[2024-01-24 11:50:47,987] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:50:47,989] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:50:47,989] [INFO] DQC Reference Directory: /var/lib/cwl/stg47e3c3e9-b4a4-4a94-b782-206ac80e543b/dqc_reference
[2024-01-24 11:50:49,283] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:50:49,284] [INFO] Task started: Prodigal
[2024-01-24 11:50:49,285] [INFO] Running command: gunzip -c /var/lib/cwl/stg5417a893-4c60-4802-a022-f56d2859600c/GCF_011761265.1_ASM1176126v1_genomic.fna.gz | prodigal -d GCF_011761265.1_ASM1176126v1_genomic.fna/cds.fna -a GCF_011761265.1_ASM1176126v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:50:58,499] [INFO] Task succeeded: Prodigal
[2024-01-24 11:50:58,499] [INFO] Task started: HMMsearch
[2024-01-24 11:50:58,499] [INFO] Running command: hmmsearch --tblout GCF_011761265.1_ASM1176126v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47e3c3e9-b4a4-4a94-b782-206ac80e543b/dqc_reference/reference_markers.hmm GCF_011761265.1_ASM1176126v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:50:58,736] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:50:58,738] [INFO] Found 6/6 markers.
[2024-01-24 11:50:58,768] [INFO] Query marker FASTA was written to GCF_011761265.1_ASM1176126v1_genomic.fna/markers.fasta
[2024-01-24 11:50:58,769] [INFO] Task started: Blastn
[2024-01-24 11:50:58,769] [INFO] Running command: blastn -query GCF_011761265.1_ASM1176126v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47e3c3e9-b4a4-4a94-b782-206ac80e543b/dqc_reference/reference_markers.fasta -out GCF_011761265.1_ASM1176126v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:50:59,536] [INFO] Task succeeded: Blastn
[2024-01-24 11:50:59,540] [INFO] Selected 12 target genomes.
[2024-01-24 11:50:59,540] [INFO] Target genome list was writen to GCF_011761265.1_ASM1176126v1_genomic.fna/target_genomes.txt
[2024-01-24 11:50:59,573] [INFO] Task started: fastANI
[2024-01-24 11:50:59,573] [INFO] Running command: fastANI --query /var/lib/cwl/stg5417a893-4c60-4802-a022-f56d2859600c/GCF_011761265.1_ASM1176126v1_genomic.fna.gz --refList GCF_011761265.1_ASM1176126v1_genomic.fna/target_genomes.txt --output GCF_011761265.1_ASM1176126v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:06,347] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:06,348] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47e3c3e9-b4a4-4a94-b782-206ac80e543b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:06,348] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47e3c3e9-b4a4-4a94-b782-206ac80e543b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:06,404] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:51:06,404] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:06,404] [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
Microbacterium halimionae	strain=CECT 8593	GCA_011761265.1	1526413	1526413	type	True	100.0	977	977	95	conclusive
Microbacterium halimionae	strain=DSM 27576	GCA_014137985.1	1526413	1526413	type	True	99.9971	966	977	95	conclusive
Microbacterium endophyticum	strain=DSM 27099	GCA_011047135.1	1526412	1526412	type	True	85.6698	734	977	95	below_threshold
Microbacterium endophyticum	strain=DSM 27099	GCA_014191465.1	1526412	1526412	type	True	85.6658	728	977	95	below_threshold
Microbacterium endophyticum	strain=CECT 8354	GCA_011761445.1	1526412	1526412	type	True	85.6332	745	977	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	77.8827	248	977	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	77.8774	162	977	95	below_threshold
Microbacterium invictum	strain=JCM 17023	GCA_015278285.1	515415	515415	type	True	77.7831	217	977	95	below_threshold
Microbacterium invictum	strain=DSM 19600	GCA_023155715.1	515415	515415	type	True	77.7825	221	977	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	77.6232	258	977	95	below_threshold
Microbacterium ginsengiterrae	strain=JCM 15516	GCA_015278215.1	546115	546115	type	True	77.5724	163	977	95	below_threshold
Microbacterium ginsengiterrae	strain=DSM 24823	GCA_014205075.1	546115	546115	type	True	77.4926	166	977	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:06,407] [INFO] DFAST Taxonomy check result was written to GCF_011761265.1_ASM1176126v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:06,408] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:06,408] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:06,408] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47e3c3e9-b4a4-4a94-b782-206ac80e543b/dqc_reference/checkm_data
[2024-01-24 11:51:06,416] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:06,447] [INFO] Task started: CheckM
[2024-01-24 11:51:06,447] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011761265.1_ASM1176126v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011761265.1_ASM1176126v1_genomic.fna/checkm_input GCF_011761265.1_ASM1176126v1_genomic.fna/checkm_result
[2024-01-24 11:51:39,768] [INFO] Task succeeded: CheckM
[2024-01-24 11:51:39,769] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:51:39,796] [INFO] ===== Completeness check finished =====
[2024-01-24 11:51:39,797] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:51:39,797] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011761265.1_ASM1176126v1_genomic.fna/markers.fasta)
[2024-01-24 11:51:39,798] [INFO] Task started: Blastn
[2024-01-24 11:51:39,798] [INFO] Running command: blastn -query GCF_011761265.1_ASM1176126v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47e3c3e9-b4a4-4a94-b782-206ac80e543b/dqc_reference/reference_markers_gtdb.fasta -out GCF_011761265.1_ASM1176126v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:41,315] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:41,319] [INFO] Selected 23 target genomes.
[2024-01-24 11:51:41,319] [INFO] Target genome list was writen to GCF_011761265.1_ASM1176126v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:51:41,340] [INFO] Task started: fastANI
[2024-01-24 11:51:41,340] [INFO] Running command: fastANI --query /var/lib/cwl/stg5417a893-4c60-4802-a022-f56d2859600c/GCF_011761265.1_ASM1176126v1_genomic.fna.gz --refList GCF_011761265.1_ASM1176126v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011761265.1_ASM1176126v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:51:54,905] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:54,946] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:51:54,946] [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_011761265.1	s__Microbacterium halimionae	100.0	977	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_011047135.1	s__Microbacterium endophyticum	85.6636	733	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	0.99	3	-
GCF_014201255.1	s__Microbacterium sp014201255	78.1152	181	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003095395.1	s__Microbacterium sp003095395	77.9829	232	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248655.1	s__Microbacterium sp003248655	77.9712	220	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799385.1	s__Microbacterium sp000799385	77.9312	268	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001456955.1	s__Microbacterium enclense	77.8608	249	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.78	97.57	0.95	0.89	3	-
GCF_013282805.1	s__Microbacterium hominis_B	77.83	249	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017968845.1	s__Microbacterium sp017968845	77.8181	165	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011046485.1	s__Microbacterium sp011046485	77.7924	248	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014197265.1	s__Microbacterium invictum	77.7911	220	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003386735.1	s__Microbacterium trichothecenolyticum_A	77.7865	271	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900078385.1	s__Microbacterium sp900078385	77.7621	224	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012847295.1	s__Microbacterium sp012847295	77.7542	225	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001476285.1	s__Microbacterium testaceum_B	77.7245	237	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.43	98.38	0.88	0.88	4	-
GCF_014873155.1	s__Microbacterium sp014873155	77.7194	248	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715145.1	s__Microbacterium sp006715145	77.7102	233	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005347485.1	s__Microbacterium sp005347485	77.6567	252	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018588945.1	s__Microbacterium flavescens	77.6503	252	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907815.1	s__Microbacterium aurum	77.6248	234	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.09	96.17	0.91	0.83	3	-
GCF_014837165.1	s__Microbacterium sp014837165	77.611	259	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003850245.1	s__Microbacterium sp003850245	77.6022	200	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205075.1	s__Microbacterium ginsengiterrae	77.5332	163	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.21	98.43	0.95	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:51:54,948] [INFO] GTDB search result was written to GCF_011761265.1_ASM1176126v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:51:54,949] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:51:54,952] [INFO] DFAST_QC result json was written to GCF_011761265.1_ASM1176126v1_genomic.fna/dqc_result.json
[2024-01-24 11:51:54,952] [INFO] DFAST_QC completed!
[2024-01-24 11:51:54,953] [INFO] Total running time: 0h1m7s