[2023-06-29 14:15:59,730] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:15:59,748] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:15:59,749] [INFO] DQC Reference Directory: /var/lib/cwl/stg9afce17c-fd4b-4c00-8916-22a557c1ffcc/dqc_reference
[2023-06-29 14:16:02,288] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:16:02,290] [INFO] Task started: Prodigal
[2023-06-29 14:16:02,290] [INFO] Running command: gunzip -c /var/lib/cwl/stg319313ec-9bed-4695-a4e2-00d4e7671d02/GCA_937873005.1_SRR2107216_bin.86_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937873005.1_SRR2107216_bin.86_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937873005.1_SRR2107216_bin.86_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:16:08,858] [INFO] Task succeeded: Prodigal
[2023-06-29 14:16:08,859] [INFO] Task started: HMMsearch
[2023-06-29 14:16:08,859] [INFO] Running command: hmmsearch --tblout GCA_937873005.1_SRR2107216_bin.86_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9afce17c-fd4b-4c00-8916-22a557c1ffcc/dqc_reference/reference_markers.hmm GCA_937873005.1_SRR2107216_bin.86_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:16:09,125] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:16:09,126] [INFO] Found 6/6 markers.
[2023-06-29 14:16:09,153] [INFO] Query marker FASTA was written to GCA_937873005.1_SRR2107216_bin.86_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 14:16:09,154] [INFO] Task started: Blastn
[2023-06-29 14:16:09,154] [INFO] Running command: blastn -query GCA_937873005.1_SRR2107216_bin.86_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg9afce17c-fd4b-4c00-8916-22a557c1ffcc/dqc_reference/reference_markers.fasta -out GCA_937873005.1_SRR2107216_bin.86_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:16:09,839] [INFO] Task succeeded: Blastn
[2023-06-29 14:16:09,843] [INFO] Selected 26 target genomes.
[2023-06-29 14:16:09,844] [INFO] Target genome list was writen to GCA_937873005.1_SRR2107216_bin.86_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 14:16:09,852] [INFO] Task started: fastANI
[2023-06-29 14:16:09,853] [INFO] Running command: fastANI --query /var/lib/cwl/stg319313ec-9bed-4695-a4e2-00d4e7671d02/GCA_937873005.1_SRR2107216_bin.86_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937873005.1_SRR2107216_bin.86_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937873005.1_SRR2107216_bin.86_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:16:26,489] [INFO] Task succeeded: fastANI
[2023-06-29 14:16:26,490] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9afce17c-fd4b-4c00-8916-22a557c1ffcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:16:26,490] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9afce17c-fd4b-4c00-8916-22a557c1ffcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:16:26,501] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:16:26,501] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 14:16:26,502] [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
Aeromicrobium camelliae	strain=YS17T	GCA_003850045.1	1538144	1538144	type	True	76.9381	75	595	95	below_threshold
Aeromicrobium tamlense	strain=SSW1-57	GCA_014672995.1	375541	375541	type	True	76.6671	105	595	95	below_threshold
Aeromicrobium tamlense	strain=DSM 19087	GCA_013408555.1	375541	375541	type	True	76.666	107	595	95	below_threshold
Aeromicrobium erythreum	strain=AR18	GCA_001509405.1	2041	2041	type	True	76.628	75	595	95	below_threshold
Aeromicrobium piscarium	strain=Co35	GCA_007421815.1	2590901	2590901	type	True	76.6246	76	595	95	below_threshold
Aeromicrobium fastidiosum	strain=DSM 10552	GCA_017876595.1	52699	52699	type	True	76.5793	77	595	95	below_threshold
Aeromicrobium stalagmiti	strain=YC3-14	GCA_013283745.1	2738988	2738988	type	True	76.4834	69	595	95	below_threshold
Aeromicrobium terrae	strain=CC-CFT486	GCA_008039565.1	2498846	2498846	type	True	76.4822	62	595	95	below_threshold
Aeromicrobium endophyticum	strain=M2KJ-4	GCA_003586285.1	2292704	2292704	type	True	76.348	76	595	95	below_threshold
Aeromicrobium chenweiae	strain=592	GCA_003065605.1	2079793	2079793	type	True	76.3363	80	595	95	below_threshold
Aeromicrobium ginsengisoli	strain=JCM 14732	GCA_004134905.2	363867	363867	type	True	76.1371	73	595	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 14:16:26,504] [INFO] DFAST Taxonomy check result was written to GCA_937873005.1_SRR2107216_bin.86_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 14:16:26,505] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:16:26,505] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:16:26,505] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9afce17c-fd4b-4c00-8916-22a557c1ffcc/dqc_reference/checkm_data
[2023-06-29 14:16:26,506] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:16:26,539] [INFO] Task started: CheckM
[2023-06-29 14:16:26,539] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937873005.1_SRR2107216_bin.86_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937873005.1_SRR2107216_bin.86_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937873005.1_SRR2107216_bin.86_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 14:16:52,132] [INFO] Task succeeded: CheckM
[2023-06-29 14:16:52,133] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 14:16:52,171] [INFO] ===== Completeness check finished =====
[2023-06-29 14:16:52,171] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:16:52,172] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937873005.1_SRR2107216_bin.86_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 14:16:52,172] [INFO] Task started: Blastn
[2023-06-29 14:16:52,172] [INFO] Running command: blastn -query GCA_937873005.1_SRR2107216_bin.86_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg9afce17c-fd4b-4c00-8916-22a557c1ffcc/dqc_reference/reference_markers_gtdb.fasta -out GCA_937873005.1_SRR2107216_bin.86_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:16:53,045] [INFO] Task succeeded: Blastn
[2023-06-29 14:16:53,050] [INFO] Selected 25 target genomes.
[2023-06-29 14:16:53,050] [INFO] Target genome list was writen to GCA_937873005.1_SRR2107216_bin.86_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:16:53,121] [INFO] Task started: fastANI
[2023-06-29 14:16:53,121] [INFO] Running command: fastANI --query /var/lib/cwl/stg319313ec-9bed-4695-a4e2-00d4e7671d02/GCA_937873005.1_SRR2107216_bin.86_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937873005.1_SRR2107216_bin.86_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937873005.1_SRR2107216_bin.86_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:17:09,269] [INFO] Task succeeded: fastANI
[2023-06-29 14:17:09,293] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 14:17:09,294] [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_008017265.1	s__Aeromicrobium sp008017265	94.3236	419	595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012513165.1	s__Aeromicrobium sp012513165	79.0251	120	595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003850045.1	s__Aeromicrobium camelliae	76.9381	75	595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408555.1	s__Aeromicrobium tamlense	76.666	107	595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014334735.1	s__Aeromicrobium sp014334735	76.6424	93	595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	99.41	98.82	0.96	0.93	3	-
GCF_001509405.1	s__Aeromicrobium erythreum	76.628	75	595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	98.57	98.39	0.93	0.92	6	-
GCF_007421815.1	s__Aeromicrobium piscarium	76.6246	76	595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	97.34	97.34	0.85	0.85	2	-
GCF_007992115.1	s__Aeromicrobium flavum	76.5319	89	595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008039565.1	s__Aeromicrobium terrae	76.5127	61	595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506105.1	s__Aeromicrobium sp902506105	76.4722	82	595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002174305.1	s__Aeromicrobium sp002174305	76.4413	64	595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004336805.1	s__Aeromicrobium sp004336805	76.3149	71	595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425755.1	s__Aeromicrobium sp001425755	76.3058	73	595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426485.1	s__Aeromicrobium sp001426485	76.2701	83	595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	97.44	97.44	0.91	0.91	2	-
GCF_004134905.2	s__Aeromicrobium ginsengisoli	76.1371	73	595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014378035.1	s__Aeromicrobium sp014378035	75.8709	51	595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 14:17:09,296] [INFO] GTDB search result was written to GCA_937873005.1_SRR2107216_bin.86_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 14:17:09,297] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:17:09,301] [INFO] DFAST_QC result json was written to GCA_937873005.1_SRR2107216_bin.86_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 14:17:09,302] [INFO] DFAST_QC completed!
[2023-06-29 14:17:09,302] [INFO] Total running time: 0h1m10s