[2023-06-30 10:21:44,094] [INFO] DFAST_QC pipeline started.
[2023-06-30 10:21:44,097] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 10:21:44,097] [INFO] DQC Reference Directory: /var/lib/cwl/stg73ed9062-1e36-45b7-b3b4-19332e9bb795/dqc_reference
[2023-06-30 10:21:46,023] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 10:21:46,024] [INFO] Task started: Prodigal
[2023-06-30 10:21:46,024] [INFO] Running command: gunzip -c /var/lib/cwl/stg985aee82-5d71-46a3-9442-422ed05d0c00/GCA_903822765.1_freshwater_MAG_---_Umea3p2_bin-0279_genomic.fna.gz | prodigal -d GCA_903822765.1_freshwater_MAG_---_Umea3p2_bin-0279_genomic.fna/cds.fna -a GCA_903822765.1_freshwater_MAG_---_Umea3p2_bin-0279_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 10:22:00,027] [INFO] Task succeeded: Prodigal
[2023-06-30 10:22:00,028] [INFO] Task started: HMMsearch
[2023-06-30 10:22:00,028] [INFO] Running command: hmmsearch --tblout GCA_903822765.1_freshwater_MAG_---_Umea3p2_bin-0279_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg73ed9062-1e36-45b7-b3b4-19332e9bb795/dqc_reference/reference_markers.hmm GCA_903822765.1_freshwater_MAG_---_Umea3p2_bin-0279_genomic.fna/protein.faa > /dev/null
[2023-06-30 10:22:00,329] [INFO] Task succeeded: HMMsearch
[2023-06-30 10:22:00,331] [INFO] Found 6/6 markers.
[2023-06-30 10:22:00,387] [INFO] Query marker FASTA was written to GCA_903822765.1_freshwater_MAG_---_Umea3p2_bin-0279_genomic.fna/markers.fasta
[2023-06-30 10:22:00,388] [INFO] Task started: Blastn
[2023-06-30 10:22:00,388] [INFO] Running command: blastn -query GCA_903822765.1_freshwater_MAG_---_Umea3p2_bin-0279_genomic.fna/markers.fasta -db /var/lib/cwl/stg73ed9062-1e36-45b7-b3b4-19332e9bb795/dqc_reference/reference_markers.fasta -out GCA_903822765.1_freshwater_MAG_---_Umea3p2_bin-0279_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:22:01,312] [INFO] Task succeeded: Blastn
[2023-06-30 10:22:01,318] [INFO] Selected 27 target genomes.
[2023-06-30 10:22:01,319] [INFO] Target genome list was writen to GCA_903822765.1_freshwater_MAG_---_Umea3p2_bin-0279_genomic.fna/target_genomes.txt
[2023-06-30 10:22:01,342] [INFO] Task started: fastANI
[2023-06-30 10:22:01,342] [INFO] Running command: fastANI --query /var/lib/cwl/stg985aee82-5d71-46a3-9442-422ed05d0c00/GCA_903822765.1_freshwater_MAG_---_Umea3p2_bin-0279_genomic.fna.gz --refList GCA_903822765.1_freshwater_MAG_---_Umea3p2_bin-0279_genomic.fna/target_genomes.txt --output GCA_903822765.1_freshwater_MAG_---_Umea3p2_bin-0279_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 10:22:27,457] [INFO] Task succeeded: fastANI
[2023-06-30 10:22:27,458] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg73ed9062-1e36-45b7-b3b4-19332e9bb795/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 10:22:27,458] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg73ed9062-1e36-45b7-b3b4-19332e9bb795/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 10:22:27,479] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 10:22:27,479] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 10:22:27,479] [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
Aliidongia dinghuensis	strain=CGMCC 1.15725	GCA_014643535.1	1867774	1867774	type	True	76.9502	287	1587	95	below_threshold
Hypericibacter terrae	strain=R5913	GCA_008728855.1	2602015	2602015	type	True	76.7637	278	1587	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	76.7323	286	1587	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.6825	186	1587	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.55	182	1587	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	76.5298	252	1587	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	76.5266	248	1587	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.4885	170	1587	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	76.3449	249	1587	95	below_threshold
Azospirillum thiophilum	strain=BV-S	GCA_001305595.1	528244	528244	type	True	76.3188	252	1587	95	below_threshold
Azospirillum humicireducens	strain=SgZ-5	GCA_001639105.2	1226968	1226968	type	True	76.3081	233	1587	95	below_threshold
Azospirillum oryzae	strain=COC8	GCA_008364795.1	286727	286727	type	True	76.2839	221	1587	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	76.2714	264	1587	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	76.2406	227	1587	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	76.2134	131	1587	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	76.2112	199	1587	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.1869	276	1587	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.1688	277	1587	95	below_threshold
Skermanella rosea	strain=KEMB 2255-458	GCA_016806835.2	1817965	1817965	type	True	76.1378	225	1587	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.0473	175	1587	95	below_threshold
Rhizobium lentis	strain=BLR27	GCA_017352135.1	1138194	1138194	type	True	75.9951	136	1587	95	below_threshold
Aurantimonas manganoxydans	strain=SI85-9A1	GCA_000153465.1	651183	651183	type	True	75.9862	151	1587	95	below_threshold
Rhizobium lentis	strain=BLR27	GCA_019684715.1	1138194	1138194	type	True	75.9417	133	1587	95	below_threshold
Aurantimonas manganoxydans	strain=DSM 21871	GCA_001463865.1	651183	651183	type	True	75.9186	151	1587	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	75.9037	201	1587	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	75.6518	225	1587	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	75.4662	177	1587	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 10:22:27,482] [INFO] DFAST Taxonomy check result was written to GCA_903822765.1_freshwater_MAG_---_Umea3p2_bin-0279_genomic.fna/tc_result.tsv
[2023-06-30 10:22:27,483] [INFO] ===== Taxonomy check completed =====
[2023-06-30 10:22:27,483] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 10:22:27,483] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg73ed9062-1e36-45b7-b3b4-19332e9bb795/dqc_reference/checkm_data
[2023-06-30 10:22:27,485] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 10:22:27,534] [INFO] Task started: CheckM
[2023-06-30 10:22:27,535] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903822765.1_freshwater_MAG_---_Umea3p2_bin-0279_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903822765.1_freshwater_MAG_---_Umea3p2_bin-0279_genomic.fna/checkm_input GCA_903822765.1_freshwater_MAG_---_Umea3p2_bin-0279_genomic.fna/checkm_result
[2023-06-30 10:23:09,838] [INFO] Task succeeded: CheckM
[2023-06-30 10:23:09,839] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 10:23:09,879] [INFO] ===== Completeness check finished =====
[2023-06-30 10:23:09,879] [INFO] ===== Start GTDB Search =====
[2023-06-30 10:23:09,880] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903822765.1_freshwater_MAG_---_Umea3p2_bin-0279_genomic.fna/markers.fasta)
[2023-06-30 10:23:09,880] [INFO] Task started: Blastn
[2023-06-30 10:23:09,880] [INFO] Running command: blastn -query GCA_903822765.1_freshwater_MAG_---_Umea3p2_bin-0279_genomic.fna/markers.fasta -db /var/lib/cwl/stg73ed9062-1e36-45b7-b3b4-19332e9bb795/dqc_reference/reference_markers_gtdb.fasta -out GCA_903822765.1_freshwater_MAG_---_Umea3p2_bin-0279_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:23:11,535] [INFO] Task succeeded: Blastn
[2023-06-30 10:23:11,541] [INFO] Selected 21 target genomes.
[2023-06-30 10:23:11,541] [INFO] Target genome list was writen to GCA_903822765.1_freshwater_MAG_---_Umea3p2_bin-0279_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 10:23:11,553] [INFO] Task started: fastANI
[2023-06-30 10:23:11,553] [INFO] Running command: fastANI --query /var/lib/cwl/stg985aee82-5d71-46a3-9442-422ed05d0c00/GCA_903822765.1_freshwater_MAG_---_Umea3p2_bin-0279_genomic.fna.gz --refList GCA_903822765.1_freshwater_MAG_---_Umea3p2_bin-0279_genomic.fna/target_genomes_gtdb.txt --output GCA_903822765.1_freshwater_MAG_---_Umea3p2_bin-0279_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 10:23:30,478] [INFO] Task succeeded: fastANI
[2023-06-30 10:23:30,507] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 10:23:30,508] [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_903828515.1	s__CAIKMD01 sp903828515	99.9991	1583	1587	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__CAIKMD01	95.0	99.99	99.96	1.00	0.99	5	conclusive
GCA_903822185.1	s__CAIKMD01 sp903822185	79.1499	729	1587	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__CAIKMD01	95.0	99.70	99.51	0.99	0.98	4	-
GCA_018971215.1	s__REEB95 sp018971215	77.8319	312	1587	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__REEB95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000518365.1	s__URHD0088 sp000518365	77.5171	378	1587	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__URHD0088	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015654725.1	s__JAATGI01 sp015654725	76.9933	198	1587	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__JAATGI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643535.1	s__Aliidongia dinghuensis	76.9595	284	1587	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Aliidongia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728855.1	s__Hypericibacter terrae	76.754	279	1587	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Hypericibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903897565.1	s__CAIXXC01 sp903897565	76.5951	150	1587	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__CAIXXC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006738865.1	s__Stella sp006738865	76.5905	258	1587	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869645.1	s__SHVW01 sp016869645	76.5101	248	1587	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVW01;f__SHVW01;g__SHVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793045.1	s__JAEUKZ01 sp016793045	76.5065	260	1587	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__JAEUKZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620685.1	s__Dongia sp000620685	76.4535	191	1587	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Dongia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006739055.1	s__Stella vacuolata	76.4354	269	1587	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377445.1	s__WHUA01 sp009377445	76.3806	188	1587	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__WHUA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899285.1	s__Pseudolabrys sp001899285	76.3413	197	1587	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	99.99	99.99	1.00	1.00	2	-
GCF_017876095.1	s__Azospirillum agricola	76.2852	262	1587	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	96.88	96.88	0.87	0.87	2	-
GCA_017307375.1	s__JAFKFH01 sp017307375	76.2463	294	1587	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__JAFKFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876115.1	s__Azospirillum picis	76.2247	229	1587	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793965.1	s__JAEULF01 sp016793965	76.0915	161	1587	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__JAEULF01;f__JAEULF01;g__JAEULF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011759535.1	s__Pleomorphomonas sp011759535	75.8751	112	1587	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003135415.1	s__Palsa-892 sp003135415	75.8526	114	1587	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Palsa-892	95.0	96.11	96.04	0.87	0.83	3	-
--------------------------------------------------------------------------------
[2023-06-30 10:23:30,510] [INFO] GTDB search result was written to GCA_903822765.1_freshwater_MAG_---_Umea3p2_bin-0279_genomic.fna/result_gtdb.tsv
[2023-06-30 10:23:30,510] [INFO] ===== GTDB Search completed =====
[2023-06-30 10:23:30,515] [INFO] DFAST_QC result json was written to GCA_903822765.1_freshwater_MAG_---_Umea3p2_bin-0279_genomic.fna/dqc_result.json
[2023-06-30 10:23:30,515] [INFO] DFAST_QC completed!
[2023-06-30 10:23:30,515] [INFO] Total running time: 0h1m46s