[2023-03-18 10:32:24,478] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:32:24,478] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:32:24,478] [INFO] DQC Reference Directory: /var/lib/cwl/stg7340d679-bdd3-4366-aa40-bc1e5aa65c81/dqc_reference
[2023-03-18 10:32:25,616] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:32:25,617] [INFO] Task started: Prodigal
[2023-03-18 10:32:25,617] [INFO] Running command: cat /var/lib/cwl/stg33c1a284-1531-4310-afa1-b51a02d68a76/OceanDNA-b38.fa | prodigal -d OceanDNA-b38/cds.fna -a OceanDNA-b38/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:32:53,071] [INFO] Task succeeded: Prodigal
[2023-03-18 10:32:53,071] [INFO] Task started: HMMsearch
[2023-03-18 10:32:53,071] [INFO] Running command: hmmsearch --tblout OceanDNA-b38/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7340d679-bdd3-4366-aa40-bc1e5aa65c81/dqc_reference/reference_markers.hmm OceanDNA-b38/protein.faa > /dev/null
[2023-03-18 10:32:53,294] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:32:53,294] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg33c1a284-1531-4310-afa1-b51a02d68a76/OceanDNA-b38.fa]
[2023-03-18 10:32:53,326] [INFO] Query marker FASTA was written to OceanDNA-b38/markers.fasta
[2023-03-18 10:32:53,327] [INFO] Task started: Blastn
[2023-03-18 10:32:53,328] [INFO] Running command: blastn -query OceanDNA-b38/markers.fasta -db /var/lib/cwl/stg7340d679-bdd3-4366-aa40-bc1e5aa65c81/dqc_reference/reference_markers.fasta -out OceanDNA-b38/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:32:53,981] [INFO] Task succeeded: Blastn
[2023-03-18 10:32:53,982] [INFO] Selected 26 target genomes.
[2023-03-18 10:32:53,982] [INFO] Target genome list was writen to OceanDNA-b38/target_genomes.txt
[2023-03-18 10:32:54,068] [INFO] Task started: fastANI
[2023-03-18 10:32:54,068] [INFO] Running command: fastANI --query /var/lib/cwl/stg33c1a284-1531-4310-afa1-b51a02d68a76/OceanDNA-b38.fa --refList OceanDNA-b38/target_genomes.txt --output OceanDNA-b38/fastani_result.tsv --threads 1
[2023-03-18 10:33:13,119] [INFO] Task succeeded: fastANI
[2023-03-18 10:33:13,120] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7340d679-bdd3-4366-aa40-bc1e5aa65c81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:33:13,120] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7340d679-bdd3-4366-aa40-bc1e5aa65c81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:33:13,127] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:33:13,127] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 10:33:13,127] [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
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	74.8747	88	1522	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	74.8571	58	1522	95	below_threshold
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	74.8183	62	1522	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	74.7882	51	1522	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_012987025.1	287	287	type	True	74.7671	55	1522	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_900167195.1	287	287	type	True	74.7671	55	1522	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	74.757	66	1522	95	below_threshold
Persicimonas caeni	strain=YN101	GCA_006517175.1	2292766	2292766	type	True	74.7502	64	1522	95	below_threshold
Stigmatella aurantiaca	strain=DSM 17044	GCA_900109545.1	41	41	type	True	74.6952	60	1522	95	below_threshold
Stigmatella hybrida	strain=DSM 14722	GCA_020103775.1	394097	394097	type	True	74.6586	59	1522	95	below_threshold
Burkholderia plantarii	strain=LMG 9035	GCA_902832905.1	41899	41899	type	True	74.6411	72	1522	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 10:33:13,128] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38/tc_result.tsv
[2023-03-18 10:33:13,128] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:33:13,128] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:33:13,128] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7340d679-bdd3-4366-aa40-bc1e5aa65c81/dqc_reference/checkm_data
[2023-03-18 10:33:13,129] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:33:13,135] [INFO] Task started: CheckM
[2023-03-18 10:33:13,135] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38/checkm_input OceanDNA-b38/checkm_result
[2023-03-18 10:34:20,108] [INFO] Task succeeded: CheckM
[2023-03-18 10:34:20,109] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.02%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 10:34:20,112] [INFO] ===== Completeness check finished =====
[2023-03-18 10:34:20,112] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:34:20,112] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38/markers.fasta)
[2023-03-18 10:34:20,113] [INFO] Task started: Blastn
[2023-03-18 10:34:20,113] [INFO] Running command: blastn -query OceanDNA-b38/markers.fasta -db /var/lib/cwl/stg7340d679-bdd3-4366-aa40-bc1e5aa65c81/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:34:21,315] [INFO] Task succeeded: Blastn
[2023-03-18 10:34:21,315] [INFO] Selected 21 target genomes.
[2023-03-18 10:34:21,316] [INFO] Target genome list was writen to OceanDNA-b38/target_genomes_gtdb.txt
[2023-03-18 10:34:21,499] [INFO] Task started: fastANI
[2023-03-18 10:34:21,499] [INFO] Running command: fastANI --query /var/lib/cwl/stg33c1a284-1531-4310-afa1-b51a02d68a76/OceanDNA-b38.fa --refList OceanDNA-b38/target_genomes_gtdb.txt --output OceanDNA-b38/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:34:36,553] [INFO] Task succeeded: fastANI
[2023-03-18 10:34:36,564] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 10:34:36,564] [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_003388555.1	s__QQVD01 sp003388555	76.7103	307	1522	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__QQVD01	95.0	99.97	99.97	0.99	0.99	2	-
GCA_009837085.1	s__WTGL01 sp009837085	76.0449	126	1522	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	99.78	99.78	0.96	0.95	3	-
GCA_009837885.1	s__WTGL01 sp009837885	75.8025	140	1522	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	99.92	99.92	0.99	0.99	2	-
GCA_009845425.1	s__WTGL01 sp009845425	75.7583	143	1522	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	99.99	99.99	0.99	0.99	3	-
GCA_012270995.1	s__WTGL01 sp012270995	75.7568	134	1522	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003697015.1	s__J023 sp003697015	75.7262	135	1522	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__J023	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525365.1	s__WTGL01 sp011525365	75.7167	137	1522	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479655.1	s__CAJQNK01 sp905479655	75.6756	97	1522	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__CAJQNK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009836625.1	s__WTGL01 sp009836625	75.5743	141	1522	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	99.03	98.03	0.95	0.91	5	-
GCA_014584695.1	s__JACTMI01 sp014584695	75.5726	119	1522	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JACTMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525905.1	s__JACTMI01 sp011525905	75.5513	110	1522	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JACTMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016699405.1	s__JAAYLR01 sp016699405	75.5126	113	1522	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JAAYLR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002420005.1	s__UBA5704 sp002420005	75.3426	122	1522	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__UBA5704	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719485.1	s__UBA5066 sp016719485	74.9523	66	1522	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5066;f__UBA5066;g__UBA5066	95.0	97.48	97.48	0.88	0.88	2	-
GCF_018398425.1	s__Pseudomonas_E lalucatii	74.8571	58	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	99.28	0.97	0.92	4	-
GCA_016779205.1	s__GCA-2862085 sp016779205	74.7502	52	1522	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2862085	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016703535.1	s__JADJBV01 sp016703535	74.7394	66	1522	d__Bacteria;p__Myxococcota;c__WYAZ01;o__WYAZ01;f__WYAZ01;g__JADJBV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875225.1	s__VGRW01 sp016875225	74.6556	57	1522	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__SZUA-336;f__SZUA-336;g__VGRW01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 10:34:36,564] [INFO] GTDB search result was written to OceanDNA-b38/result_gtdb.tsv
[2023-03-18 10:34:36,564] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:34:36,566] [INFO] DFAST_QC result json was written to OceanDNA-b38/dqc_result.json
[2023-03-18 10:34:36,566] [INFO] DFAST_QC completed!
[2023-03-18 10:34:36,566] [INFO] Total running time: 0h2m12s