[2023-03-17 03:11:36,308] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:11:36,308] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:11:36,309] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8d2f9be-0666-4592-910a-f9fd2f3df64c/dqc_reference
[2023-03-17 03:11:37,506] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:11:37,506] [INFO] Task started: Prodigal
[2023-03-17 03:11:37,506] [INFO] Running command: cat /var/lib/cwl/stg1d0cd82c-033c-4545-967d-291ebc500fa6/OceanDNA-b17188.fa | prodigal -d OceanDNA-b17188/cds.fna -a OceanDNA-b17188/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:11:51,539] [INFO] Task succeeded: Prodigal
[2023-03-17 03:11:51,540] [INFO] Task started: HMMsearch
[2023-03-17 03:11:51,540] [INFO] Running command: hmmsearch --tblout OceanDNA-b17188/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8d2f9be-0666-4592-910a-f9fd2f3df64c/dqc_reference/reference_markers.hmm OceanDNA-b17188/protein.faa > /dev/null
[2023-03-17 03:11:51,793] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:11:51,794] [INFO] Found 6/6 markers.
[2023-03-17 03:11:51,820] [INFO] Query marker FASTA was written to OceanDNA-b17188/markers.fasta
[2023-03-17 03:11:51,821] [INFO] Task started: Blastn
[2023-03-17 03:11:51,821] [INFO] Running command: blastn -query OceanDNA-b17188/markers.fasta -db /var/lib/cwl/stgc8d2f9be-0666-4592-910a-f9fd2f3df64c/dqc_reference/reference_markers.fasta -out OceanDNA-b17188/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:11:52,368] [INFO] Task succeeded: Blastn
[2023-03-17 03:11:52,369] [INFO] Selected 19 target genomes.
[2023-03-17 03:11:52,369] [INFO] Target genome list was writen to OceanDNA-b17188/target_genomes.txt
[2023-03-17 03:11:52,415] [INFO] Task started: fastANI
[2023-03-17 03:11:52,416] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d0cd82c-033c-4545-967d-291ebc500fa6/OceanDNA-b17188.fa --refList OceanDNA-b17188/target_genomes.txt --output OceanDNA-b17188/fastani_result.tsv --threads 1
[2023-03-17 03:12:08,352] [INFO] Task succeeded: fastANI
[2023-03-17 03:12:08,352] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8d2f9be-0666-4592-910a-f9fd2f3df64c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:12:08,353] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8d2f9be-0666-4592-910a-f9fd2f3df64c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:12:08,360] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:12:08,360] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 03:12:08,360] [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
Paenibacillus turicensis	strain=DSM 14349	GCA_017873435.1	160487	160487	type	True	89.0668	784	844	95	below_threshold
Paenibacillus sanguinis	strain=DSM 16941	GCA_000374825.1	225906	225906	type	True	78.0634	76	844	95	below_threshold
Paenibacillus senegalimassiliensis	strain=SIT18	GCA_001486585.1	1737426	1737426	type	True	77.9838	77	844	95	below_threshold
Paenibacillus segetis	strain=CGMCC 1.12769	GCA_014639155.1	1325360	1325360	type	True	77.6936	128	844	95	below_threshold
Paenibacillus anaericanus	strain=DSM 15890	GCA_003994475.1	170367	170367	type	True	77.366	124	844	95	below_threshold
Paenibacillus barengoltzii	strain=NBRC 101215	GCA_004000745.1	343517	343517	type	True	77.1058	61	844	95	below_threshold
Paenibacillus ottowii	strain=MS2379	GCA_006874425.1	2315729	2315729	type	True	77.0548	52	844	95	below_threshold
Paenibacillus shirakamiensis	strain=DSM 26806	GCA_017874255.1	1265935	1265935	type	True	76.7789	68	844	95	below_threshold
Paenibacillus nuruki	strain=TI45-13ar	GCA_001721045.1	1886670	1886670	type	True	76.6682	61	844	95	below_threshold
Paenibacillus gallinarum	strain=Sa2BVA9	GCA_014836635.1	2762232	2762232	type	True	76.4803	62	844	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 03:12:08,361] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17188/tc_result.tsv
[2023-03-17 03:12:08,361] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:12:08,361] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:12:08,361] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8d2f9be-0666-4592-910a-f9fd2f3df64c/dqc_reference/checkm_data
[2023-03-17 03:12:08,362] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:12:08,372] [INFO] Task started: CheckM
[2023-03-17 03:12:08,372] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17188/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17188/checkm_input OceanDNA-b17188/checkm_result
[2023-03-17 03:12:46,852] [INFO] Task succeeded: CheckM
[2023-03-17 03:12:46,852] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.95%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 03:12:46,855] [INFO] ===== Completeness check finished =====
[2023-03-17 03:12:46,855] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:12:46,855] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17188/markers.fasta)
[2023-03-17 03:12:46,856] [INFO] Task started: Blastn
[2023-03-17 03:12:46,856] [INFO] Running command: blastn -query OceanDNA-b17188/markers.fasta -db /var/lib/cwl/stgc8d2f9be-0666-4592-910a-f9fd2f3df64c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17188/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:12:47,596] [INFO] Task succeeded: Blastn
[2023-03-17 03:12:47,597] [INFO] Selected 24 target genomes.
[2023-03-17 03:12:47,597] [INFO] Target genome list was writen to OceanDNA-b17188/target_genomes_gtdb.txt
[2023-03-17 03:12:47,723] [INFO] Task started: fastANI
[2023-03-17 03:12:47,723] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d0cd82c-033c-4545-967d-291ebc500fa6/OceanDNA-b17188.fa --refList OceanDNA-b17188/target_genomes_gtdb.txt --output OceanDNA-b17188/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:13:09,839] [INFO] Task succeeded: fastANI
[2023-03-17 03:13:09,848] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 03:13:09,848] [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
GCF_017873435.1	s__Paenibacillus_A turicensis	89.0668	784	844	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374825.1	s__Paenibacillus_A sanguinis	78.0634	76	844	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001486585.1	s__Paenibacillus_A senegalimassiliensis	77.9838	77	844	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014639155.1	s__Paenibacillus_A segetis	77.6936	128	844	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337355.1	s__Paenibacillus_A phaseoli	77.42	81	844	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003994475.1	s__Paenibacillus_A anaericanus	77.366	124	844	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005217525.1	s__Paenibacillus terrae_C	77.2514	51	844	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003991425.1	s__Paenibacillus_A lutimineralis	77.1117	75	844	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006874425.1	s__Paenibacillus ottowii	76.9725	52	844	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.10	96.87	0.92	0.88	5	-
GCF_002240415.1	s__Paenibacillus kribbensis	76.9076	54	844	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.18	95.13	0.90	0.86	4	-
GCF_000159955.1	s__Paenibacillus_A sp000159955	76.8669	67	844	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000237325.1	s__Paenibacillus polymyxa_C	76.7871	59	844	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.50	97.87	0.93	0.89	15	-
GCF_016908805.1	s__Paenibacillus_J nicotianae	76.676	50	844	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_J	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001721045.1	s__Paenibacillus_J nuruki	76.6682	61	844	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_J	95.0	98.40	98.40	0.93	0.93	2	-
GCF_014836635.1	s__Paenibacillus sp014836635	76.4803	62	844	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 03:13:09,848] [INFO] GTDB search result was written to OceanDNA-b17188/result_gtdb.tsv
[2023-03-17 03:13:09,848] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:13:09,849] [INFO] DFAST_QC result json was written to OceanDNA-b17188/dqc_result.json
[2023-03-17 03:13:09,850] [INFO] DFAST_QC completed!
[2023-03-17 03:13:09,850] [INFO] Total running time: 0h1m34s