[2023-06-05 00:38:10,121] [INFO] DFAST_QC pipeline started.
[2023-06-05 00:38:10,127] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 00:38:10,128] [INFO] DQC Reference Directory: /var/lib/cwl/stga871fc1e-f335-4fbe-9465-b76414b611c9/dqc_reference
[2023-06-05 00:38:11,526] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 00:38:11,527] [INFO] Task started: Prodigal
[2023-06-05 00:38:11,528] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa75f60f-3331-4130-9866-8f48e6ad3213/GCA_934149125.1_ERR7746030_bin.173_genomic.fna.gz | prodigal -d GCA_934149125.1_ERR7746030_bin.173_genomic.fna/cds.fna -a GCA_934149125.1_ERR7746030_bin.173_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 00:38:14,561] [INFO] Task succeeded: Prodigal
[2023-06-05 00:38:14,562] [INFO] Task started: HMMsearch
[2023-06-05 00:38:14,562] [INFO] Running command: hmmsearch --tblout GCA_934149125.1_ERR7746030_bin.173_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga871fc1e-f335-4fbe-9465-b76414b611c9/dqc_reference/reference_markers.hmm GCA_934149125.1_ERR7746030_bin.173_genomic.fna/protein.faa > /dev/null
[2023-06-05 00:38:14,798] [INFO] Task succeeded: HMMsearch
[2023-06-05 00:38:14,800] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfa75f60f-3331-4130-9866-8f48e6ad3213/GCA_934149125.1_ERR7746030_bin.173_genomic.fna.gz]
[2023-06-05 00:38:14,820] [INFO] Query marker FASTA was written to GCA_934149125.1_ERR7746030_bin.173_genomic.fna/markers.fasta
[2023-06-05 00:38:14,821] [INFO] Task started: Blastn
[2023-06-05 00:38:14,821] [INFO] Running command: blastn -query GCA_934149125.1_ERR7746030_bin.173_genomic.fna/markers.fasta -db /var/lib/cwl/stga871fc1e-f335-4fbe-9465-b76414b611c9/dqc_reference/reference_markers.fasta -out GCA_934149125.1_ERR7746030_bin.173_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:38:15,427] [INFO] Task succeeded: Blastn
[2023-06-05 00:38:15,431] [INFO] Selected 20 target genomes.
[2023-06-05 00:38:15,431] [INFO] Target genome list was writen to GCA_934149125.1_ERR7746030_bin.173_genomic.fna/target_genomes.txt
[2023-06-05 00:38:15,432] [INFO] Task started: fastANI
[2023-06-05 00:38:15,433] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa75f60f-3331-4130-9866-8f48e6ad3213/GCA_934149125.1_ERR7746030_bin.173_genomic.fna.gz --refList GCA_934149125.1_ERR7746030_bin.173_genomic.fna/target_genomes.txt --output GCA_934149125.1_ERR7746030_bin.173_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 00:38:25,076] [INFO] Task succeeded: fastANI
[2023-06-05 00:38:25,076] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga871fc1e-f335-4fbe-9465-b76414b611c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 00:38:25,076] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga871fc1e-f335-4fbe-9465-b76414b611c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 00:38:25,087] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 00:38:25,087] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 00:38:25,088] [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 moniliforme	strain=DSM 3984	GCA_017873235.1	39489	39489	type	True	74.9606	61	553	95	below_threshold
Clostridium thermobutyricum	strain=DSM 4928	GCA_002050515.1	29372	29372	type	True	74.9417	83	553	95	below_threshold
Clostridium sporogenes	strain=NCTC13020	GCA_900461305.1	1509	1509	type	True	74.9169	61	553	95	below_threshold
Clostridium sporogenes	strain=DSM 795	GCA_001020205.1	1509	1509	type	True	74.9087	62	553	95	below_threshold
Clostridium muellerianum	strain=P21	GCA_012926525.1	2716538	2716538	type	True	74.908	60	553	95	below_threshold
Clostridium sporogenes	strain=DSM 795	GCA_000685115.1	1509	1509	type	True	74.9004	63	553	95	below_threshold
Clostridium sporogenes	strain=NCIMB 10696	GCA_000973705.1	1509	1509	type	True	74.9004	63	553	95	below_threshold
Clostridium hydrogenum	strain=CUEA01	GCA_021432385.1	2855764	2855764	type	True	74.8354	54	553	95	below_threshold
Fusobacterium canifelinum	strain=FDAARGOS_1126	GCA_016724785.1	285729	285729	type	True	74.7117	63	553	95	below_threshold
Fusobacterium massiliense	strain=Marseille-P2749	GCA_900095705.1	1852365	1852365	type	True	74.6485	52	553	95	below_threshold
Clostridium niameyense	strain=MT5	GCA_001243045.1	1622073	1622073	type	True	74.6267	52	553	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 00:38:25,090] [INFO] DFAST Taxonomy check result was written to GCA_934149125.1_ERR7746030_bin.173_genomic.fna/tc_result.tsv
[2023-06-05 00:38:25,090] [INFO] ===== Taxonomy check completed =====
[2023-06-05 00:38:25,090] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 00:38:25,091] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga871fc1e-f335-4fbe-9465-b76414b611c9/dqc_reference/checkm_data
[2023-06-05 00:38:25,092] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 00:38:25,116] [INFO] Task started: CheckM
[2023-06-05 00:38:25,116] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934149125.1_ERR7746030_bin.173_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934149125.1_ERR7746030_bin.173_genomic.fna/checkm_input GCA_934149125.1_ERR7746030_bin.173_genomic.fna/checkm_result
[2023-06-05 00:38:42,777] [INFO] Task succeeded: CheckM
[2023-06-05 00:38:42,779] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 00:38:42,799] [INFO] ===== Completeness check finished =====
[2023-06-05 00:38:42,799] [INFO] ===== Start GTDB Search =====
[2023-06-05 00:38:42,800] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934149125.1_ERR7746030_bin.173_genomic.fna/markers.fasta)
[2023-06-05 00:38:42,800] [INFO] Task started: Blastn
[2023-06-05 00:38:42,800] [INFO] Running command: blastn -query GCA_934149125.1_ERR7746030_bin.173_genomic.fna/markers.fasta -db /var/lib/cwl/stga871fc1e-f335-4fbe-9465-b76414b611c9/dqc_reference/reference_markers_gtdb.fasta -out GCA_934149125.1_ERR7746030_bin.173_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:38:43,549] [INFO] Task succeeded: Blastn
[2023-06-05 00:38:43,553] [INFO] Selected 8 target genomes.
[2023-06-05 00:38:43,553] [INFO] Target genome list was writen to GCA_934149125.1_ERR7746030_bin.173_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 00:38:43,554] [INFO] Task started: fastANI
[2023-06-05 00:38:43,554] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa75f60f-3331-4130-9866-8f48e6ad3213/GCA_934149125.1_ERR7746030_bin.173_genomic.fna.gz --refList GCA_934149125.1_ERR7746030_bin.173_genomic.fna/target_genomes_gtdb.txt --output GCA_934149125.1_ERR7746030_bin.173_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 00:38:46,306] [INFO] Task succeeded: fastANI
[2023-06-05 00:38:46,314] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 00:38:46,314] [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_003525075.1	s__CAG-269 sp003525075	98.1945	457	553	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	conclusive
GCA_001915995.1	s__CAG-269 sp001915995	93.6418	386	553	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_001916055.1	s__CAG-269 sp001916055	81.3117	249	553	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.37	97.96	0.88	0.86	4	-
GCA_900555615.1	s__CAG-269 sp900555615	81.2669	251	553	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	97.95	97.78	0.76	0.74	3	-
GCA_017409455.1	s__CAG-269 sp017409455	80.584	219	553	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_900551615.1	s__CAG-269 sp900551615	79.0029	200	553	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.20	98.20	0.87	0.87	2	-
GCA_904384245.1	s__CAG-269 sp904384245	78.4686	192	553	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_904387305.1	s__CAG-269 sp904387305	78.0954	185	553	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	-
--------------------------------------------------------------------------------
[2023-06-05 00:38:46,316] [INFO] GTDB search result was written to GCA_934149125.1_ERR7746030_bin.173_genomic.fna/result_gtdb.tsv
[2023-06-05 00:38:46,316] [INFO] ===== GTDB Search completed =====
[2023-06-05 00:38:46,319] [INFO] DFAST_QC result json was written to GCA_934149125.1_ERR7746030_bin.173_genomic.fna/dqc_result.json
[2023-06-05 00:38:46,320] [INFO] DFAST_QC completed!
[2023-06-05 00:38:46,320] [INFO] Total running time: 0h0m36s