[2023-03-16 08:10:35,175] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:10:35,178] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:10:35,178] [INFO] DQC Reference Directory: /var/lib/cwl/stg59cfc5ef-1562-4a7e-b487-345b7e6c9d2f/dqc_reference
[2023-03-16 08:10:36,329] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:10:36,329] [INFO] Task started: Prodigal
[2023-03-16 08:10:36,329] [INFO] Running command: cat /var/lib/cwl/stg9156d8b4-5837-4d02-880e-b69dffdcbc13/OceanDNA-b24044.fa | prodigal -d OceanDNA-b24044/cds.fna -a OceanDNA-b24044/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:10:52,839] [INFO] Task succeeded: Prodigal
[2023-03-16 08:10:52,839] [INFO] Task started: HMMsearch
[2023-03-16 08:10:52,839] [INFO] Running command: hmmsearch --tblout OceanDNA-b24044/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg59cfc5ef-1562-4a7e-b487-345b7e6c9d2f/dqc_reference/reference_markers.hmm OceanDNA-b24044/protein.faa > /dev/null
[2023-03-16 08:10:53,046] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:10:53,046] [INFO] Found 6/6 markers.
[2023-03-16 08:10:53,128] [INFO] Query marker FASTA was written to OceanDNA-b24044/markers.fasta
[2023-03-16 08:10:53,129] [INFO] Task started: Blastn
[2023-03-16 08:10:53,129] [INFO] Running command: blastn -query OceanDNA-b24044/markers.fasta -db /var/lib/cwl/stg59cfc5ef-1562-4a7e-b487-345b7e6c9d2f/dqc_reference/reference_markers.fasta -out OceanDNA-b24044/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:10:53,747] [INFO] Task succeeded: Blastn
[2023-03-16 08:10:53,771] [INFO] Selected 37 target genomes.
[2023-03-16 08:10:53,771] [INFO] Target genome list was writen to OceanDNA-b24044/target_genomes.txt
[2023-03-16 08:10:53,793] [INFO] Task started: fastANI
[2023-03-16 08:10:53,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg9156d8b4-5837-4d02-880e-b69dffdcbc13/OceanDNA-b24044.fa --refList OceanDNA-b24044/target_genomes.txt --output OceanDNA-b24044/fastani_result.tsv --threads 1
[2023-03-16 08:11:21,056] [INFO] Task succeeded: fastANI
[2023-03-16 08:11:21,056] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg59cfc5ef-1562-4a7e-b487-345b7e6c9d2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:11:21,056] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg59cfc5ef-1562-4a7e-b487-345b7e6c9d2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:11:21,066] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:11:21,066] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 08:11:21,066] [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
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	76.1544	51	858	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	76.1537	54	858	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.131	84	858	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.0615	64	858	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.0227	95	858	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.0198	95	858	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	75.9363	59	858	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	75.924	66	858	95	below_threshold
Aliidongia dinghuensis	strain=CGMCC 1.15725	GCA_014643535.1	1867774	1867774	type	True	75.8834	66	858	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	75.8777	73	858	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	75.7805	58	858	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	75.7502	83	858	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	75.6785	78	858	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	75.6765	69	858	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	75.6009	71	858	95	below_threshold
Propylenella binzhouense	strain=L72	GCA_009866965.1	2555902	2555902	type	True	75.2978	54	858	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 08:11:21,071] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24044/tc_result.tsv
[2023-03-16 08:11:21,077] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:11:21,077] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:11:21,077] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg59cfc5ef-1562-4a7e-b487-345b7e6c9d2f/dqc_reference/checkm_data
[2023-03-16 08:11:21,077] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:11:21,091] [INFO] Task started: CheckM
[2023-03-16 08:11:21,091] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24044/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24044/checkm_input OceanDNA-b24044/checkm_result
[2023-03-16 08:12:04,538] [INFO] Task succeeded: CheckM
[2023-03-16 08:12:04,538] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.63%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 08:12:04,755] [INFO] ===== Completeness check finished =====
[2023-03-16 08:12:04,755] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:12:04,755] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24044/markers.fasta)
[2023-03-16 08:12:04,756] [INFO] Task started: Blastn
[2023-03-16 08:12:04,756] [INFO] Running command: blastn -query OceanDNA-b24044/markers.fasta -db /var/lib/cwl/stg59cfc5ef-1562-4a7e-b487-345b7e6c9d2f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24044/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:12:05,763] [INFO] Task succeeded: Blastn
[2023-03-16 08:12:05,775] [INFO] Selected 39 target genomes.
[2023-03-16 08:12:05,776] [INFO] Target genome list was writen to OceanDNA-b24044/target_genomes_gtdb.txt
[2023-03-16 08:12:05,826] [INFO] Task started: fastANI
[2023-03-16 08:12:05,826] [INFO] Running command: fastANI --query /var/lib/cwl/stg9156d8b4-5837-4d02-880e-b69dffdcbc13/OceanDNA-b24044.fa --refList OceanDNA-b24044/target_genomes_gtdb.txt --output OceanDNA-b24044/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:12:33,740] [INFO] Task succeeded: fastANI
[2023-03-16 08:12:33,752] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 08:12:33,752] [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_002239065.1	s__MPNO01 sp002239065	76.592	208	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__MPNO01;g__MPNO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018971215.1	s__REEB95 sp018971215	76.4794	55	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__REEB95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869145.1	s__VGEU01 sp016869145	76.4316	147	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__VGEU01;g__VGEU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377375.1	s__WHUE01 sp009377375	76.378	112	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__WHUE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000518365.1	s__URHD0088 sp000518365	76.3511	86	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__URHD0088	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869645.1	s__SHVW01 sp016869645	76.1932	74	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVW01;f__SHVW01;g__SHVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870055.1	s__Reyranella sp016870055	76.1785	53	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902729435.1	s__Magnetospirillum sp902729435	76.1625	68	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652915.1	s__Thalassobaculum_A fulvum	76.1508	83	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401495.1	s__Thalassobaculum_A sp018401495	76.0269	80	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	76.0057	96	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_016467395.1	s__Reyranella sp016467395	75.9667	84	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423185.1	s__Inquilinus limosus	75.924	66	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__Inquilinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001657395.1	s__Pelagibius sp001657395	75.9071	58	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__Pelagibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643535.1	s__Aliidongia dinghuensis	75.8618	67	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Aliidongia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002195995.1	s__Inquilinus limosus_C	75.7498	55	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__Inquilinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009694025.1	s__SHVZ01 sp009694025	75.6986	56	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVZ01;f__SHVZ01;g__SHVZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362745.1	s__Oharaeibacter diazotrophicus	75.6785	78	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Oharaeibacter	95.0	99.98	99.97	1.00	1.00	3	-
GCA_018660305.1	s__JABJKO01 sp018660305	75.6239	63	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__JABJKO01	95.0	99.60	99.60	0.81	0.81	2	-
GCF_005938675.2	s__Inquilinus sp005938675	75.611	71	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__Inquilinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903839865.1	s__Reyranella aerosaccus_A	75.5638	53	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	99.29	98.98	0.87	0.83	3	-
GCF_000282615.1	s__Bradyrhizobium sp000282615	75.4801	55	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 08:12:33,757] [INFO] GTDB search result was written to OceanDNA-b24044/result_gtdb.tsv
[2023-03-16 08:12:33,765] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:12:33,775] [INFO] DFAST_QC result json was written to OceanDNA-b24044/dqc_result.json
[2023-03-16 08:12:33,775] [INFO] DFAST_QC completed!
[2023-03-16 08:12:33,775] [INFO] Total running time: 0h1m59s