[2023-03-15 05:29:10,768] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:29:10,768] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:29:10,768] [INFO] DQC Reference Directory: /var/lib/cwl/stg03a887bb-0f82-42d6-a7d6-275337bc2a97/dqc_reference
[2023-03-15 05:29:12,383] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:29:12,384] [INFO] Task started: Prodigal
[2023-03-15 05:29:12,384] [INFO] Running command: cat /var/lib/cwl/stg96e779b5-f730-42c0-9302-80ab50fba0ac/OceanDNA-b26646.fa | prodigal -d OceanDNA-b26646/cds.fna -a OceanDNA-b26646/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:29:40,902] [INFO] Task succeeded: Prodigal
[2023-03-15 05:29:40,902] [INFO] Task started: HMMsearch
[2023-03-15 05:29:40,902] [INFO] Running command: hmmsearch --tblout OceanDNA-b26646/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03a887bb-0f82-42d6-a7d6-275337bc2a97/dqc_reference/reference_markers.hmm OceanDNA-b26646/protein.faa > /dev/null
[2023-03-15 05:29:41,246] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:29:41,247] [INFO] Found 6/6 markers.
[2023-03-15 05:29:41,275] [INFO] Query marker FASTA was written to OceanDNA-b26646/markers.fasta
[2023-03-15 05:29:41,275] [INFO] Task started: Blastn
[2023-03-15 05:29:41,275] [INFO] Running command: blastn -query OceanDNA-b26646/markers.fasta -db /var/lib/cwl/stg03a887bb-0f82-42d6-a7d6-275337bc2a97/dqc_reference/reference_markers.fasta -out OceanDNA-b26646/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:29:42,287] [INFO] Task succeeded: Blastn
[2023-03-15 05:29:42,288] [INFO] Selected 26 target genomes.
[2023-03-15 05:29:42,288] [INFO] Target genome list was writen to OceanDNA-b26646/target_genomes.txt
[2023-03-15 05:29:42,298] [INFO] Task started: fastANI
[2023-03-15 05:29:42,298] [INFO] Running command: fastANI --query /var/lib/cwl/stg96e779b5-f730-42c0-9302-80ab50fba0ac/OceanDNA-b26646.fa --refList OceanDNA-b26646/target_genomes.txt --output OceanDNA-b26646/fastani_result.tsv --threads 1
[2023-03-15 05:30:07,838] [INFO] Task succeeded: fastANI
[2023-03-15 05:30:07,839] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03a887bb-0f82-42d6-a7d6-275337bc2a97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:30:07,839] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03a887bb-0f82-42d6-a7d6-275337bc2a97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:30:07,853] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:30:07,853] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 05:30:07,853] [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
Amorphus coralli	strain=DSM 19760	GCA_000374525.1	340680	340680	type	True	83.7388	1119	1539	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_014197785.1	34017	34017	type	True	78.0815	434	1539	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_016653375.1	34017	34017	type	True	78.0779	438	1539	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	77.9856	431	1539	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_003258835.1	34017	34017	type	True	77.9721	434	1539	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	77.737	511	1539	95	below_threshold
Acuticoccus kandeliae	strain=J103	GCA_003073115.1	2073160	2073160	type	True	77.6132	461	1539	95	below_threshold
Acuticoccus mangrovi	strain=B2012	GCA_016411865.1	2796142	2796142	type	True	77.5537	498	1539	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	77.4145	390	1539	95	below_threshold
Kaistia granuli	strain=Ko04	GCA_000380505.1	363259	363259	type	True	77.4136	335	1539	95	below_threshold
Pleomorphomonas carboxyditropha	strain=SVCO-16	GCA_002770725.1	2023338	2023338	type	True	77.381	383	1539	95	below_threshold
Ancylobacter sonchi	strain=VKM B-3145	GCA_018390695.1	1937790	1937790	type	True	77.3799	431	1539	95	below_threshold
Ancylobacter dichloromethanicus	strain=VKM B-2484	GCA_018390645.1	518825	518825	type	True	77.3688	395	1539	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	77.2926	437	1539	95	below_threshold
Microvirga lotononidis	strain=WSM3557	GCA_000262405.1	864069	864069	type	True	77.2724	274	1539	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	77.1986	367	1539	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	77.1652	273	1539	95	below_threshold
Bosea caraganae	strain=RCAM 04680	GCA_003351345.1	2763117	2763117	type	True	77.1235	413	1539	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	77.0766	440	1539	95	below_threshold
Mesorhizobium silamurunense	strain=CCBAU 01550	GCA_014843825.1	499528	499528	type	True	77.0156	326	1539	95	below_threshold
Rhodoplanes piscinae	strain=DSM 19946	GCA_003258855.1	444923	444923	type	True	76.9699	379	1539	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	76.9651	322	1539	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	76.963	422	1539	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	76.8694	336	1539	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	76.8341	298	1539	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	76.8184	343	1539	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 05:30:07,854] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26646/tc_result.tsv
[2023-03-15 05:30:07,854] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:30:07,854] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:30:07,854] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03a887bb-0f82-42d6-a7d6-275337bc2a97/dqc_reference/checkm_data
[2023-03-15 05:30:07,855] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:30:07,860] [INFO] Task started: CheckM
[2023-03-15 05:30:07,861] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26646/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26646/checkm_input OceanDNA-b26646/checkm_result
[2023-03-15 05:31:18,154] [INFO] Task succeeded: CheckM
[2023-03-15 05:31:18,154] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:31:18,157] [INFO] ===== Completeness check finished =====
[2023-03-15 05:31:18,157] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:31:18,158] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26646/markers.fasta)
[2023-03-15 05:31:18,159] [INFO] Task started: Blastn
[2023-03-15 05:31:18,159] [INFO] Running command: blastn -query OceanDNA-b26646/markers.fasta -db /var/lib/cwl/stg03a887bb-0f82-42d6-a7d6-275337bc2a97/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26646/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:31:20,224] [INFO] Task succeeded: Blastn
[2023-03-15 05:31:20,225] [INFO] Selected 25 target genomes.
[2023-03-15 05:31:20,225] [INFO] Target genome list was writen to OceanDNA-b26646/target_genomes_gtdb.txt
[2023-03-15 05:31:20,246] [INFO] Task started: fastANI
[2023-03-15 05:31:20,246] [INFO] Running command: fastANI --query /var/lib/cwl/stg96e779b5-f730-42c0-9302-80ab50fba0ac/OceanDNA-b26646.fa --refList OceanDNA-b26646/target_genomes_gtdb.txt --output OceanDNA-b26646/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:31:41,251] [INFO] Task succeeded: fastANI
[2023-03-15 05:31:41,267] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 05:31:41,268] [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_000374525.1	s__Amorphus coralli	83.7257	1120	1539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Amorphaceae;g__Amorphus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001696535.1	s__Stappia indica	78.0913	462	1539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	97.23	96.79	0.94	0.94	3	-
GCF_003610575.1	s__Stappia sp003610575	78.0377	451	1539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	98.18	98.18	0.97	0.97	2	-
GCF_003258835.1	s__Rhodobium orientis	78.0044	430	1539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodobiaceae;g__Rhodobium	95.0	99.99	99.98	0.99	0.98	3	-
GCF_009789575.1	s__Stappia indica_A	77.9449	504	1539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900185725.1	s__Stappia sp900185725	77.9379	502	1539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	98.18	97.99	0.94	0.94	3	-
GCF_015904235.1	s__L22 sp015904235	77.7775	478	1539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__L22	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362745.1	s__Oharaeibacter diazotrophicus	77.7724	505	1539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Oharaeibacter	95.0	99.98	99.97	1.00	1.00	3	-
GCF_900148505.1	s__Pseudoxanthobacter soli	77.7507	396	1539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pseudoxanthobacteraceae;g__Pseudoxanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907975.1	s__Methylopila capsulata	77.6433	365	1539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Methylopila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009600605.1	s__Pseudoxanthobacter spirostomi	77.6122	425	1539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pseudoxanthobacteraceae;g__Pseudoxanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722295.1	s__Stappia sp002722295	77.6106	341	1539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	99.88	99.88	0.88	0.88	2	-
GCF_003432385.1	s__Breoghania sp003432385	77.5938	391	1539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Breoghania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526315.1	s__Methylopila sp000526315	77.5389	359	1539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Methylopila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423225.1	s__Kaistia adipata	77.3859	394	1539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002770725.1	s__Pleomorphomonas carboxyditropha	77.3801	385	1539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	98.10	98.10	0.89	0.89	2	-
GCF_014635285.1	s__Stappia taiwanensis	77.3416	363	1539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000425185.1	s__Pleomorphomonas koreensis	77.2858	385	1539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	95.03	95.03	0.88	0.88	2	-
GCA_017305635.1	s__Bauldia sp017305635	77.2519	342	1539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Bauldia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007922615.2	s__Nitratireductor_D sp007922615	77.2451	339	1539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716745.1	s__GCA-013693735 sp016716745	77.0265	351	1539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__GCA-013693735	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258865.1	s__Rhodoplanes roseus	76.9792	424	1539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196455.1	s__Kaistia hirudinis	76.9658	322	1539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	96.80	96.80	0.96	0.96	2	-
GCF_003173715.1	s__Methylobacterium durans	76.8169	315	1539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018262575.1	s__Pleomorphomonas sp018262575	76.6453	239	1539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 05:31:41,268] [INFO] GTDB search result was written to OceanDNA-b26646/result_gtdb.tsv
[2023-03-15 05:31:41,268] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:31:41,271] [INFO] DFAST_QC result json was written to OceanDNA-b26646/dqc_result.json
[2023-03-15 05:31:41,271] [INFO] DFAST_QC completed!
[2023-03-15 05:31:41,271] [INFO] Total running time: 0h2m31s