[2024-01-24 11:51:10,713] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:10,715] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:10,715] [INFO] DQC Reference Directory: /var/lib/cwl/stg030e50f9-549a-45e7-b569-2ff451621e49/dqc_reference
[2024-01-24 11:51:12,188] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:12,189] [INFO] Task started: Prodigal
[2024-01-24 11:51:12,190] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ca1d350-c361-4052-9f6c-c18208328256/GCF_014635185.1_ASM1463518v1_genomic.fna.gz | prodigal -d GCF_014635185.1_ASM1463518v1_genomic.fna/cds.fna -a GCF_014635185.1_ASM1463518v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:23,904] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:23,905] [INFO] Task started: HMMsearch
[2024-01-24 11:51:23,905] [INFO] Running command: hmmsearch --tblout GCF_014635185.1_ASM1463518v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg030e50f9-549a-45e7-b569-2ff451621e49/dqc_reference/reference_markers.hmm GCF_014635185.1_ASM1463518v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:24,178] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:24,179] [INFO] Found 6/6 markers.
[2024-01-24 11:51:24,227] [INFO] Query marker FASTA was written to GCF_014635185.1_ASM1463518v1_genomic.fna/markers.fasta
[2024-01-24 11:51:24,227] [INFO] Task started: Blastn
[2024-01-24 11:51:24,227] [INFO] Running command: blastn -query GCF_014635185.1_ASM1463518v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg030e50f9-549a-45e7-b569-2ff451621e49/dqc_reference/reference_markers.fasta -out GCF_014635185.1_ASM1463518v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:25,300] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:25,304] [INFO] Selected 15 target genomes.
[2024-01-24 11:51:25,304] [INFO] Target genome list was writen to GCF_014635185.1_ASM1463518v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:25,310] [INFO] Task started: fastANI
[2024-01-24 11:51:25,310] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ca1d350-c361-4052-9f6c-c18208328256/GCF_014635185.1_ASM1463518v1_genomic.fna.gz --refList GCF_014635185.1_ASM1463518v1_genomic.fna/target_genomes.txt --output GCF_014635185.1_ASM1463518v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:37,855] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:37,855] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg030e50f9-549a-45e7-b569-2ff451621e49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:37,856] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg030e50f9-549a-45e7-b569-2ff451621e49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:37,869] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:37,869] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:37,869] [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 murale	strain=CCM 7640	GCA_014635185.1	1081040	1081040	type	True	100.0	1290	1291	95	conclusive
Microbacterium profundi	strain=Shh49	GCA_000763375.1	450380	450380	type	True	90.9144	868	1291	95	below_threshold
Microbacterium aerolatum	strain=NBRC 103071	GCA_007988825.1	153731	153731	type	True	83.2831	779	1291	95	below_threshold
Microbacterium aerolatum	strain=CCM 4955	GCA_014635005.1	153731	153731	type	True	83.1617	793	1291	95	below_threshold
Microbacterium ginsengiterrae	strain=JCM 15516	GCA_015278215.1	546115	546115	type	True	82.0039	670	1291	95	below_threshold
Microbacterium saperdae	strain=JCM 1352	GCA_014646775.1	69368	69368	type	True	81.3819	651	1291	95	below_threshold
Microbacterium liquefaciens	strain=NBRC 15037	GCA_006539765.1	33918	33918	type	True	81.353	613	1291	95	below_threshold
Microbacterium liquefaciens	strain=JCM 3879	GCA_014648755.1	33918	33918	type	True	81.3294	619	1291	95	below_threshold
Microbacterium saperdae	strain=DSM 20169	GCA_006716345.1	69368	69368	type	True	81.3269	651	1291	95	below_threshold
Microbacterium foliorum	strain=NRRL B-24224	GCA_003367705.1	104336	104336	suspected-type	True	81.2337	641	1291	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	80.771	593	1291	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	79.8124	464	1291	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	79.682	381	1291	95	below_threshold
Microbacterium pullorum	strain=Sa4CUA7	GCA_014836535.1	2762236	2762236	type	True	79.3295	453	1291	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	79.1946	489	1291	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:37,871] [INFO] DFAST Taxonomy check result was written to GCF_014635185.1_ASM1463518v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:37,874] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:37,874] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:37,874] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg030e50f9-549a-45e7-b569-2ff451621e49/dqc_reference/checkm_data
[2024-01-24 11:51:37,876] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:37,915] [INFO] Task started: CheckM
[2024-01-24 11:51:37,915] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014635185.1_ASM1463518v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014635185.1_ASM1463518v1_genomic.fna/checkm_input GCF_014635185.1_ASM1463518v1_genomic.fna/checkm_result
[2024-01-24 11:52:36,748] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:36,749] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:36,771] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:36,771] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:36,772] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014635185.1_ASM1463518v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:36,772] [INFO] Task started: Blastn
[2024-01-24 11:52:36,772] [INFO] Running command: blastn -query GCF_014635185.1_ASM1463518v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg030e50f9-549a-45e7-b569-2ff451621e49/dqc_reference/reference_markers_gtdb.fasta -out GCF_014635185.1_ASM1463518v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:38,350] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:38,353] [INFO] Selected 17 target genomes.
[2024-01-24 11:52:38,353] [INFO] Target genome list was writen to GCF_014635185.1_ASM1463518v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:38,363] [INFO] Task started: fastANI
[2024-01-24 11:52:38,363] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ca1d350-c361-4052-9f6c-c18208328256/GCF_014635185.1_ASM1463518v1_genomic.fna.gz --refList GCF_014635185.1_ASM1463518v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014635185.1_ASM1463518v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:51,144] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:51,158] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:51,159] [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_014635185.1	s__Microbacterium murale	100.0	1290	1291	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000763375.1	s__Microbacterium profundi	90.8947	869	1291	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.00	98.00	0.85	0.85	2	-
GCF_015277895.1	s__Microbacterium sp015277895	83.4381	794	1291	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	83.3101	777	1291	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014205075.1	s__Microbacterium ginsengiterrae	82.0034	674	1291	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	81.6947	645	1291	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002979655.1	s__Microbacterium sp002979655	81.4365	656	1291	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	97.69	97.67	0.91	0.90	5	-
GCF_011752045.1	s__Microbacterium sp001639925	81.4213	629	1291	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.61	99.21	0.98	0.97	3	-
GCF_002872075.1	s__Microbacterium kitamiense	81.4202	646	1291	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716345.1	s__Microbacterium saperdae	81.3407	649	1291	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003610275.1	s__Microbacterium ginsengiterrae_A	81.3208	688	1291	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003367705.1	s__Microbacterium foliorum	81.236	640	1291	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004216995.1	s__Microbacterium sp004216995	81.2016	669	1291	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009758255.1	s__Microbacterium sp009758255	80.6473	610	1291	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	80.6443	484	1291	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	80.3829	487	1291	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506375.1	s__Microbacterium sp902506375	80.3748	558	1291	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 11:52:51,162] [INFO] GTDB search result was written to GCF_014635185.1_ASM1463518v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:51,163] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:51,167] [INFO] DFAST_QC result json was written to GCF_014635185.1_ASM1463518v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:51,167] [INFO] DFAST_QC completed!
[2024-01-24 11:52:51,167] [INFO] Total running time: 0h1m40s