[2024-01-24 11:43:39,056] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:39,075] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:39,075] [INFO] DQC Reference Directory: /var/lib/cwl/stg06d0945b-4637-4d63-b3c3-edc924521348/dqc_reference
[2024-01-24 11:43:40,291] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:40,292] [INFO] Task started: Prodigal
[2024-01-24 11:43:40,293] [INFO] Running command: gunzip -c /var/lib/cwl/stgcff6f5c6-50c1-4415-a990-b413fa0047da/GCF_000763375.1_ASM76337v1_genomic.fna.gz | prodigal -d GCF_000763375.1_ASM76337v1_genomic.fna/cds.fna -a GCF_000763375.1_ASM76337v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:50,422] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:50,422] [INFO] Task started: HMMsearch
[2024-01-24 11:43:50,422] [INFO] Running command: hmmsearch --tblout GCF_000763375.1_ASM76337v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06d0945b-4637-4d63-b3c3-edc924521348/dqc_reference/reference_markers.hmm GCF_000763375.1_ASM76337v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:50,815] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:50,816] [INFO] Found 6/6 markers.
[2024-01-24 11:43:50,846] [INFO] Query marker FASTA was written to GCF_000763375.1_ASM76337v1_genomic.fna/markers.fasta
[2024-01-24 11:43:50,847] [INFO] Task started: Blastn
[2024-01-24 11:43:50,847] [INFO] Running command: blastn -query GCF_000763375.1_ASM76337v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06d0945b-4637-4d63-b3c3-edc924521348/dqc_reference/reference_markers.fasta -out GCF_000763375.1_ASM76337v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:51,980] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:51,984] [INFO] Selected 14 target genomes.
[2024-01-24 11:43:51,984] [INFO] Target genome list was writen to GCF_000763375.1_ASM76337v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:52,001] [INFO] Task started: fastANI
[2024-01-24 11:43:52,001] [INFO] Running command: fastANI --query /var/lib/cwl/stgcff6f5c6-50c1-4415-a990-b413fa0047da/GCF_000763375.1_ASM76337v1_genomic.fna.gz --refList GCF_000763375.1_ASM76337v1_genomic.fna/target_genomes.txt --output GCF_000763375.1_ASM76337v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:03,191] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:03,192] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06d0945b-4637-4d63-b3c3-edc924521348/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:03,192] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06d0945b-4637-4d63-b3c3-edc924521348/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:03,204] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:03,205] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:03,205] [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 profundi	strain=Shh49	GCA_000763375.1	450380	450380	type	True	100.0	1119	1120	95	conclusive
Microbacterium murale	strain=CCM 7640	GCA_014635185.1	1081040	1081040	type	True	91.0855	854	1120	95	below_threshold
Microbacterium aerolatum	strain=NBRC 103071	GCA_007988825.1	153731	153731	type	True	83.4876	716	1120	95	below_threshold
Microbacterium aerolatum	strain=CCM 4955	GCA_014635005.1	153731	153731	type	True	83.4127	725	1120	95	below_threshold
Microbacterium ginsengiterrae	strain=JCM 15516	GCA_015278215.1	546115	546115	type	True	82.3825	638	1120	95	below_threshold
Microbacterium ginsengiterrae	strain=DSM 24823	GCA_014205075.1	546115	546115	type	True	82.2863	641	1120	95	below_threshold
Microbacterium liquefaciens	strain=JCM 3879	GCA_014648755.1	33918	33918	type	True	81.44	572	1120	95	below_threshold
Microbacterium saperdae	strain=JCM 1352	GCA_014646775.1	69368	69368	type	True	81.4356	603	1120	95	below_threshold
Microbacterium liquefaciens	strain=NBRC 15037	GCA_006539765.1	33918	33918	type	True	81.4279	578	1120	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	80.8001	574	1120	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	79.6076	456	1120	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	79.4619	386	1120	95	below_threshold
Microbacterium invictum	strain=DSM 19600	GCA_023155715.1	515415	515415	type	True	79.4304	418	1120	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	79.3545	450	1120	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:03,207] [INFO] DFAST Taxonomy check result was written to GCF_000763375.1_ASM76337v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:03,208] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:03,208] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:03,208] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06d0945b-4637-4d63-b3c3-edc924521348/dqc_reference/checkm_data
[2024-01-24 11:44:03,209] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:03,245] [INFO] Task started: CheckM
[2024-01-24 11:44:03,245] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000763375.1_ASM76337v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000763375.1_ASM76337v1_genomic.fna/checkm_input GCF_000763375.1_ASM76337v1_genomic.fna/checkm_result
[2024-01-24 11:44:43,207] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:43,208] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:43,230] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:43,230] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:43,230] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000763375.1_ASM76337v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:43,231] [INFO] Task started: Blastn
[2024-01-24 11:44:43,231] [INFO] Running command: blastn -query GCF_000763375.1_ASM76337v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06d0945b-4637-4d63-b3c3-edc924521348/dqc_reference/reference_markers_gtdb.fasta -out GCF_000763375.1_ASM76337v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:45,068] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:45,071] [INFO] Selected 14 target genomes.
[2024-01-24 11:44:45,071] [INFO] Target genome list was writen to GCF_000763375.1_ASM76337v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:45,081] [INFO] Task started: fastANI
[2024-01-24 11:44:45,082] [INFO] Running command: fastANI --query /var/lib/cwl/stgcff6f5c6-50c1-4415-a990-b413fa0047da/GCF_000763375.1_ASM76337v1_genomic.fna.gz --refList GCF_000763375.1_ASM76337v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000763375.1_ASM76337v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:55,919] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:55,936] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:55,937] [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_000763375.1	s__Microbacterium profundi	100.0	1119	1120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.00	98.00	0.85	0.85	2	conclusive
GCF_014635185.1	s__Microbacterium murale	91.0889	853	1120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007988825.1	s__Microbacterium aerolatum	83.4964	715	1120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_015277895.1	s__Microbacterium sp015277895	83.1546	700	1120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903645325.1	s__Microbacterium sp903645325	82.9978	632	1120	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	82.2745	642	1120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.21	98.43	0.95	0.89	3	-
GCF_000685355.1	s__Microbacterium sp000685355	81.643	644	1120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900095745.1	s__Microbacterium oxydans_B	81.4169	612	1120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.33	97.96	0.92	0.90	3	-
GCF_006716345.1	s__Microbacterium saperdae	81.3887	605	1120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002872075.1	s__Microbacterium kitamiense	81.225	624	1120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007954505.1	s__Microbacterium sp000800925	80.9899	583	1120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.26	97.84	0.89	0.86	5	-
GCF_009758255.1	s__Microbacterium sp009758255	80.7455	581	1120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744855.1	s__Microbacterium sp017744855	80.7284	453	1120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003524435.1	s__Microbacterium sp003524435	80.2743	446	1120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:55,938] [INFO] GTDB search result was written to GCF_000763375.1_ASM76337v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:55,939] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:55,942] [INFO] DFAST_QC result json was written to GCF_000763375.1_ASM76337v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:55,943] [INFO] DFAST_QC completed!
[2024-01-24 11:44:55,943] [INFO] Total running time: 0h1m17s