[2023-03-14 11:13:58,985] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:13:58,986] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:13:58,986] [INFO] DQC Reference Directory: /var/lib/cwl/stgd7914714-9b49-440f-ac9b-c157ae5ca449/dqc_reference
[2023-03-14 11:14:00,597] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:14:00,597] [INFO] Task started: Prodigal
[2023-03-14 11:14:00,598] [INFO] Running command: cat /var/lib/cwl/stgbd009b12-1bca-47ea-9ef6-1746e97c1361/OceanDNA-b41.fa | prodigal -d OceanDNA-b41/cds.fna -a OceanDNA-b41/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:15:11,369] [INFO] Task succeeded: Prodigal
[2023-03-14 11:15:11,369] [INFO] Task started: HMMsearch
[2023-03-14 11:15:11,369] [INFO] Running command: hmmsearch --tblout OceanDNA-b41/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd7914714-9b49-440f-ac9b-c157ae5ca449/dqc_reference/reference_markers.hmm OceanDNA-b41/protein.faa > /dev/null
[2023-03-14 11:15:11,735] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:15:11,735] [INFO] Found 6/6 markers.
[2023-03-14 11:15:11,790] [INFO] Query marker FASTA was written to OceanDNA-b41/markers.fasta
[2023-03-14 11:15:11,791] [INFO] Task started: Blastn
[2023-03-14 11:15:11,791] [INFO] Running command: blastn -query OceanDNA-b41/markers.fasta -db /var/lib/cwl/stgd7914714-9b49-440f-ac9b-c157ae5ca449/dqc_reference/reference_markers.fasta -out OceanDNA-b41/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:15:12,356] [INFO] Task succeeded: Blastn
[2023-03-14 11:15:12,357] [INFO] Selected 30 target genomes.
[2023-03-14 11:15:12,357] [INFO] Target genome list was writen to OceanDNA-b41/target_genomes.txt
[2023-03-14 11:15:12,379] [INFO] Task started: fastANI
[2023-03-14 11:15:12,379] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd009b12-1bca-47ea-9ef6-1746e97c1361/OceanDNA-b41.fa --refList OceanDNA-b41/target_genomes.txt --output OceanDNA-b41/fastani_result.tsv --threads 1
[2023-03-14 11:15:32,386] [INFO] Task succeeded: fastANI
[2023-03-14 11:15:32,386] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd7914714-9b49-440f-ac9b-c157ae5ca449/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:15:32,386] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd7914714-9b49-440f-ac9b-c157ae5ca449/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:15:32,393] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:15:32,393] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 11:15:32,394] [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
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	74.875	72	3422	95	below_threshold
Cryptosporangium phraense	strain=A-T 5661	GCA_006912135.1	2593070	2593070	type	True	74.8265	96	3422	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	74.8259	59	3422	95	below_threshold
Halomonas nitroreducens	strain=11S	GCA_003966155.1	447425	447425	type	True	74.8157	56	3422	95	below_threshold
Nocardiopsis potens	strain=DSM 45234	GCA_000341105.1	1246458	1246458	type	True	74.7565	98	3422	95	below_threshold
Actinomadura bangladeshensis	strain=DSM 45347	GCA_004348335.1	453573	453573	type	True	74.7192	101	3422	95	below_threshold
Actinomadura roseirufa		GCA_900659635.1	2094049	2094049	type	True	74.6923	123	3422	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	74.6759	107	3422	95	below_threshold
Actinomadura soli	strain=14C53	GCA_005889715.1	2508997	2508997	type	True	74.6438	101	3422	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:15:32,394] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41/tc_result.tsv
[2023-03-14 11:15:32,394] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:15:32,394] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:15:32,394] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd7914714-9b49-440f-ac9b-c157ae5ca449/dqc_reference/checkm_data
[2023-03-14 11:15:32,395] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:15:32,405] [INFO] Task started: CheckM
[2023-03-14 11:15:32,406] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41/checkm_input OceanDNA-b41/checkm_result
[2023-03-14 11:18:18,981] [INFO] Task succeeded: CheckM
[2023-03-14 11:18:18,982] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:18:18,994] [INFO] ===== Completeness check finished =====
[2023-03-14 11:18:18,994] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:18:18,994] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41/markers.fasta)
[2023-03-14 11:18:18,995] [INFO] Task started: Blastn
[2023-03-14 11:18:18,995] [INFO] Running command: blastn -query OceanDNA-b41/markers.fasta -db /var/lib/cwl/stgd7914714-9b49-440f-ac9b-c157ae5ca449/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:18:19,845] [INFO] Task succeeded: Blastn
[2023-03-14 11:18:19,846] [INFO] Selected 28 target genomes.
[2023-03-14 11:18:19,846] [INFO] Target genome list was writen to OceanDNA-b41/target_genomes_gtdb.txt
[2023-03-14 11:18:19,891] [INFO] Task started: fastANI
[2023-03-14 11:18:19,892] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd009b12-1bca-47ea-9ef6-1746e97c1361/OceanDNA-b41.fa --refList OceanDNA-b41/target_genomes_gtdb.txt --output OceanDNA-b41/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:18:38,089] [INFO] Task succeeded: fastANI
[2023-03-14 11:18:38,099] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:18:38,099] [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_003697015.1	s__J023 sp003697015	75.9484	274	3422	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__J023	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009837085.1	s__WTGL01 sp009837085	75.7689	84	3422	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	75.7141	88	3422	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	75.7054	92	3422	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	99.99	99.99	0.99	0.99	3	-
GCA_012521815.1	s__JAAYLR01 sp012521815	75.6017	80	3422	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JAAYLR01	95.0	99.12	98.38	0.89	0.78	5	-
GCA_016699405.1	s__JAAYLR01 sp016699405	75.5902	115	3422	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JAAYLR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525365.1	s__WTGL01 sp011525365	75.5423	93	3422	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012270995.1	s__WTGL01 sp012270995	75.5322	82	3422	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009836625.1	s__WTGL01 sp009836625	75.5068	102	3422	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	99.03	98.03	0.95	0.91	5	-
GCA_002420005.1	s__UBA5704 sp002420005	75.4978	173	3422	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__UBA5704	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018057705.1	s__JAGPDF01 sp018057705	75.4962	123	3422	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JAGPDF01	95.0	99.73	99.73	0.94	0.94	2	-
GCA_017860005.1	s__JACTMI01 sp017860005	75.489	95	3422	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JACTMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003388555.1	s__QQVD01 sp003388555	75.4758	192	3422	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__QQVD01	95.0	99.97	99.97	0.99	0.99	2	-
GCA_014584695.1	s__JACTMI01 sp014584695	75.3204	114	3422	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JACTMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716705.1	s__UBA5066 sp016716705	75.0971	71	3422	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5066;f__UBA5066;g__UBA5066	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714815.1	s__UBA5066 sp016714815	75.0613	89	3422	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5066;f__UBA5066;g__UBA5066	95.0	99.07	99.07	0.92	0.92	2	-
GCA_003576805.1	s__PR03 sp003576805	74.8772	68	3422	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__PR03;g__PR03	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002068325.1	s__MVZH01 sp002068325	74.6104	59	3422	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__UBA1407;f__MVZH01;g__MVZH01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:18:38,101] [INFO] GTDB search result was written to OceanDNA-b41/result_gtdb.tsv
[2023-03-14 11:18:38,101] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:18:38,104] [INFO] DFAST_QC result json was written to OceanDNA-b41/dqc_result.json
[2023-03-14 11:18:38,104] [INFO] DFAST_QC completed!
[2023-03-14 11:18:38,104] [INFO] Total running time: 0h4m39s