[2023-03-17 06:30:49,800] [INFO] DFAST_QC pipeline started.
[2023-03-17 06:30:49,800] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 06:30:49,800] [INFO] DQC Reference Directory: /var/lib/cwl/stg2469bd28-f71a-4b7c-9ab7-a7ab8256b0d1/dqc_reference
[2023-03-17 06:30:51,354] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 06:30:51,355] [INFO] Task started: Prodigal
[2023-03-17 06:30:51,355] [INFO] Running command: cat /var/lib/cwl/stg6efbadc3-d059-4dee-bc87-670a478d3654/OceanDNA-b23297.fa | prodigal -d OceanDNA-b23297/cds.fna -a OceanDNA-b23297/protein.faa -g 11 -q > /dev/null
[2023-03-17 06:31:15,423] [INFO] Task succeeded: Prodigal
[2023-03-17 06:31:15,424] [INFO] Task started: HMMsearch
[2023-03-17 06:31:15,424] [INFO] Running command: hmmsearch --tblout OceanDNA-b23297/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2469bd28-f71a-4b7c-9ab7-a7ab8256b0d1/dqc_reference/reference_markers.hmm OceanDNA-b23297/protein.faa > /dev/null
[2023-03-17 06:31:15,632] [INFO] Task succeeded: HMMsearch
[2023-03-17 06:31:15,632] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6efbadc3-d059-4dee-bc87-670a478d3654/OceanDNA-b23297.fa]
[2023-03-17 06:31:15,657] [INFO] Query marker FASTA was written to OceanDNA-b23297/markers.fasta
[2023-03-17 06:31:15,657] [INFO] Task started: Blastn
[2023-03-17 06:31:15,657] [INFO] Running command: blastn -query OceanDNA-b23297/markers.fasta -db /var/lib/cwl/stg2469bd28-f71a-4b7c-9ab7-a7ab8256b0d1/dqc_reference/reference_markers.fasta -out OceanDNA-b23297/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:31:16,385] [INFO] Task succeeded: Blastn
[2023-03-17 06:31:16,386] [INFO] Selected 30 target genomes.
[2023-03-17 06:31:16,386] [INFO] Target genome list was writen to OceanDNA-b23297/target_genomes.txt
[2023-03-17 06:31:16,398] [INFO] Task started: fastANI
[2023-03-17 06:31:16,398] [INFO] Running command: fastANI --query /var/lib/cwl/stg6efbadc3-d059-4dee-bc87-670a478d3654/OceanDNA-b23297.fa --refList OceanDNA-b23297/target_genomes.txt --output OceanDNA-b23297/fastani_result.tsv --threads 1
[2023-03-17 06:31:44,097] [INFO] Task succeeded: fastANI
[2023-03-17 06:31:44,097] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2469bd28-f71a-4b7c-9ab7-a7ab8256b0d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 06:31:44,097] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2469bd28-f71a-4b7c-9ab7-a7ab8256b0d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 06:31:44,113] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 06:31:44,113] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 06:31:44,113] [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
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.2768	180	1342	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.1268	187	1342	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.1123	182	1342	95	below_threshold
Nisaea nitritireducens	strain=DSM 19540	GCA_014904795.1	568392	568392	type	True	76.0907	108	1342	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.0391	174	1342	95	below_threshold
Kaistia granuli	strain=Ko04	GCA_000380505.1	363259	363259	type	True	75.9176	174	1342	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	75.8956	233	1342	95	below_threshold
Bosea caraganae	strain=RCAM 04680	GCA_003351345.1	2763117	2763117	type	True	75.8871	219	1342	95	below_threshold
Dongia mobilis	strain=CGMCC 1.7660	GCA_004363235.1	578943	578943	type	True	75.8837	139	1342	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	75.8022	215	1342	95	below_threshold
Skermanella aerolata	strain=5416T-32	GCA_000936425.1	393310	393310	type	True	75.8006	194	1342	95	below_threshold
Neorhizobium galegae	strain=HAMBI 540	GCA_000731315.1	399	399	suspected-type	True	75.7915	130	1342	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	75.7832	228	1342	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.7763	266	1342	95	below_threshold
Nisaea denitrificans	strain=DSM 18348	GCA_000426505.1	390877	390877	type	True	75.7717	115	1342	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	75.77	199	1342	95	below_threshold
Neorhizobium vignae	strain=CCBAU 05176	GCA_000732195.1	690585	690585	type	True	75.7306	122	1342	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	75.7305	254	1342	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	75.7259	253	1342	95	below_threshold
Skermanella rosea	strain=KEMB 2255-458	GCA_016806835.2	1817965	1817965	type	True	75.7168	217	1342	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	75.7064	237	1342	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	75.6879	243	1342	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	75.6654	190	1342	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	75.6194	176	1342	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	75.5934	133	1342	95	below_threshold
Sinorhizobium medicae	strain=A321	GCA_009599935.1	110321	110321	type	True	75.5363	75	1342	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	75.52	140	1342	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	75.4748	224	1342	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	75.4022	159	1342	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	75.2964	131	1342	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 06:31:44,343] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23297/tc_result.tsv
[2023-03-17 06:31:44,343] [INFO] ===== Taxonomy check completed =====
[2023-03-17 06:31:44,343] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 06:31:44,344] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2469bd28-f71a-4b7c-9ab7-a7ab8256b0d1/dqc_reference/checkm_data
[2023-03-17 06:31:44,344] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 06:31:44,473] [INFO] Task started: CheckM
[2023-03-17 06:31:44,473] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23297/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23297/checkm_input OceanDNA-b23297/checkm_result
[2023-03-17 06:32:42,773] [INFO] Task succeeded: CheckM
[2023-03-17 06:32:42,773] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 06:32:42,776] [INFO] ===== Completeness check finished =====
[2023-03-17 06:32:42,776] [INFO] ===== Start GTDB Search =====
[2023-03-17 06:32:42,776] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23297/markers.fasta)
[2023-03-17 06:32:42,776] [INFO] Task started: Blastn
[2023-03-17 06:32:42,776] [INFO] Running command: blastn -query OceanDNA-b23297/markers.fasta -db /var/lib/cwl/stg2469bd28-f71a-4b7c-9ab7-a7ab8256b0d1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23297/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:32:44,114] [INFO] Task succeeded: Blastn
[2023-03-17 06:32:44,115] [INFO] Selected 28 target genomes.
[2023-03-17 06:32:44,115] [INFO] Target genome list was writen to OceanDNA-b23297/target_genomes_gtdb.txt
[2023-03-17 06:32:44,658] [INFO] Task started: fastANI
[2023-03-17 06:32:44,658] [INFO] Running command: fastANI --query /var/lib/cwl/stg6efbadc3-d059-4dee-bc87-670a478d3654/OceanDNA-b23297.fa --refList OceanDNA-b23297/target_genomes_gtdb.txt --output OceanDNA-b23297/fastani_result_gtdb.tsv --threads 1
[2023-03-17 06:33:07,780] [INFO] Task succeeded: fastANI
[2023-03-17 06:33:07,795] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 06:33:07,795] [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_017640745.1	s__Nisaea sp017640745	76.224	174	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401495.1	s__Thalassobaculum_A sp018401495	76.1986	240	1342	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_014904705.1	s__Nisaea sp014904705	76.1401	180	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018823745.1	s__Oceanibaculum sp018823745	76.0757	167	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	99.98	99.98	1.00	1.00	4	-
GCF_014904795.1	s__Nisaea nitritireducens	76.0587	110	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003336875.1	s__Oleisolibacter albus	75.9718	137	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Oleisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018971215.1	s__REEB95 sp018971215	75.9698	130	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__REEB95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009909005.1	s__JAAAOG01 sp009909005	75.9546	137	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__JAAAOG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006738865.1	s__Stella sp006738865	75.9407	240	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380505.1	s__Kaistia granuli	75.9181	174	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006739055.1	s__Stella vacuolata	75.9173	266	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002195995.1	s__Inquilinus limosus_C	75.9072	260	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__Inquilinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016765655.1	s__Skermanella mucosa	75.8698	229	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423185.1	s__Inquilinus limosus	75.852	263	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__Inquilinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016629525.1	s__Kaistia sp016629525	75.8499	204	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869645.1	s__SHVW01 sp016869645	75.8096	171	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVW01;f__SHVW01;g__SHVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876155.1	s__Azospirillum rugosum	75.783	228	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008843145.1	s__Skermanella pratensis	75.7618	200	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000732195.1	s__Neorhizobium vignae	75.7205	123	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938675.2	s__Inquilinus sp005938675	75.7185	273	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__Inquilinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992495.1	s__Reyranella soli	75.702	242	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595245.1	s__Azospirillum sp016595245	75.6763	251	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794165.1	s__Dongia sp016794165	75.6304	115	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Dongia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307955.1	s__Kaistia sp017307955	75.6071	210	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003693905.1	s__J153 sp003693905	75.5508	65	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__J153;g__J153	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003122325.1	s__Rhizobium album	75.5475	137	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859895.1	s__JACZKS01 sp014859895	75.2346	128	1342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JACZKS01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 06:33:07,795] [INFO] GTDB search result was written to OceanDNA-b23297/result_gtdb.tsv
[2023-03-17 06:33:07,795] [INFO] ===== GTDB Search completed =====
[2023-03-17 06:33:07,798] [INFO] DFAST_QC result json was written to OceanDNA-b23297/dqc_result.json
[2023-03-17 06:33:07,798] [INFO] DFAST_QC completed!
[2023-03-17 06:33:07,798] [INFO] Total running time: 0h2m18s