[2023-03-14 10:55:58,911] [INFO] DFAST_QC pipeline started.
[2023-03-14 10:55:58,911] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 10:55:58,911] [INFO] DQC Reference Directory: /var/lib/cwl/stg503c9166-de43-4581-a93a-45bf8b87a932/dqc_reference
[2023-03-14 10:56:00,749] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 10:56:00,749] [INFO] Task started: Prodigal
[2023-03-14 10:56:00,750] [INFO] Running command: cat /var/lib/cwl/stge546577f-eb32-4d64-b6d2-dbf9e2438cfd/OceanDNA-b2866.fa | prodigal -d OceanDNA-b2866/cds.fna -a OceanDNA-b2866/protein.faa -g 11 -q > /dev/null
[2023-03-14 10:56:19,718] [INFO] Task succeeded: Prodigal
[2023-03-14 10:56:19,718] [INFO] Task started: HMMsearch
[2023-03-14 10:56:19,718] [INFO] Running command: hmmsearch --tblout OceanDNA-b2866/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg503c9166-de43-4581-a93a-45bf8b87a932/dqc_reference/reference_markers.hmm OceanDNA-b2866/protein.faa > /dev/null
[2023-03-14 10:56:19,980] [INFO] Task succeeded: HMMsearch
[2023-03-14 10:56:19,980] [INFO] Found 6/6 markers.
[2023-03-14 10:56:20,001] [INFO] Query marker FASTA was written to OceanDNA-b2866/markers.fasta
[2023-03-14 10:56:20,001] [INFO] Task started: Blastn
[2023-03-14 10:56:20,001] [INFO] Running command: blastn -query OceanDNA-b2866/markers.fasta -db /var/lib/cwl/stg503c9166-de43-4581-a93a-45bf8b87a932/dqc_reference/reference_markers.fasta -out OceanDNA-b2866/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:20,998] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:20,999] [INFO] Selected 26 target genomes.
[2023-03-14 10:56:20,999] [INFO] Target genome list was writen to OceanDNA-b2866/target_genomes.txt
[2023-03-14 10:56:21,026] [INFO] Task started: fastANI
[2023-03-14 10:56:21,026] [INFO] Running command: fastANI --query /var/lib/cwl/stge546577f-eb32-4d64-b6d2-dbf9e2438cfd/OceanDNA-b2866.fa --refList OceanDNA-b2866/target_genomes.txt --output OceanDNA-b2866/fastani_result.tsv --threads 1
[2023-03-14 10:56:45,772] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:45,772] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg503c9166-de43-4581-a93a-45bf8b87a932/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 10:56:45,772] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg503c9166-de43-4581-a93a-45bf8b87a932/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 10:56:45,786] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 10:56:45,786] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 10:56:45,787] [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
Candidatus Mycolicibacterium alkanivorans		GCA_022760805.1	2954114	2954114	type	True	79.1386	497	989	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	78.9398	537	989	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	78.7379	516	989	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	78.7091	535	989	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	78.6783	516	989	95	below_threshold
Mycolicibacterium fallax	strain=DSM 44179	GCA_002101995.1	1793	1793	type	True	78.6068	422	989	95	below_threshold
Mycolicibacterium fallax	strain=JCM 6405	GCA_010726955.1	1793	1793	type	True	78.5938	429	989	95	below_threshold
Mycobacterium palauense	strain=CECT 8779	GCA_002592005.1	2034511	2034511	type	True	78.4898	463	989	95	below_threshold
Mycolicibacterium helvum	strain=JCM 30396	GCA_010731895.1	1534349	1534349	type	True	78.4525	509	989	95	below_threshold
Mycolicibacterium aromaticivorans	strain=JS19b1	GCA_000559085.2	318425	318425	type	True	78.4469	523	989	95	below_threshold
Mycolicibacterium canariasense	strain=JCM15298	GCA_001570445.1	228230	228230	type	True	78.2821	427	989	95	below_threshold
Mycolicibacterium canariasense	strain=CCUG 47953	GCA_002101555.1	228230	228230	type	True	78.2699	419	989	95	below_threshold
Mycolicibacterium thermoresistibile	strain=NCTC10409	GCA_900187065.1	1797	1797	type	True	78.1183	423	989	95	below_threshold
Mycolicibacterium thermoresistibile	strain=ATCC 19527	GCA_000234585.2	1797	1797	type	True	78.1137	429	989	95	below_threshold
Mycolicibacterium thermoresistibile	strain=JCM6362	GCA_001570505.1	1797	1797	type	True	78.095	425	989	95	below_threshold
Mycolicibacterium sarraceniae	strain=JCM 30395	GCA_010731875.1	1534348	1534348	type	True	78.0717	466	989	95	below_threshold
Mycobacterium arosiense	strain=DSM 45069	GCA_002086125.1	425468	425468	type	True	77.9451	368	989	95	below_threshold
Mycolicibacterium arabiense	strain=JCM 18538	GCA_010731815.2	1286181	1286181	type	True	77.9412	410	989	95	below_threshold
Mycolicibacterium pulveris	strain=JCM 6370	GCA_010725725.1	36813	36813	type	True	77.9372	414	989	95	below_threshold
Mycolicibacterium boenickei	strain=JCM 15653	GCA_010731295.1	146017	146017	type	True	77.9194	428	989	95	below_threshold
Mycolicibacterium malmesburyense	strain=WCM 7299	GCA_001050015.1	1566886	1566886	type	True	77.9175	390	989	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	77.912	413	989	95	below_threshold
Mycolicibacterium llatzerense	strain=MG13	GCA_025331195.1	280871	280871	type	True	77.8221	386	989	95	below_threshold
Mycobacterium saskatchewanense	strain=DSM 44616	GCA_002101875.1	220927	220927	type	True	77.8058	372	989	95	below_threshold
Mycobacterium saskatchewanense	strain=JCM 13016	GCA_010729105.1	220927	220927	type	True	77.8015	383	989	95	below_threshold
Mycobacterium noviomagense	strain=DSM 45145	GCA_002086415.1	459858	459858	type	True	77.603	327	989	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 10:56:45,787] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2866/tc_result.tsv
[2023-03-14 10:56:45,787] [INFO] ===== Taxonomy check completed =====
[2023-03-14 10:56:45,787] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 10:56:45,787] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg503c9166-de43-4581-a93a-45bf8b87a932/dqc_reference/checkm_data
[2023-03-14 10:56:45,788] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 10:56:45,792] [INFO] Task started: CheckM
[2023-03-14 10:56:45,792] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2866/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2866/checkm_input OceanDNA-b2866/checkm_result
[2023-03-14 10:57:33,357] [INFO] Task succeeded: CheckM
[2023-03-14 10:57:33,358] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.22%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 10:57:33,361] [INFO] ===== Completeness check finished =====
[2023-03-14 10:57:33,361] [INFO] ===== Start GTDB Search =====
[2023-03-14 10:57:33,361] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2866/markers.fasta)
[2023-03-14 10:57:33,361] [INFO] Task started: Blastn
[2023-03-14 10:57:33,361] [INFO] Running command: blastn -query OceanDNA-b2866/markers.fasta -db /var/lib/cwl/stg503c9166-de43-4581-a93a-45bf8b87a932/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2866/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:57:34,761] [INFO] Task succeeded: Blastn
[2023-03-14 10:57:34,762] [INFO] Selected 20 target genomes.
[2023-03-14 10:57:34,762] [INFO] Target genome list was writen to OceanDNA-b2866/target_genomes_gtdb.txt
[2023-03-14 10:57:34,780] [INFO] Task started: fastANI
[2023-03-14 10:57:34,781] [INFO] Running command: fastANI --query /var/lib/cwl/stge546577f-eb32-4d64-b6d2-dbf9e2438cfd/OceanDNA-b2866.fa --refList OceanDNA-b2866/target_genomes_gtdb.txt --output OceanDNA-b2866/fastani_result_gtdb.tsv --threads 1
[2023-03-14 10:57:51,143] [INFO] Task succeeded: fastANI
[2023-03-14 10:57:51,155] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 10:57:51,155] [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_018401645.1	s__Mycobacterium sp018401645	98.5426	804	989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903911165.1	s__Mycobacterium sp903911165	83.0531	597	989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005789055.1	s__Mycobacterium sp005789055	82.438	412	989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016462945.1	s__Mycobacterium sp016462945	81.0073	647	989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001510415.1	s__Mycobacterium sp001510415	79.9831	361	989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017853185.1	s__Mycobacterium sp017853185	79.8668	538	989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903884065.1	s__Mycobacterium sp903884065	79.638	619	989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.70	99.70	0.92	0.92	2	-
GCA_903877095.1	s__Mycobacterium sp903877095	79.3104	562	989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.96	99.94	0.97	0.96	4	-
GCA_018883075.1	s__Mycobacterium sp018883075	79.1579	442	989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903862565.1	s__Mycobacterium sp903862565	79.0105	520	989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002723835.1	s__Mycobacterium sp002723835	78.8411	561	989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745805.1	s__Mycobacterium sp004745805	78.8406	528	989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018882545.1	s__Mycobacterium sp018882545	78.7014	343	989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886515.1	s__Mycobacterium sp001886515	78.6973	513	989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.54	98.54	0.94	0.94	2	-
GCA_900078375.1	s__Mycobacterium sp900078375	78.4935	517	989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018455725.1	s__Mycobacterium sp018455725	78.3407	393	989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101555.1	s__Mycobacterium canariasense	78.287	417	989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_008329565.1	s__Mycobacterium sp008329565	78.2569	493	989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001722335.1	s__Mycobacterium flavescens_A	78.2218	439	989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187065.1	s__Mycobacterium thermoresistibile	78.1239	423	989	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.97	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2023-03-14 10:57:51,155] [INFO] GTDB search result was written to OceanDNA-b2866/result_gtdb.tsv
[2023-03-14 10:57:51,155] [INFO] ===== GTDB Search completed =====
[2023-03-14 10:57:51,158] [INFO] DFAST_QC result json was written to OceanDNA-b2866/dqc_result.json
[2023-03-14 10:57:51,158] [INFO] DFAST_QC completed!
[2023-03-14 10:57:51,158] [INFO] Total running time: 0h1m52s