[2023-06-29 23:48:23,969] [INFO] DFAST_QC pipeline started.
[2023-06-29 23:48:23,971] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 23:48:23,971] [INFO] DQC Reference Directory: /var/lib/cwl/stgb931897a-db71-4354-bc30-3fae90ec923e/dqc_reference
[2023-06-29 23:48:25,157] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 23:48:25,158] [INFO] Task started: Prodigal
[2023-06-29 23:48:25,158] [INFO] Running command: gunzip -c /var/lib/cwl/stg7a634e4c-3178-457e-9166-507f39b90bef/GCA_016869375.1_JGI_2017-08-21_genomic.fna.gz | prodigal -d GCA_016869375.1_JGI_2017-08-21_genomic.fna/cds.fna -a GCA_016869375.1_JGI_2017-08-21_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 23:48:37,342] [INFO] Task succeeded: Prodigal
[2023-06-29 23:48:37,343] [INFO] Task started: HMMsearch
[2023-06-29 23:48:37,344] [INFO] Running command: hmmsearch --tblout GCA_016869375.1_JGI_2017-08-21_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb931897a-db71-4354-bc30-3fae90ec923e/dqc_reference/reference_markers.hmm GCA_016869375.1_JGI_2017-08-21_genomic.fna/protein.faa > /dev/null
[2023-06-29 23:48:37,657] [INFO] Task succeeded: HMMsearch
[2023-06-29 23:48:37,658] [INFO] Found 6/6 markers.
[2023-06-29 23:48:37,703] [INFO] Query marker FASTA was written to GCA_016869375.1_JGI_2017-08-21_genomic.fna/markers.fasta
[2023-06-29 23:48:37,703] [INFO] Task started: Blastn
[2023-06-29 23:48:37,703] [INFO] Running command: blastn -query GCA_016869375.1_JGI_2017-08-21_genomic.fna/markers.fasta -db /var/lib/cwl/stgb931897a-db71-4354-bc30-3fae90ec923e/dqc_reference/reference_markers.fasta -out GCA_016869375.1_JGI_2017-08-21_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:48:38,716] [INFO] Task succeeded: Blastn
[2023-06-29 23:48:38,720] [INFO] Selected 28 target genomes.
[2023-06-29 23:48:38,720] [INFO] Target genome list was writen to GCA_016869375.1_JGI_2017-08-21_genomic.fna/target_genomes.txt
[2023-06-29 23:48:38,721] [INFO] Task started: fastANI
[2023-06-29 23:48:38,721] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a634e4c-3178-457e-9166-507f39b90bef/GCA_016869375.1_JGI_2017-08-21_genomic.fna.gz --refList GCA_016869375.1_JGI_2017-08-21_genomic.fna/target_genomes.txt --output GCA_016869375.1_JGI_2017-08-21_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 23:49:04,385] [INFO] Task succeeded: fastANI
[2023-06-29 23:49:04,386] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb931897a-db71-4354-bc30-3fae90ec923e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 23:49:04,387] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb931897a-db71-4354-bc30-3fae90ec923e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 23:49:04,408] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 23:49:04,408] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 23:49:04,409] [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
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	77.3521	394	1510	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	77.2838	291	1510	95	below_threshold
Hypericibacter terrae	strain=R5913	GCA_008728855.1	2602015	2602015	type	True	77.1031	364	1510	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	77.0427	434	1510	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.9828	295	1510	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	76.9026	336	1510	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.8643	351	1510	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.863	487	1510	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.8568	493	1510	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.8406	288	1510	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_001315015.1	192	192	type	True	76.8133	326	1510	95	below_threshold
Skermanella rosea	strain=KEMB 2255-458	GCA_016806835.2	1817965	1817965	type	True	76.8111	340	1510	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	76.8032	295	1510	95	below_threshold
Azospirillum humicireducens	strain=SgZ-5	GCA_001639105.2	1226968	1226968	type	True	76.7972	309	1510	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_008274945.1	192	192	type	True	76.7895	331	1510	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_007827425.1	192	192	type	True	76.7816	336	1510	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.7524	243	1510	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	76.7494	326	1510	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	76.747	401	1510	95	below_threshold
Azospirillum doebereinerae	strain=GSF71	GCA_003989665.1	92933	92933	type	True	76.7026	345	1510	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	76.643	336	1510	95	below_threshold
Nitrospirillum iridis	strain=DSM 22198	GCA_014205765.1	765888	765888	type	True	76.308	194	1510	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	76.2783	255	1510	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.1406	290	1510	95	below_threshold
Stappia taiwanensis	strain=CCM 7757	GCA_014635285.1	992267	992267	type	True	76.0535	176	1510	95	below_threshold
Stappia taiwanensis	strain=DSM 23284	GCA_013868145.1	992267	992267	type	True	76.0521	179	1510	95	below_threshold
Gemmobacter megaterium	strain=DSM 26375	GCA_900156815.1	1086013	1086013	type	True	75.4861	74	1510	95	below_threshold
Gemmobacter megaterium	strain=CGMCC 1.11024	GCA_014636395.1	1086013	1086013	type	True	75.4725	75	1510	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 23:49:04,411] [INFO] DFAST Taxonomy check result was written to GCA_016869375.1_JGI_2017-08-21_genomic.fna/tc_result.tsv
[2023-06-29 23:49:04,412] [INFO] ===== Taxonomy check completed =====
[2023-06-29 23:49:04,412] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 23:49:04,412] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb931897a-db71-4354-bc30-3fae90ec923e/dqc_reference/checkm_data
[2023-06-29 23:49:04,413] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 23:49:04,468] [INFO] Task started: CheckM
[2023-06-29 23:49:04,468] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016869375.1_JGI_2017-08-21_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016869375.1_JGI_2017-08-21_genomic.fna/checkm_input GCA_016869375.1_JGI_2017-08-21_genomic.fna/checkm_result
[2023-06-29 23:49:42,351] [INFO] Task succeeded: CheckM
[2023-06-29 23:49:42,353] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.04%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 23:49:42,376] [INFO] ===== Completeness check finished =====
[2023-06-29 23:49:42,377] [INFO] ===== Start GTDB Search =====
[2023-06-29 23:49:42,377] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016869375.1_JGI_2017-08-21_genomic.fna/markers.fasta)
[2023-06-29 23:49:42,377] [INFO] Task started: Blastn
[2023-06-29 23:49:42,378] [INFO] Running command: blastn -query GCA_016869375.1_JGI_2017-08-21_genomic.fna/markers.fasta -db /var/lib/cwl/stgb931897a-db71-4354-bc30-3fae90ec923e/dqc_reference/reference_markers_gtdb.fasta -out GCA_016869375.1_JGI_2017-08-21_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:49:44,374] [INFO] Task succeeded: Blastn
[2023-06-29 23:49:44,378] [INFO] Selected 12 target genomes.
[2023-06-29 23:49:44,379] [INFO] Target genome list was writen to GCA_016869375.1_JGI_2017-08-21_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 23:49:44,381] [INFO] Task started: fastANI
[2023-06-29 23:49:44,382] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a634e4c-3178-457e-9166-507f39b90bef/GCA_016869375.1_JGI_2017-08-21_genomic.fna.gz --refList GCA_016869375.1_JGI_2017-08-21_genomic.fna/target_genomes_gtdb.txt --output GCA_016869375.1_JGI_2017-08-21_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 23:49:56,462] [INFO] Task succeeded: fastANI
[2023-06-29 23:49:56,476] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 23:49:56,476] [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_016869375.1	s__SHVZ01 sp016869375	100.0	1493	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVZ01;f__SHVZ01;g__SHVZ01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016869285.1	s__SHVZ01 sp016869285	86.4251	1060	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVZ01;f__SHVZ01;g__SHVZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792585.1	s__SHVZ01 sp016792585	85.0189	1110	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVZ01;f__SHVZ01;g__SHVZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009694025.1	s__SHVZ01 sp009694025	83.2359	777	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVZ01;f__SHVZ01;g__SHVZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016195085.1	s__JACQAG01 sp016195085	77.9267	511	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVZ01;f__SHVZ01;g__JACQAG01	95.0	99.88	99.88	0.96	0.96	2	-
GCA_016869645.1	s__SHVW01 sp016869645	77.7146	444	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVW01;f__SHVW01;g__SHVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728835.1	s__Hypericibacter adhaerens	77.3121	399	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Hypericibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	76.8972	480	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCA_016792765.1	s__SBBV01 sp016792765	76.6353	323	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Bin65;f__Bin65;g__SBBV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869275.1	s__SHVV01 sp016869275	76.3982	231	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVV01;f__SHVV01;g__SHVV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903927615.1	s__BOG-933 sp903927615	75.4243	92	1510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__BOG-933	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872815.1	s__SIAN01 sp016872815	75.0071	149	1510	d__Bacteria;p__Planctomycetota;c__B15-G4;o__B15-G4;f__SIAN01;g__SIAN01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 23:49:56,500] [INFO] GTDB search result was written to GCA_016869375.1_JGI_2017-08-21_genomic.fna/result_gtdb.tsv
[2023-06-29 23:49:56,501] [INFO] ===== GTDB Search completed =====
[2023-06-29 23:49:56,506] [INFO] DFAST_QC result json was written to GCA_016869375.1_JGI_2017-08-21_genomic.fna/dqc_result.json
[2023-06-29 23:49:56,507] [INFO] DFAST_QC completed!
[2023-06-29 23:49:56,507] [INFO] Total running time: 0h1m33s