[2023-06-29 14:05:30,432] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:05:30,435] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:05:30,435] [INFO] DQC Reference Directory: /var/lib/cwl/stg1039e260-40fc-47c7-8055-a01c062482da/dqc_reference
[2023-06-29 14:05:31,745] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:05:31,746] [INFO] Task started: Prodigal
[2023-06-29 14:05:31,746] [INFO] Running command: gunzip -c /var/lib/cwl/stgca94e3e5-79cd-469d-a462-68cf124ba7b9/GCA_937973095.1_SRR6231220_bin.40_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937973095.1_SRR6231220_bin.40_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937973095.1_SRR6231220_bin.40_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:05:35,253] [INFO] Task succeeded: Prodigal
[2023-06-29 14:05:35,254] [INFO] Task started: HMMsearch
[2023-06-29 14:05:35,254] [INFO] Running command: hmmsearch --tblout GCA_937973095.1_SRR6231220_bin.40_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1039e260-40fc-47c7-8055-a01c062482da/dqc_reference/reference_markers.hmm GCA_937973095.1_SRR6231220_bin.40_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:05:35,487] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:05:35,488] [INFO] Found 6/6 markers.
[2023-06-29 14:05:35,510] [INFO] Query marker FASTA was written to GCA_937973095.1_SRR6231220_bin.40_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 14:05:35,510] [INFO] Task started: Blastn
[2023-06-29 14:05:35,510] [INFO] Running command: blastn -query GCA_937973095.1_SRR6231220_bin.40_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg1039e260-40fc-47c7-8055-a01c062482da/dqc_reference/reference_markers.fasta -out GCA_937973095.1_SRR6231220_bin.40_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:05:36,449] [INFO] Task succeeded: Blastn
[2023-06-29 14:05:36,453] [INFO] Selected 30 target genomes.
[2023-06-29 14:05:36,454] [INFO] Target genome list was writen to GCA_937973095.1_SRR6231220_bin.40_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 14:05:36,461] [INFO] Task started: fastANI
[2023-06-29 14:05:36,461] [INFO] Running command: fastANI --query /var/lib/cwl/stgca94e3e5-79cd-469d-a462-68cf124ba7b9/GCA_937973095.1_SRR6231220_bin.40_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937973095.1_SRR6231220_bin.40_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937973095.1_SRR6231220_bin.40_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:05:51,099] [INFO] Task succeeded: fastANI
[2023-06-29 14:05:51,099] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1039e260-40fc-47c7-8055-a01c062482da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:05:51,100] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1039e260-40fc-47c7-8055-a01c062482da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:05:51,117] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:05:51,117] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 14:05:51,118] [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
Microcella putealis	strain=CV2	GCA_004216575.1	337005	337005	type	True	77.5384	76	268	95	below_threshold
Microcella putealis	strain=DSM 19627	GCA_006716545.1	337005	337005	type	True	77.4572	75	268	95	below_threshold
Conyzicola nivalis	strain=CGMCC 1.12813	GCA_014639655.1	1477021	1477021	type	True	77.1912	60	268	95	below_threshold
Protaetiibacter larvae	strain=KACC 19322	GCA_008365275.1	2592654	2592654	type	True	77.1463	72	268	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	77.0446	56	268	95	below_threshold
Clavibacter zhangzhiyongii	strain=DM1	GCA_014775655.1	2768071	2768071	type	True	76.8264	65	268	95	below_threshold
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	76.8257	82	268	95	below_threshold
Microbacterium humi	strain=DSM 21799	GCA_900105715.1	640635	640635	type	True	76.7834	53	268	95	below_threshold
Microbacterium hominis	strain=LCDC 84-0209	GCA_001553805.1	162426	162426	type	True	76.7757	54	268	95	below_threshold
Agrococcus jejuensis	strain=DSM 22002	GCA_900099705.1	399736	399736	type	True	76.761	65	268	95	below_threshold
Agromyces humi	strain=ANK073	GCA_009720255.2	1766800	1766800	type	True	76.7102	65	268	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	76.7042	73	268	95	below_threshold
Agrococcus sediminis	strain=NS18	GCA_007923295.1	2599924	2599924	type	True	76.6161	58	268	95	below_threshold
Rathayibacter caricis	strain=DSM 15933	GCA_003044275.1	110936	110936	type	True	76.57	68	268	95	below_threshold
Leucobacter zeae	strain=CC-MF41	GCA_016758175.1	1257004	1257004	type	True	76.4793	52	268	95	below_threshold
Microbacterium luteum	strain=A18JL200	GCA_015277875.1	2782167	2782167	type	True	76.4007	50	268	95	below_threshold
Curtobacterium citreum	strain=JCM 1345	GCA_014646735.1	2036	2036	type	True	76.3942	63	268	95	below_threshold
Curtobacterium citreum	strain=LMG8786T	GCA_024997915.1	2036	2036	type	True	76.36	64	268	95	below_threshold
Curtobacterium citreum	strain=DSM 20528	GCA_006715175.1	2036	2036	type	True	76.3021	66	268	95	below_threshold
Agrococcus pavilionensis	strain=RW1	GCA_000400485.1	1346502	1346502	type	True	76.2623	66	268	95	below_threshold
Microbacterium sulfonylureivorans	strain=LAM7116	GCA_003999995.1	2486854	2486854	type	True	76.147	65	268	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 14:05:51,120] [INFO] DFAST Taxonomy check result was written to GCA_937973095.1_SRR6231220_bin.40_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 14:05:51,121] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:05:51,121] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:05:51,121] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1039e260-40fc-47c7-8055-a01c062482da/dqc_reference/checkm_data
[2023-06-29 14:05:51,122] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:05:51,142] [INFO] Task started: CheckM
[2023-06-29 14:05:51,142] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937973095.1_SRR6231220_bin.40_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937973095.1_SRR6231220_bin.40_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937973095.1_SRR6231220_bin.40_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 14:06:09,008] [INFO] Task succeeded: CheckM
[2023-06-29 14:06:09,009] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 1.30%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-29 14:06:09,031] [INFO] ===== Completeness check finished =====
[2023-06-29 14:06:09,031] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:06:09,032] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937973095.1_SRR6231220_bin.40_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 14:06:09,032] [INFO] Task started: Blastn
[2023-06-29 14:06:09,032] [INFO] Running command: blastn -query GCA_937973095.1_SRR6231220_bin.40_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg1039e260-40fc-47c7-8055-a01c062482da/dqc_reference/reference_markers_gtdb.fasta -out GCA_937973095.1_SRR6231220_bin.40_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:06:10,607] [INFO] Task succeeded: Blastn
[2023-06-29 14:06:10,611] [INFO] Selected 24 target genomes.
[2023-06-29 14:06:10,612] [INFO] Target genome list was writen to GCA_937973095.1_SRR6231220_bin.40_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:06:10,688] [INFO] Task started: fastANI
[2023-06-29 14:06:10,688] [INFO] Running command: fastANI --query /var/lib/cwl/stgca94e3e5-79cd-469d-a462-68cf124ba7b9/GCA_937973095.1_SRR6231220_bin.40_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937973095.1_SRR6231220_bin.40_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937973095.1_SRR6231220_bin.40_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:06:19,613] [INFO] Task succeeded: fastANI
[2023-06-29 14:06:19,637] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 14:06:19,637] [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_016463265.1	s__MWH-TA3 sp016463265	80.4899	115	268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__MWH-TA3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903882245.1	s__MWH-TA3 sp903882245	80.0284	84	268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__MWH-TA3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009704225.1	s__MWH-TA3 sp009704225	79.4685	86	268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__MWH-TA3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009703545.1	s__MWH-TA3 sp009703545	78.8747	97	268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__MWH-TA3	95.0	99.00	99.00	0.78	0.78	2	-
GCA_903940225.1	s__MWH-TA3 sp903940225	78.4928	117	268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__MWH-TA3	95.0	99.80	99.50	0.95	0.95	7	-
GCA_009704155.1	s__MWH-TA3 sp009704155	77.9835	60	268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__MWH-TA3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003053925.1	s__MWH-TA3 sp003053925	77.9216	85	268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__MWH-TA3	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014639655.1	s__Conyzicola nivalis	77.1912	60	268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Conyzicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008365275.1	s__Protaetiibacter larvae	77.1463	72	268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002245215.1	s__Microbacterium sp002245215	77.0896	55	268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364285.1	s__Frigoribacterium sp004364285	77.0725	60	268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	96.77	95.63	0.92	0.87	5	-
GCF_014483895.1	s__Protaetiibacter sp014483895	76.9751	83	268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003384945.1	s__Clavibacter sp003384945	76.963	62	268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003289625.1	s__Microbacterium sp003289625	76.8353	51	268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.69	98.69	0.93	0.93	2	-
GCF_016907085.1	s__Clavibacter michiganensis_O	76.7955	65	268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002074055.1	s__Frondihabitans sp002074055	76.7677	63	268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frondihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102175.1	s__Microbacterium sp900102175	76.7402	59	268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003651225.1	s__Microbacterium telephonicum	76.6238	61	268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000333395.1	s__Microbacterium sp000333395	76.6195	54	268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007923295.1	s__Agrococcus sediminis	76.6161	58	268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	97.99	97.99	0.92	0.92	2	-
GCF_005484985.1	s__Agrococcus sp005484985	76.4152	59	268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 14:06:19,639] [INFO] GTDB search result was written to GCA_937973095.1_SRR6231220_bin.40_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 14:06:19,640] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:06:19,644] [INFO] DFAST_QC result json was written to GCA_937973095.1_SRR6231220_bin.40_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 14:06:19,645] [INFO] DFAST_QC completed!
[2023-06-29 14:06:19,645] [INFO] Total running time: 0h0m49s