[2023-06-28 20:48:50,728] [INFO] DFAST_QC pipeline started.
[2023-06-28 20:48:50,731] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 20:48:50,732] [INFO] DQC Reference Directory: /var/lib/cwl/stg78c4896b-ffc9-40bd-9158-99514e083d49/dqc_reference
[2023-06-28 20:48:53,137] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 20:48:53,138] [INFO] Task started: Prodigal
[2023-06-28 20:48:53,139] [INFO] Running command: gunzip -c /var/lib/cwl/stg4bb84266-8adb-4b9c-9609-8e379f5c1592/GCA_913055885.1_SRR6193124_bin.73_MetaBAT_v2.12.1_MAG_genomic.fna.gz | prodigal -d GCA_913055885.1_SRR6193124_bin.73_MetaBAT_v2.12.1_MAG_genomic.fna/cds.fna -a GCA_913055885.1_SRR6193124_bin.73_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 20:49:00,890] [INFO] Task succeeded: Prodigal
[2023-06-28 20:49:00,891] [INFO] Task started: HMMsearch
[2023-06-28 20:49:00,891] [INFO] Running command: hmmsearch --tblout GCA_913055885.1_SRR6193124_bin.73_MetaBAT_v2.12.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78c4896b-ffc9-40bd-9158-99514e083d49/dqc_reference/reference_markers.hmm GCA_913055885.1_SRR6193124_bin.73_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 20:49:01,141] [INFO] Task succeeded: HMMsearch
[2023-06-28 20:49:01,143] [INFO] Found 6/6 markers.
[2023-06-28 20:49:01,170] [INFO] Query marker FASTA was written to GCA_913055885.1_SRR6193124_bin.73_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta
[2023-06-28 20:49:01,171] [INFO] Task started: Blastn
[2023-06-28 20:49:01,171] [INFO] Running command: blastn -query GCA_913055885.1_SRR6193124_bin.73_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg78c4896b-ffc9-40bd-9158-99514e083d49/dqc_reference/reference_markers.fasta -out GCA_913055885.1_SRR6193124_bin.73_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:49:02,030] [INFO] Task succeeded: Blastn
[2023-06-28 20:49:02,034] [INFO] Selected 31 target genomes.
[2023-06-28 20:49:02,034] [INFO] Target genome list was writen to GCA_913055885.1_SRR6193124_bin.73_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt
[2023-06-28 20:49:02,035] [INFO] Task started: fastANI
[2023-06-28 20:49:02,035] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bb84266-8adb-4b9c-9609-8e379f5c1592/GCA_913055885.1_SRR6193124_bin.73_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913055885.1_SRR6193124_bin.73_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt --output GCA_913055885.1_SRR6193124_bin.73_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 20:49:28,128] [INFO] Task succeeded: fastANI
[2023-06-28 20:49:28,129] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78c4896b-ffc9-40bd-9158-99514e083d49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 20:49:28,130] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78c4896b-ffc9-40bd-9158-99514e083d49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 20:49:28,154] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 20:49:28,154] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 20:49:28,155] [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
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	77.1543	219	777	95	below_threshold
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	77.1342	243	777	95	below_threshold
Roseospira navarrensis	strain=DSM 15114	GCA_009601025.1	140058	140058	type	True	76.9317	204	777	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.8755	213	777	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.7258	210	777	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	76.6402	174	777	95	below_threshold
Roseospira goensis	strain=JA135	GCA_014197795.1	391922	391922	type	True	76.622	235	777	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	76.4346	273	777	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	76.3652	201	777	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	76.3317	191	777	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	76.3304	214	777	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	76.3104	204	777	95	below_threshold
Azospirillum formosense	strain=CC-NFb-7	GCA_013340925.1	861533	861533	type	True	76.2797	203	777	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.2628	220	777	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.253	225	777	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	76.2352	180	777	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	76.2009	199	777	95	below_threshold
Roseospira marina	strain=DSM 15113	GCA_014203135.1	140057	140057	type	True	76.1732	158	777	95	below_threshold
Roseospira marina	strain=DSM 15113	GCA_014197855.1	140057	140057	type	True	76.1626	156	777	95	below_threshold
Azospirillum doebereinerae	strain=GSF71	GCA_003989665.1	92933	92933	type	True	76.1484	211	777	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	76.0993	162	777	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	75.9888	190	777	95	below_threshold
Elioraea thermophila	strain=YIM 72297	GCA_003336755.1	2185104	2185104	type	True	75.9768	106	777	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	75.9442	77	777	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	75.8566	145	777	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	75.7994	136	777	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	75.6152	217	777	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	75.5991	151	777	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	75.557	91	777	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	75.5036	122	777	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	75.2932	79	777	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 20:49:28,167] [INFO] DFAST Taxonomy check result was written to GCA_913055885.1_SRR6193124_bin.73_MetaBAT_v2.12.1_MAG_genomic.fna/tc_result.tsv
[2023-06-28 20:49:28,168] [INFO] ===== Taxonomy check completed =====
[2023-06-28 20:49:28,168] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 20:49:28,168] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78c4896b-ffc9-40bd-9158-99514e083d49/dqc_reference/checkm_data
[2023-06-28 20:49:28,170] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 20:49:28,217] [INFO] Task started: CheckM
[2023-06-28 20:49:28,217] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913055885.1_SRR6193124_bin.73_MetaBAT_v2.12.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913055885.1_SRR6193124_bin.73_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_input GCA_913055885.1_SRR6193124_bin.73_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_result
[2023-06-28 20:49:56,426] [INFO] Task succeeded: CheckM
[2023-06-28 20:49:56,428] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.51%
Contamintation: 4.69%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 20:49:56,458] [INFO] ===== Completeness check finished =====
[2023-06-28 20:49:56,458] [INFO] ===== Start GTDB Search =====
[2023-06-28 20:49:56,458] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913055885.1_SRR6193124_bin.73_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta)
[2023-06-28 20:49:56,459] [INFO] Task started: Blastn
[2023-06-28 20:49:56,459] [INFO] Running command: blastn -query GCA_913055885.1_SRR6193124_bin.73_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg78c4896b-ffc9-40bd-9158-99514e083d49/dqc_reference/reference_markers_gtdb.fasta -out GCA_913055885.1_SRR6193124_bin.73_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:49:58,461] [INFO] Task succeeded: Blastn
[2023-06-28 20:49:58,466] [INFO] Selected 28 target genomes.
[2023-06-28 20:49:58,466] [INFO] Target genome list was writen to GCA_913055885.1_SRR6193124_bin.73_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 20:49:58,473] [INFO] Task started: fastANI
[2023-06-28 20:49:58,474] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bb84266-8adb-4b9c-9609-8e379f5c1592/GCA_913055885.1_SRR6193124_bin.73_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913055885.1_SRR6193124_bin.73_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_913055885.1_SRR6193124_bin.73_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 20:50:19,962] [INFO] Task succeeded: fastANI
[2023-06-28 20:50:19,989] [INFO] Found 28 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 20:50:19,989] [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_900100455.1	s__Roseospirillum parvum	77.2286	213	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Roseospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902729435.1	s__Magnetospirillum sp902729435	77.0991	236	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900230255.1	s__Caenispirillum bisanense	76.8819	285	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Caenispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001511835.1	s__Phaeospirillum sp001511835	76.8363	209	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000342045.1	s__Phaeospirillum caucaseum	76.7996	220	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184795.1	s__Phaeospirillum sp900184795	76.7917	204	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014925385.1	s__WHTV01 sp014925385	76.715	211	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197795.1	s__Rhodospira goensis	76.6558	233	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650715.1	s__Phaeospirillum marisnigri	76.6289	175	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006980715.1	s__Oleiliquidispirillum nitrogeniifigens	76.622	148	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Oleiliquidispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008365405.1	s__Azospirillum brasilense_D	76.4956	189	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197915.1	s__Rhodospira visakhapatnamensis	76.4929	218	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006969625.1	s__Algihabitans sp006969625	76.4424	188	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Algihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015232485.1	s__JADFZP01 sp015232485	76.4356	138	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	96.70	95.97	0.70	0.69	3	-
GCA_016792605.1	s__JAEULC01 sp016792605	76.4258	114	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__JAEULC01;f__JAEULC01;g__JAEULC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903853455.1	s__Phaeospirillum sp903853455	76.4176	192	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	99.97	99.97	0.98	0.98	2	-
GCA_002781745.1	s__UBA1479 sp002781745	76.3889	136	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827795.1	s__Azospirillum brasilense_E	76.3564	182	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	98.90	98.81	0.89	0.86	3	-
GCF_003116015.1	s__Azospirillum sp003116015	76.3064	260	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018432935.1	s__JAHDSF01 sp018432935	76.3033	139	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JAHDSF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	76.2947	220	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003349955.1	s__Azospirillum brasilense_B	76.2331	206	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	95.36	95.36	0.89	0.89	2	-
GCF_014197855.1	s__Rhodospira marina	76.1643	156	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	100.00	99.99	1.00	1.00	3	-
GCA_900079695.1	s__Alpha-05 sp900079695	76.1428	135	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Alpha-05	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006738865.1	s__Stella sp006738865	76.1301	162	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355985.1	s__Desertibacter sp017355985	76.1051	163	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Desertibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003250275.1	s__Alpha-05 sp003250275	75.8189	117	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Alpha-05	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116135.1	s__Roseomonas aestuarii	75.7482	198	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 20:50:19,992] [INFO] GTDB search result was written to GCA_913055885.1_SRR6193124_bin.73_MetaBAT_v2.12.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 20:50:19,992] [INFO] ===== GTDB Search completed =====
[2023-06-28 20:50:19,998] [INFO] DFAST_QC result json was written to GCA_913055885.1_SRR6193124_bin.73_MetaBAT_v2.12.1_MAG_genomic.fna/dqc_result.json
[2023-06-28 20:50:19,998] [INFO] DFAST_QC completed!
[2023-06-28 20:50:19,998] [INFO] Total running time: 0h1m29s