[2023-06-29 14:27:03,621] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:27:03,631] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:27:03,632] [INFO] DQC Reference Directory: /var/lib/cwl/stg138f8e76-cf54-4892-a83b-2dadac18a64f/dqc_reference
[2023-06-29 14:27:04,976] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:27:04,977] [INFO] Task started: Prodigal
[2023-06-29 14:27:04,977] [INFO] Running command: gunzip -c /var/lib/cwl/stg08ad4e24-d310-4314-96c0-d98f341dba77/GCA_937910285.1_SRR1561992_bin.48_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937910285.1_SRR1561992_bin.48_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937910285.1_SRR1561992_bin.48_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:27:23,738] [INFO] Task succeeded: Prodigal
[2023-06-29 14:27:23,739] [INFO] Task started: HMMsearch
[2023-06-29 14:27:23,739] [INFO] Running command: hmmsearch --tblout GCA_937910285.1_SRR1561992_bin.48_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg138f8e76-cf54-4892-a83b-2dadac18a64f/dqc_reference/reference_markers.hmm GCA_937910285.1_SRR1561992_bin.48_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:27:24,142] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:27:24,144] [INFO] Found 6/6 markers.
[2023-06-29 14:27:24,201] [INFO] Query marker FASTA was written to GCA_937910285.1_SRR1561992_bin.48_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 14:27:24,202] [INFO] Task started: Blastn
[2023-06-29 14:27:24,202] [INFO] Running command: blastn -query GCA_937910285.1_SRR1561992_bin.48_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg138f8e76-cf54-4892-a83b-2dadac18a64f/dqc_reference/reference_markers.fasta -out GCA_937910285.1_SRR1561992_bin.48_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:27:25,209] [INFO] Task succeeded: Blastn
[2023-06-29 14:27:25,213] [INFO] Selected 39 target genomes.
[2023-06-29 14:27:25,213] [INFO] Target genome list was writen to GCA_937910285.1_SRR1561992_bin.48_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 14:27:25,215] [INFO] Task started: fastANI
[2023-06-29 14:27:25,215] [INFO] Running command: fastANI --query /var/lib/cwl/stg08ad4e24-d310-4314-96c0-d98f341dba77/GCA_937910285.1_SRR1561992_bin.48_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937910285.1_SRR1561992_bin.48_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937910285.1_SRR1561992_bin.48_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:28:07,983] [INFO] Task succeeded: fastANI
[2023-06-29 14:28:07,984] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg138f8e76-cf54-4892-a83b-2dadac18a64f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:28:07,984] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg138f8e76-cf54-4892-a83b-2dadac18a64f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:28:08,012] [INFO] Found 38 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:28:08,013] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 14:28:08,013] [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
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	76.1514	341	2416	95	below_threshold
Stigmatella aurantiaca	strain=DSM 17044	GCA_900109545.1	41	41	type	True	76.1163	329	2416	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	76.0373	467	2416	95	below_threshold
Myxococcus stipitatus	strain=DSM 14675	GCA_000331735.1	83455	83455	neotype	True	75.9737	339	2416	95	below_threshold
Archangium violaceum	strain=Cb vi76	GCA_000733295.1	83451	83451	type	True	75.9337	407	2416	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_001027285.1	48	48	type	True	75.92	429	2416	95	below_threshold
Pyxidicoccus fallax	strain=DSM 14698	GCA_012933655.1	394095	394095	type	True	75.9155	435	2416	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_003387095.1	48	48	type	True	75.915	430	2416	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	75.8278	344	2416	95	below_threshold
Myxococcus fulvus	strain=DSM 16525	GCA_900111765.1	33	33	type	True	75.815	394	2416	95	below_threshold
Myxococcus fulvus	strain=NBRC 100333	GCA_007991095.1	33	33	type	True	75.809	399	2416	95	below_threshold
Corallococcus llansteffanensis	strain=CA051B	GCA_003612055.1	2316731	2316731	type	True	75.8081	351	2416	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	75.8055	341	2416	95	below_threshold
Pseudoxanthomonas kaohsiungensis	strain=DSM 17583	GCA_010211765.1	283923	283923	type	True	75.2101	129	2416	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	75.1364	149	2416	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	75.1232	91	2416	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	75.1172	230	2416	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	75.1002	218	2416	95	below_threshold
Oleiagrimonas soli	strain=3.5X	GCA_000761445.1	1543381	1543381	type	True	75.0744	109	2416	95	below_threshold
Stenotrophomonas nitritireducens	strain=DSM 12575	GCA_001431425.1	83617	83617	type	True	75.0248	129	2416	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	75.0164	148	2416	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	75.0122	130	2416	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_008801845.1	36863	36863	type	True	75.0037	126	2416	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	74.9965	132	2416	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_007827425.1	192	192	type	True	74.9858	161	2416	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	74.948	155	2416	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	74.9347	214	2416	95	below_threshold
Sandaracinus amylolyticus	strain=DSM 53668	GCA_000737325.2	927083	927083	type	True	74.9305	575	2416	95	below_threshold
Ideonella livida	strain=TBM-1	GCA_010499455.1	2707176	2707176	type	True	74.9205	121	2416	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	74.9118	235	2416	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	74.911	297	2416	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	74.8846	215	2416	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	74.8824	156	2416	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	74.8368	179	2416	95	below_threshold
Saccharothrix australiensis	strain=DSM 43800	GCA_003634935.1	2072	2072	type	True	74.8277	283	2416	95	below_threshold
Solirubrobacter pauli	strain=DSM 14954	GCA_003633755.1	166793	166793	type	True	74.7259	337	2416	95	below_threshold
Truepera radiovictrix	strain=DSM 17093	GCA_000092425.1	332249	332249	type	True	74.7253	115	2416	95	below_threshold
Actinomadura oligospora	strain=ATCC 43269	GCA_000518265.1	111804	111804	type	True	74.7039	292	2416	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 14:28:08,015] [INFO] DFAST Taxonomy check result was written to GCA_937910285.1_SRR1561992_bin.48_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 14:28:08,016] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:28:08,016] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:28:08,016] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg138f8e76-cf54-4892-a83b-2dadac18a64f/dqc_reference/checkm_data
[2023-06-29 14:28:08,017] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:28:08,086] [INFO] Task started: CheckM
[2023-06-29 14:28:08,086] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937910285.1_SRR1561992_bin.48_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937910285.1_SRR1561992_bin.48_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937910285.1_SRR1561992_bin.48_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 14:29:01,365] [INFO] Task succeeded: CheckM
[2023-06-29 14:29:01,367] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 14:29:01,390] [INFO] ===== Completeness check finished =====
[2023-06-29 14:29:01,390] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:29:01,391] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937910285.1_SRR1561992_bin.48_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 14:29:01,391] [INFO] Task started: Blastn
[2023-06-29 14:29:01,391] [INFO] Running command: blastn -query GCA_937910285.1_SRR1561992_bin.48_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg138f8e76-cf54-4892-a83b-2dadac18a64f/dqc_reference/reference_markers_gtdb.fasta -out GCA_937910285.1_SRR1561992_bin.48_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:29:03,038] [INFO] Task succeeded: Blastn
[2023-06-29 14:29:03,043] [INFO] Selected 32 target genomes.
[2023-06-29 14:29:03,043] [INFO] Target genome list was writen to GCA_937910285.1_SRR1561992_bin.48_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:29:03,053] [INFO] Task started: fastANI
[2023-06-29 14:29:03,053] [INFO] Running command: fastANI --query /var/lib/cwl/stg08ad4e24-d310-4314-96c0-d98f341dba77/GCA_937910285.1_SRR1561992_bin.48_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937910285.1_SRR1561992_bin.48_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937910285.1_SRR1561992_bin.48_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:29:42,643] [INFO] Task succeeded: fastANI
[2023-06-29 14:29:42,669] [INFO] Found 32 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 14:29:42,669] [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_002408385.1	s__UBA10939 sp002408385	99.9192	2308	2416	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__UBA5297;g__UBA10939	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017500825.1	s__UBA1203 sp017500825	77.2915	261	2416	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__UBA5297;g__UBA1203	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016718565.1	s__JADKCZ01 sp016718565	76.2448	353	2416	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__JADKCZ01	95.0	99.81	99.81	0.97	0.97	2	-
GCA_002309695.1	s__UBA1203 sp002309695	76.2443	126	2416	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__UBA5297;g__UBA1203	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009659535.1	s__Aggregicoccus sp009659535	76.1857	486	2416	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Aggregicoccus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018266075.1	s__SZAS-1 sp018266075	76.1818	459	2416	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__SZAS-1;g__SZAS-1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000964525.1	s__Anaeromyxobacter sp000964525	76.1343	395	2416	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__Anaeromyxobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016214955.1	s__JACRMN01 sp016214955	76.101	364	2416	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__JACRMN01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002305855.1	s__Melittangium boletus	76.0207	351	2416	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Melittangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001887355.1	s__Cystobacter ferrugineus	76.0099	394	2416	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Cystobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016904885.1	s__Melittangium primigenium	76.0015	426	2416	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Melittangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013340205.1	s__R267 sp013340205	75.9933	426	2416	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__R267	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003044305.1	s__Archangium sp003044305	75.9618	411	2416	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Archangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001027285.1	s__Archangium gephyra	75.9362	424	2416	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Archangium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000737315.1	s__Hyalangium minutum	75.9315	338	2416	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Hyalangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010894435.1	s__Myxococcus trucidator	75.908	414	2416	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656495.1	s__Myxococcus sp014656495	75.8511	344	2416	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000017505.1	s__Anaeromyxobacter sp000017505	75.841	430	2416	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__Anaeromyxobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001768075.1	s__R267 sp001768075	75.829	282	2416	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__R267	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010894405.1	s__Myxococcus caerfyrddinensis	75.7018	449	2416	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793095.1	s__JAEUJQ01 sp016793095	75.639	451	2416	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__JAEUJQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016879935.1	s__JAEUJQ01 sp016879935	75.6188	393	2416	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__JAEUJQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793725.1	s__JAEUJP01 sp016793725	75.5316	491	2416	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__JAEUJP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900696455.1	s__UBA2376 sp900696455	75.1805	548	2416	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	98.40	97.29	0.91	0.90	3	-
GCA_002841825.1	s__HGW-17 sp002841825	75.1496	117	2416	d__Bacteria;p__Myxococcota;c__Polyangia;o__HGW-17;f__HGW-17;g__HGW-17	95.0	97.98	97.84	0.81	0.78	4	-
GCA_011526095.1	s__WYBA01 sp011526095	75.1093	616	2416	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__WYBA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768335.1	s__Lysobacter arseniciresistens	74.998	133	2416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903919045.1	s__CAILLO01 sp903919045	74.9757	119	2416	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__UBA5734;g__CAILLO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002345845.1	s__Azonexus sp002345845	74.9269	87	2416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903866365.1	s__Chromatium sp903866365	74.8988	85	2416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Chromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005884455.1	s__VBDM01 sp005884455	74.8422	83	2416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__VBDM01	95.0	99.10	99.10	0.85	0.85	2	-
GCA_007750655.1	s__Pla163 sp007750655	74.8209	182	2416	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__Pla163	95.0	N/A	N/A	N/A	N/A	1	-
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[2023-06-29 14:29:42,675] [INFO] GTDB search result was written to GCA_937910285.1_SRR1561992_bin.48_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 14:29:42,675] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:29:42,682] [INFO] DFAST_QC result json was written to GCA_937910285.1_SRR1561992_bin.48_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 14:29:42,682] [INFO] DFAST_QC completed!
[2023-06-29 14:29:42,682] [INFO] Total running time: 0h2m39s