[2024-01-24 12:31:58,379] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:58,381] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:58,382] [INFO] DQC Reference Directory: /var/lib/cwl/stg936a2434-4ced-4c5b-90c2-6f38b098cfbc/dqc_reference
[2024-01-24 12:31:59,777] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:59,778] [INFO] Task started: Prodigal
[2024-01-24 12:31:59,778] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ff9684e-c17b-4dd3-a376-2633b5d0d0be/GCF_028875885.1_ASM2887588v1_genomic.fna.gz | prodigal -d GCF_028875885.1_ASM2887588v1_genomic.fna/cds.fna -a GCF_028875885.1_ASM2887588v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:09,684] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:09,684] [INFO] Task started: HMMsearch
[2024-01-24 12:32:09,684] [INFO] Running command: hmmsearch --tblout GCF_028875885.1_ASM2887588v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg936a2434-4ced-4c5b-90c2-6f38b098cfbc/dqc_reference/reference_markers.hmm GCF_028875885.1_ASM2887588v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:09,949] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:09,950] [INFO] Found 6/6 markers.
[2024-01-24 12:32:09,998] [INFO] Query marker FASTA was written to GCF_028875885.1_ASM2887588v1_genomic.fna/markers.fasta
[2024-01-24 12:32:09,998] [INFO] Task started: Blastn
[2024-01-24 12:32:09,999] [INFO] Running command: blastn -query GCF_028875885.1_ASM2887588v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg936a2434-4ced-4c5b-90c2-6f38b098cfbc/dqc_reference/reference_markers.fasta -out GCF_028875885.1_ASM2887588v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:10,733] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:10,737] [INFO] Selected 26 target genomes.
[2024-01-24 12:32:10,737] [INFO] Target genome list was writen to GCF_028875885.1_ASM2887588v1_genomic.fna/target_genomes.txt
[2024-01-24 12:32:10,747] [INFO] Task started: fastANI
[2024-01-24 12:32:10,747] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ff9684e-c17b-4dd3-a376-2633b5d0d0be/GCF_028875885.1_ASM2887588v1_genomic.fna.gz --refList GCF_028875885.1_ASM2887588v1_genomic.fna/target_genomes.txt --output GCF_028875885.1_ASM2887588v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:31,579] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:31,579] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg936a2434-4ced-4c5b-90c2-6f38b098cfbc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:31,579] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg936a2434-4ced-4c5b-90c2-6f38b098cfbc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:31,591] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:32:31,591] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:32:31,591] [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
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	75.3389	196	1167	95	below_threshold
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	75.2222	102	1167	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	75.0679	97	1167	95	below_threshold
Longimicrobium terrae	strain=DSM 29007	GCA_014202995.1	1639882	1639882	type	True	75.0611	102	1167	95	below_threshold
Longimicrobium terrae	strain=CECT 8660	GCA_014198875.1	1639882	1639882	type	True	75.0551	103	1167	95	below_threshold
Rubrivirga marina	strain=SAORIC-28	GCA_002283365.1	1196024	1196024	type	True	75.0158	102	1167	95	below_threshold
Aeromicrobium choanae	strain=9H-4	GCA_900167475.1	1736691	1736691	type	True	74.9607	62	1167	95	below_threshold
Rathayibacter caricis	strain=DSM 15933	GCA_003044275.1	110936	110936	type	True	74.8593	64	1167	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	74.7801	97	1167	95	below_threshold
Mumia flava	strain=DSM 27763	GCA_002797495.1	1348852	1348852	type	True	74.7782	72	1167	95	below_threshold
Lentzea atacamensis	strain=DSM 45479	GCA_003269295.1	531938	531938	type	True	74.763	84	1167	95	below_threshold
Streptomyces goshikiensis	strain=JCM 4640	GCA_014650555.1	1942	1942	type	True	74.7441	120	1167	95	below_threshold
Cellulomonas iranensis	strain=NBRC 101100	GCA_001552375.1	76862	76862	type	True	74.7362	97	1167	95	below_threshold
Amycolatopsis pithecellobii	strain=RM579	GCA_009707865.1	664692	664692	type	True	74.7215	61	1167	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:31,593] [INFO] DFAST Taxonomy check result was written to GCF_028875885.1_ASM2887588v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:31,594] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:31,594] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:31,594] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg936a2434-4ced-4c5b-90c2-6f38b098cfbc/dqc_reference/checkm_data
[2024-01-24 12:32:31,595] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:31,643] [INFO] Task started: CheckM
[2024-01-24 12:32:31,643] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028875885.1_ASM2887588v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028875885.1_ASM2887588v1_genomic.fna/checkm_input GCF_028875885.1_ASM2887588v1_genomic.fna/checkm_result
[2024-01-24 12:33:05,924] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:05,925] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:05,949] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:05,950] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:05,950] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028875885.1_ASM2887588v1_genomic.fna/markers.fasta)
[2024-01-24 12:33:05,951] [INFO] Task started: Blastn
[2024-01-24 12:33:05,951] [INFO] Running command: blastn -query GCF_028875885.1_ASM2887588v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg936a2434-4ced-4c5b-90c2-6f38b098cfbc/dqc_reference/reference_markers_gtdb.fasta -out GCF_028875885.1_ASM2887588v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:06,991] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:06,996] [INFO] Selected 5 target genomes.
[2024-01-24 12:33:06,996] [INFO] Target genome list was writen to GCF_028875885.1_ASM2887588v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:07,001] [INFO] Task started: fastANI
[2024-01-24 12:33:07,001] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ff9684e-c17b-4dd3-a376-2633b5d0d0be/GCF_028875885.1_ASM2887588v1_genomic.fna.gz --refList GCF_028875885.1_ASM2887588v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028875885.1_ASM2887588v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:11,563] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:11,572] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:33:11,572] [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_009841015.1	s__JAAXHJ01 sp009841015	92.8056	924	1167	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__KS3-K002;f__JABDQB01;g__JAAXHJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009840115.1	s__JAAXHJ01 sp009840115	92.4325	974	1167	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__KS3-K002;f__JABDQB01;g__JAAXHJ01	95.0	99.91	99.91	0.95	0.95	2	-
GCA_009838765.1	s__JAAXHJ01 sp009838765	91.2721	963	1167	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__KS3-K002;f__JABDQB01;g__JAAXHJ01	95.0	99.96	99.96	0.97	0.96	3	-
GCA_009841005.1	s__JAAXHJ01 sp009841005	90.1822	845	1167	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__KS3-K002;f__JABDQB01;g__JAAXHJ01	95.0	96.67	96.60	0.84	0.81	5	-
GCA_012270965.1	s__JAAXHJ01 sp012270965	88.7085	881	1167	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__KS3-K002;f__JABDQB01;g__JAAXHJ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:11,574] [INFO] GTDB search result was written to GCF_028875885.1_ASM2887588v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:11,575] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:11,577] [INFO] DFAST_QC result json was written to GCF_028875885.1_ASM2887588v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:11,578] [INFO] DFAST_QC completed!
[2024-01-24 12:33:11,578] [INFO] Total running time: 0h1m13s