO] Running command: blastn -query GCA_934087265.1_ERR7737966_bin.113_genomic.fna/markers.fasta -db /var/lib/cwl/stge63a49fc-4e21-445a-b87d-bfe14da6bce4/dqc_reference/reference_markers.fasta -out GCA_934087265.1_ERR7737966_bin.113_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:12:34,376] [INFO] Task succeeded: Blastn
[2023-06-05 02:12:34,381] [INFO] Selected 26 target genomes.
[2023-06-05 02:12:34,382] [INFO] Target genome list was writen to GCA_934087265.1_ERR7737966_bin.113_genomic.fna/target_genomes.txt
[2023-06-05 02:12:34,459] [INFO] Task started: fastANI
[2023-06-05 02:12:34,460] [INFO] Running command: fastANI --query /var/lib/cwl/stg322d65ce-f760-45bd-9a1e-7b9702b0d71e/GCA_934087265.1_ERR7737966_bin.113_genomic.fna.gz --refList GCA_934087265.1_ERR7737966_bin.113_genomic.fna/target_genomes.txt --output GCA_934087265.1_ERR7737966_bin.113_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 02:12:46,509] [INFO] Task succeeded: fastANI
[2023-06-05 02:12:46,510] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge63a49fc-4e21-445a-b87d-bfe14da6bce4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 02:12:46,510] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge63a49fc-4e21-445a-b87d-bfe14da6bce4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 02:12:46,517] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 02:12:46,517] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 02:12:46,517] [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
Clostridium thermobutyricum	strain=DSM 4928	GCA_002050515.1	29372	29372	type	True	74.664	50	418	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 02:12:46,519] [INFO] DFAST Taxonomy check result was written to GCA_934087265.1_ERR7737966_bin.113_genomic.fna/tc_result.tsv
[2023-06-05 02:12:46,520] [INFO] ===== Taxonomy check completed =====
[2023-06-05 02:12:46,520] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 02:12:46,521] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge63a49fc-4e21-445a-b87d-bfe14da6bce4/dqc_reference/checkm_data
[2023-06-05 02:12:46,522] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 02:12:46,542] [INFO] Task started: CheckM
[2023-06-05 02:12:46,543] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934087265.1_ERR7737966_bin.113_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934087265.1_ERR7737966_bin.113_genomic.fna/checkm_input GCA_934087265.1_ERR7737966_bin.113_genomic.fna/checkm_result
[2023-06-05 02:13:00,673] [INFO] Task succeeded: CheckM
[2023-06-05 02:13:00,675] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 02:13:00,691] [INFO] ===== Completeness check finished =====
[2023-06-05 02:13:00,691] [INFO] ===== Start GTDB Search =====
[2023-06-05 02:13:00,691] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934087265.1_ERR7737966_bin.113_genomic.fna/markers.fasta)
[2023-06-05 02:13:00,692] [INFO] Task started: Blastn
[2023-06-05 02:13:00,692] [INFO] Running command: blastn -query GCA_934087265.1_ERR7737966_bin.113_genomic.fna/markers.fasta -db /var/lib/cwl/stge63a49fc-4e21-445a-b87d-bfe14da6bce4/dqc_reference/reference_markers_gtdb.fasta -out GCA_934087265.1_ERR7737966_bin.113_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:13:01,550] [INFO] Task succeeded: Blastn
[2023-06-05 02:13:01,556] [INFO] Selected 18 target genomes.
[2023-06-05 02:13:01,556] [INFO] Target genome list was writen to GCA_934087265.1_ERR7737966_bin.113_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 02:13:01,561] [INFO] Task started: fastANI
[2023-06-05 02:13:01,561] [INFO] Running command: fastANI --query /var/lib/cwl/stg322d65ce-f760-45bd-9a1e-7b9702b0d71e/GCA_934087265.1_ERR7737966_bin.113_genomic.fna.gz --refList GCA_934087265.1_ERR7737966_bin.113_genomic.fna/target_genomes_gtdb.txt --output GCA_934087265.1_ERR7737966_bin.113_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 02:13:05,688] [INFO] Task succeeded: fastANI
[2023-06-05 02:13:05,704] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 02:13:05,704] [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_900760845.1	s__CAG-582 sp900760845	95.9945	332	418	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-582	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000435515.1	s__CAG-582 sp000435515	83.1746	263	418	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-582	95.0	97.28	96.56	0.85	0.81	4	-
GCA_017626405.1	s__CAG-582 sp017626405	77.9655	85	418	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-582	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588195.1	s__CAG-582 sp910588195	77.8203	114	418	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-582	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587065.1	s__CAG-582 sp910587065	77.6313	113	418	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-582	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577075.1	s__CAG-582 sp910577075	77.1117	84	418	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-582	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017411405.1	s__UMGS1124 sp017411405	76.9235	66	418	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS1124	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015059485.1	s__RUG14121 sp015059485	76.6184	59	418	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG14121	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000437355.1	s__Onthocola_B sp000437355	76.4363	54	418	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Onthocola_B	95.0	98.35	98.06	0.89	0.84	4	-
GCA_017441065.1	s__SIG200 sp017441065	76.2963	55	418	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__SIG200	95.0	97.98	97.98	0.82	0.82	2	-
GCA_017936845.1	s__UBA5026 sp017936845	76.1642	60	418	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5026	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902783345.1	s__CAG-533 sp902783345	76.1362	59	418	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-533	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002425325.1	s__UBA5578 sp002425325	76.1089	65	418	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5578	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 02:13:05,706] [INFO] GTDB search result was written to GCA_934087265.1_ERR7737966_bin.113_genomic.fna/result_gtdb.tsv
[2023-06-05 02:13:05,707] [INFO] ===== GTDB Search completed =====
[2023-06-05 02:13:05,710] [INFO] DFAST_QC result json was written to GCA_934087265.1_ERR7737966_bin.113_genomic.fna/dqc_result.json
[2023-06-05 02:13:05,710] [INFO] DFAST_QC completed!
[2023-06-05 02:13:05,710] [INFO] Total running time: 0h0m36s