[2023-03-16 07:28:29,973] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:28:29,973] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:28:29,974] [INFO] DQC Reference Directory: /var/lib/cwl/stg64a4ee47-8828-4d34-a82e-6621752503af/dqc_reference
[2023-03-16 07:28:31,101] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:28:31,102] [INFO] Task started: Prodigal
[2023-03-16 07:28:31,102] [INFO] Running command: cat /var/lib/cwl/stge8f6deea-de42-4c65-8c64-6a1fe4a7e069/OceanDNA-b26772.fa | prodigal -d OceanDNA-b26772/cds.fna -a OceanDNA-b26772/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:28:42,540] [INFO] Task succeeded: Prodigal
[2023-03-16 07:28:42,541] [INFO] Task started: HMMsearch
[2023-03-16 07:28:42,541] [INFO] Running command: hmmsearch --tblout OceanDNA-b26772/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg64a4ee47-8828-4d34-a82e-6621752503af/dqc_reference/reference_markers.hmm OceanDNA-b26772/protein.faa > /dev/null
[2023-03-16 07:28:42,720] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:28:42,721] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge8f6deea-de42-4c65-8c64-6a1fe4a7e069/OceanDNA-b26772.fa]
[2023-03-16 07:28:42,742] [INFO] Query marker FASTA was written to OceanDNA-b26772/markers.fasta
[2023-03-16 07:28:42,743] [INFO] Task started: Blastn
[2023-03-16 07:28:42,743] [INFO] Running command: blastn -query OceanDNA-b26772/markers.fasta -db /var/lib/cwl/stg64a4ee47-8828-4d34-a82e-6621752503af/dqc_reference/reference_markers.fasta -out OceanDNA-b26772/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:28:43,600] [INFO] Task succeeded: Blastn
[2023-03-16 07:28:43,603] [INFO] Selected 30 target genomes.
[2023-03-16 07:28:43,603] [INFO] Target genome list was writen to OceanDNA-b26772/target_genomes.txt
[2023-03-16 07:28:43,622] [INFO] Task started: fastANI
[2023-03-16 07:28:43,623] [INFO] Running command: fastANI --query /var/lib/cwl/stge8f6deea-de42-4c65-8c64-6a1fe4a7e069/OceanDNA-b26772.fa --refList OceanDNA-b26772/target_genomes.txt --output OceanDNA-b26772/fastani_result.tsv --threads 1
[2023-03-16 07:29:05,668] [INFO] Task succeeded: fastANI
[2023-03-16 07:29:05,668] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg64a4ee47-8828-4d34-a82e-6621752503af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:29:05,669] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg64a4ee47-8828-4d34-a82e-6621752503af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:29:05,685] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:29:05,685] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 07:29:05,686] [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
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	77.1015	162	581	95	below_threshold
Aureimonas flava	strain=M2BS4Y-1	GCA_003583935.1	2320271	2320271	type	True	77.0443	144	581	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	76.8988	168	581	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	76.8279	94	581	95	below_threshold
Aureimonas leprariae	strain=YIM 132180	GCA_008802405.1	2615207	2615207	type	True	76.7664	150	581	95	below_threshold
Aurantimonas endophytica	strain=DSM 103570	GCA_014196845.1	1522175	1522175	type	True	76.7215	127	581	95	below_threshold
Aurantimonas manganoxydans	strain=DSM 21871	GCA_001463865.1	651183	651183	type	True	76.7149	136	581	95	below_threshold
Aurantimonas manganoxydans	strain=SI85-9A1	GCA_000153465.1	651183	651183	type	True	76.714	139	581	95	below_threshold
Bosea thiooxidans	strain=DSM 9653	GCA_900168195.1	53254	53254	type	True	76.71	108	581	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	76.7032	128	581	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	76.6248	152	581	95	below_threshold
Afifella pfennigii	strain=DSM 17143	GCA_000688515.1	209897	209897	type	True	76.6173	106	581	95	below_threshold
Aquibium carbonis	strain=B2.3	GCA_003970795.1	2495581	2495581	type	True	76.6159	136	581	95	below_threshold
Nitratireductor pacificus	strain=pht-3B	GCA_000300335.1	1231180	1231180	type	True	76.5852	139	581	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	76.5305	161	581	95	below_threshold
Chelativorans intermedius	strain=LMG 28482	GCA_025398255.1	515947	515947	type	True	76.5098	102	581	95	below_threshold
Aureimonas endophytica	strain=CGMCC 1.15367	GCA_014642635.1	2027858	2027858	type	True	76.4721	143	581	95	below_threshold
Aureimonas ureilytica	strain=DSM 18598	GCA_000382705.1	401562	401562	type	True	76.4499	145	581	95	below_threshold
Aureimonas mangrovi	strain=LMG 31693	GCA_014058705.1	2758041	2758041	type	True	76.4358	125	581	95	below_threshold
Aureimonas phyllosphaerae	strain=DSM 25024	GCA_014196405.1	1166078	1166078	type	True	76.4349	138	581	95	below_threshold
Aureimonas ureilytica	strain=NBRC 106430	GCA_001463945.1	401562	401562	type	True	76.4259	148	581	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	76.4032	103	581	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	76.3989	116	581	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	76.3863	104	581	95	below_threshold
Methylobacterium oxalidis	strain=DSM 24028	GCA_022179505.1	944322	944322	type	True	76.3806	118	581	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	76.3791	139	581	95	below_threshold
Methylobacterium oxalidis	strain=NBRC 107715	GCA_007992195.1	944322	944322	type	True	76.3587	114	581	95	below_threshold
Aureimonas psammosilenae	strain=YIM DR1026	GCA_009176975.1	2495496	2495496	type	True	76.3376	124	581	95	below_threshold
Jiella pacifica	strain=40Bstr34	GCA_010500815.1	2696469	2696469	type	True	76.1676	131	581	95	below_threshold
Martelella mediterranea	strain=DSM 17316	GCA_000376125.1	293089	293089	type	True	76.1006	93	581	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:29:05,687] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26772/tc_result.tsv
[2023-03-16 07:29:05,688] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:29:05,688] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:29:05,688] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg64a4ee47-8828-4d34-a82e-6621752503af/dqc_reference/checkm_data
[2023-03-16 07:29:05,689] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:29:05,697] [INFO] Task started: CheckM
[2023-03-16 07:29:05,697] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26772/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26772/checkm_input OceanDNA-b26772/checkm_result
[2023-03-16 07:29:37,299] [INFO] Task succeeded: CheckM
[2023-03-16 07:29:37,300] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 4.55%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 07:29:37,304] [INFO] ===== Completeness check finished =====
[2023-03-16 07:29:37,305] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:29:37,305] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26772/markers.fasta)
[2023-03-16 07:29:37,306] [INFO] Task started: Blastn
[2023-03-16 07:29:37,306] [INFO] Running command: blastn -query OceanDNA-b26772/markers.fasta -db /var/lib/cwl/stg64a4ee47-8828-4d34-a82e-6621752503af/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26772/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:29:38,967] [INFO] Task succeeded: Blastn
[2023-03-16 07:29:38,968] [INFO] Selected 38 target genomes.
[2023-03-16 07:29:38,968] [INFO] Target genome list was writen to OceanDNA-b26772/target_genomes_gtdb.txt
[2023-03-16 07:29:39,423] [INFO] Task started: fastANI
[2023-03-16 07:29:39,423] [INFO] Running command: fastANI --query /var/lib/cwl/stge8f6deea-de42-4c65-8c64-6a1fe4a7e069/OceanDNA-b26772.fa --refList OceanDNA-b26772/target_genomes_gtdb.txt --output OceanDNA-b26772/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:30:12,316] [INFO] Task succeeded: fastANI
[2023-03-16 07:30:12,337] [INFO] Found 38 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 07:30:12,337] [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
GCF_003583935.1	s__Aureimonas flava	77.0983	141	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004963905.1	s__Mesorhizobium sp004963905	77.0388	123	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114255.1	s__Mesorhizobium_F albiziae	77.0008	112	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002088275.1	s__Jiella sp002088275	76.9692	138	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004354915.1	s__Pseudohoeflea suaedae	76.7606	102	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudohoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002709005.1	s__Pseudohoeflea sp002709005	76.7546	80	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudohoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008802405.1	s__Aureimonas_A leprariae	76.7513	151	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001463765.1	s__Aureimonas sp001463765	76.7235	134	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177325.1	s__Mesorhizobium_A australicum_A	76.7142	143	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153465.1	s__Aurantimonas manganoxydans	76.714	139	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.4342	99.99	99.99	1.00	1.00	2	-
GCF_014196845.1	s__Aurantimonas endophytica	76.7049	128	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014860725.1	s__Aquamicrobium_A sp014860725	76.6951	98	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168195.1	s__Bosea thiooxidans	76.6891	109	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	99.77	99.77	0.94	0.94	2	-
GCF_900185725.1	s__Stappia sp900185725	76.6693	137	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	98.18	97.99	0.94	0.94	3	-
GCF_004331955.1	s__Roseitalea porphyridii	76.6449	129	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Roseitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970795.1	s__Mesorhizobium_E carbonis	76.6325	135	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305925.1	s__JAFKJW01 sp017305925	76.6238	137	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__JAFKJW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016591715.1	s__Mesorhizobium sp016591715	76.6192	130	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017353515.1	s__Jiella sp017353515	76.6129	153	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300335.1	s__Nitratireductor pacificus	76.6	138	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001014615.2	s__Aquamicrobium_A sp001014615	76.575	129	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016756595.1	s__Mesorhizobium sp004020105	76.5131	110	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.38	95.83	0.84	0.81	7	-
GCF_900113065.1	s__Aureimonas phyllosphaerae	76.4845	143	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	99.99	99.99	0.99	0.99	3	-
GCF_014643375.1	s__Aureimonas_A glaciei	76.4779	145	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873545.1	s__OAS926 sp014873545	76.4631	142	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__OAS926	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013358405.1	s__Oricola thermophila	76.4592	104	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014642635.1	s__Aureimonas_A endophytica	76.4587	144	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382705.1	s__Aureimonas ureilytica	76.4499	145	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014058705.1	s__Aureimonas mangrovi	76.4195	126	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015904235.1	s__L22 sp015904235	76.4121	139	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__L22	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904745.1	s__Oricola sp014904745	76.3939	116	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793485.1	s__RCIZ01 sp016793485	76.3768	97	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992195.1	s__Methylobacterium oxalidis	76.3586	114	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004959855.1	s__SPNT01 sp004959855	76.3217	106	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__SPNT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706335.1	s__Oricola sp002706335	76.3034	98	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008040035.1	s__Methylobacterium sp008040035	76.2109	95	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500815.1	s__Jiella pacifica	76.1676	131	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000019365.1	s__Methylobacterium sp000019365	75.9896	150	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.09	99.09	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-03-16 07:30:12,337] [INFO] GTDB search result was written to OceanDNA-b26772/result_gtdb.tsv
[2023-03-16 07:30:12,337] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:30:12,341] [INFO] DFAST_QC result json was written to OceanDNA-b26772/dqc_result.json
[2023-03-16 07:30:12,341] [INFO] DFAST_QC completed!
[2023-03-16 07:30:12,341] [INFO] Total running time: 0h1m42s