[2024-01-25 17:41:35,604] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:41:35,606] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:41:35,606] [INFO] DQC Reference Directory: /var/lib/cwl/stgea85164b-518d-413d-bdeb-26bc746d59c4/dqc_reference
[2024-01-25 17:41:36,768] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:41:36,769] [INFO] Task started: Prodigal
[2024-01-25 17:41:36,769] [INFO] Running command: gunzip -c /var/lib/cwl/stg72cd0429-ae72-4a90-9eba-75e8a8402255/GCF_014672995.1_ASM1467299v1_genomic.fna.gz | prodigal -d GCF_014672995.1_ASM1467299v1_genomic.fna/cds.fna -a GCF_014672995.1_ASM1467299v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:41:46,301] [INFO] Task succeeded: Prodigal
[2024-01-25 17:41:46,301] [INFO] Task started: HMMsearch
[2024-01-25 17:41:46,301] [INFO] Running command: hmmsearch --tblout GCF_014672995.1_ASM1467299v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea85164b-518d-413d-bdeb-26bc746d59c4/dqc_reference/reference_markers.hmm GCF_014672995.1_ASM1467299v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:41:46,534] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:41:46,535] [INFO] Found 6/6 markers.
[2024-01-25 17:41:46,564] [INFO] Query marker FASTA was written to GCF_014672995.1_ASM1467299v1_genomic.fna/markers.fasta
[2024-01-25 17:41:46,565] [INFO] Task started: Blastn
[2024-01-25 17:41:46,565] [INFO] Running command: blastn -query GCF_014672995.1_ASM1467299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea85164b-518d-413d-bdeb-26bc746d59c4/dqc_reference/reference_markers.fasta -out GCF_014672995.1_ASM1467299v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:47,766] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:47,770] [INFO] Selected 14 target genomes.
[2024-01-25 17:41:47,770] [INFO] Target genome list was writen to GCF_014672995.1_ASM1467299v1_genomic.fna/target_genomes.txt
[2024-01-25 17:41:47,782] [INFO] Task started: fastANI
[2024-01-25 17:41:47,782] [INFO] Running command: fastANI --query /var/lib/cwl/stg72cd0429-ae72-4a90-9eba-75e8a8402255/GCF_014672995.1_ASM1467299v1_genomic.fna.gz --refList GCF_014672995.1_ASM1467299v1_genomic.fna/target_genomes.txt --output GCF_014672995.1_ASM1467299v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:42:00,502] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:00,503] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea85164b-518d-413d-bdeb-26bc746d59c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:42:00,503] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea85164b-518d-413d-bdeb-26bc746d59c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:42:00,512] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:42:00,513] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:42:00,513] [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 tamlense	strain=SSW1-57	GCA_014672995.1	375541	375541	type	True	100.0	1197	1275	95	conclusive
Aeromicrobium tamlense	strain=DSM 19087	GCA_013408555.1	375541	375541	type	True	99.9995	1111	1275	95	conclusive
Aeromicrobium phoceense	strain=Marseille-Q0843	GCA_013868155.1	2754045	2754045	type	True	88.1746	931	1275	95	below_threshold
Aeromicrobium choanae	strain=9H-4	GCA_900167475.1	1736691	1736691	type	True	88.1674	964	1275	95	below_threshold
Aeromicrobium massiliense	strain=JC14	GCA_000312105.1	1464554	1464554	type	True	81.1645	590	1275	95	below_threshold
Aeromicrobium terrae	strain=CC-CFT486	GCA_008039565.1	2498846	2498846	type	True	80.6287	497	1275	95	below_threshold
Aeromicrobium chenweiae	strain=592	GCA_003065605.1	2079793	2079793	type	True	80.562	557	1275	95	below_threshold
Aeromicrobium stalagmiti	strain=YC3-14	GCA_013283745.1	2738988	2738988	type	True	80.5258	564	1275	95	below_threshold
Aeromicrobium erythreum	strain=AR18	GCA_001509405.1	2041	2041	type	True	80.4013	596	1275	95	below_threshold
Aeromicrobium phragmitis	strain=9W16Y-2	GCA_003674095.1	2478914	2478914	type	True	80.2657	504	1275	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	78.3558	451	1275	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	78.1751	472	1275	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	78.1083	439	1275	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	78.0062	450	1275	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:42:00,514] [INFO] DFAST Taxonomy check result was written to GCF_014672995.1_ASM1467299v1_genomic.fna/tc_result.tsv
[2024-01-25 17:42:00,515] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:42:00,515] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:42:00,515] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea85164b-518d-413d-bdeb-26bc746d59c4/dqc_reference/checkm_data
[2024-01-25 17:42:00,516] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:42:00,557] [INFO] Task started: CheckM
[2024-01-25 17:42:00,557] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014672995.1_ASM1467299v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014672995.1_ASM1467299v1_genomic.fna/checkm_input GCF_014672995.1_ASM1467299v1_genomic.fna/checkm_result
[2024-01-25 17:42:59,681] [INFO] Task succeeded: CheckM
[2024-01-25 17:42:59,682] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 16.67%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-25 17:42:59,712] [INFO] ===== Completeness check finished =====
[2024-01-25 17:42:59,712] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:42:59,714] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014672995.1_ASM1467299v1_genomic.fna/markers.fasta)
[2024-01-25 17:42:59,714] [INFO] Task started: Blastn
[2024-01-25 17:42:59,714] [INFO] Running command: blastn -query GCF_014672995.1_ASM1467299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea85164b-518d-413d-bdeb-26bc746d59c4/dqc_reference/reference_markers_gtdb.fasta -out GCF_014672995.1_ASM1467299v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:01,774] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:01,777] [INFO] Selected 5 target genomes.
[2024-01-25 17:43:01,778] [INFO] Target genome list was writen to GCF_014672995.1_ASM1467299v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:43:01,782] [INFO] Task started: fastANI
[2024-01-25 17:43:01,782] [INFO] Running command: fastANI --query /var/lib/cwl/stg72cd0429-ae72-4a90-9eba-75e8a8402255/GCF_014672995.1_ASM1467299v1_genomic.fna.gz --refList GCF_014672995.1_ASM1467299v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014672995.1_ASM1467299v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:43:06,703] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:06,708] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:43:06,708] [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_013408555.1	s__Aeromicrobium tamlense	99.9995	1111	1275	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_013868155.1	s__Aeromicrobium phoceense	88.1744	931	1275	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	97.64	97.64	0.92	0.92	2	-
GCF_900167475.1	s__Aeromicrobium choanae	88.1674	964	1275	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992115.1	s__Aeromicrobium flavum	86.7805	807	1275	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014334735.1	s__Aeromicrobium sp014334735	85.9082	824	1275	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	99.41	98.82	0.96	0.93	3	-
--------------------------------------------------------------------------------
[2024-01-25 17:43:06,709] [INFO] GTDB search result was written to GCF_014672995.1_ASM1467299v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:43:06,710] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:43:06,714] [INFO] DFAST_QC result json was written to GCF_014672995.1_ASM1467299v1_genomic.fna/dqc_result.json
[2024-01-25 17:43:06,714] [INFO] DFAST_QC completed!
[2024-01-25 17:43:06,715] [INFO] Total running time: 0h1m31s