[2024-01-24 11:04:03,324] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:04:03,326] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:04:03,326] [INFO] DQC Reference Directory: /var/lib/cwl/stga5c92a66-6af4-40a0-858d-2ba857c72a6d/dqc_reference
[2024-01-24 11:04:04,536] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:04:04,536] [INFO] Task started: Prodigal
[2024-01-24 11:04:04,537] [INFO] Running command: gunzip -c /var/lib/cwl/stg96ff7d78-ec7a-4f27-91c5-658f47d444b9/GCF_004135285.1_ASM413528v1_genomic.fna.gz | prodigal -d GCF_004135285.1_ASM413528v1_genomic.fna/cds.fna -a GCF_004135285.1_ASM413528v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:04:16,695] [INFO] Task succeeded: Prodigal
[2024-01-24 11:04:16,696] [INFO] Task started: HMMsearch
[2024-01-24 11:04:16,696] [INFO] Running command: hmmsearch --tblout GCF_004135285.1_ASM413528v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga5c92a66-6af4-40a0-858d-2ba857c72a6d/dqc_reference/reference_markers.hmm GCF_004135285.1_ASM413528v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:04:16,978] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:04:16,980] [INFO] Found 6/6 markers.
[2024-01-24 11:04:17,015] [INFO] Query marker FASTA was written to GCF_004135285.1_ASM413528v1_genomic.fna/markers.fasta
[2024-01-24 11:04:17,015] [INFO] Task started: Blastn
[2024-01-24 11:04:17,015] [INFO] Running command: blastn -query GCF_004135285.1_ASM413528v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5c92a66-6af4-40a0-858d-2ba857c72a6d/dqc_reference/reference_markers.fasta -out GCF_004135285.1_ASM413528v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:04:18,193] [INFO] Task succeeded: Blastn
[2024-01-24 11:04:18,198] [INFO] Selected 24 target genomes.
[2024-01-24 11:04:18,199] [INFO] Target genome list was writen to GCF_004135285.1_ASM413528v1_genomic.fna/target_genomes.txt
[2024-01-24 11:04:18,214] [INFO] Task started: fastANI
[2024-01-24 11:04:18,214] [INFO] Running command: fastANI --query /var/lib/cwl/stg96ff7d78-ec7a-4f27-91c5-658f47d444b9/GCF_004135285.1_ASM413528v1_genomic.fna.gz --refList GCF_004135285.1_ASM413528v1_genomic.fna/target_genomes.txt --output GCF_004135285.1_ASM413528v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:04:36,839] [INFO] Task succeeded: fastANI
[2024-01-24 11:04:36,839] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga5c92a66-6af4-40a0-858d-2ba857c72a6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:04:36,840] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga5c92a66-6af4-40a0-858d-2ba857c72a6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:04:36,858] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:04:36,858] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:04:36,859] [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 protaetiae	strain=DFW100M-13	GCA_004135285.1	2509458	2509458	type	True	100.0	1263	1263	95	conclusive
Microbacterium luticocti	strain=DSM 19459	GCA_000422405.1	451764	451764	type	True	82.0389	650	1263	95	below_threshold
Microbacterium thalassium	strain=DSM 12511	GCA_014208045.1	362649	362649	type	True	79.8015	471	1263	95	below_threshold
Microbacterium kyungheense	strain=DSM 105492	GCA_006783905.1	1263636	1263636	type	True	79.7844	529	1263	95	below_threshold
Microbacterium invictum	strain=DSM 19600	GCA_023155715.1	515415	515415	type	True	79.7724	502	1263	95	below_threshold
Microbacterium invictum	strain=JCM 17023	GCA_015278285.1	515415	515415	type	True	79.7241	498	1263	95	below_threshold
Microbacterium pullorum	strain=Sa4CUA7	GCA_014836535.1	2762236	2762236	type	True	79.6257	466	1263	95	below_threshold
Microbacterium helvum	strain=NEAU-LLC	GCA_014779795.1	2773713	2773713	type	True	79.5382	567	1263	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	79.532	496	1263	95	below_threshold
Microbacterium ginsengisoli	strain=DSM 18659	GCA_000956535.1	400772	400772	type	True	79.5062	412	1263	95	below_threshold
Microbacterium flavescens	strain=JCM 3877	GCA_018588945.1	69366	69366	type	True	79.4428	481	1263	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	79.432	494	1263	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	79.421	526	1263	95	below_threshold
Microbacterium mangrovi	strain=MUSC 115	GCA_000802305.1	1348253	1348253	type	True	79.4144	498	1263	95	below_threshold
Microbacterium pseudoresistens	strain=DSM 22185	GCA_013409745.1	640634	640634	type	True	79.3813	389	1263	95	below_threshold
Microbacterium lushaniae	strain=L-031	GCA_008727775.1	2614639	2614639	type	True	79.3792	428	1263	95	below_threshold
Microbacterium ureisolvens	strain=CFH S00084	GCA_015278315.1	2781186	2781186	type	True	79.3339	549	1263	95	below_threshold
Microbacterium ulmi	strain=JCM 14282	GCA_013004565.1	179095	179095	type	True	79.273	479	1263	95	below_threshold
Microbacterium aerolatum	strain=NBRC 103071	GCA_007988825.1	153731	153731	type	True	79.2646	409	1263	95	below_threshold
Microbacterium aerolatum	strain=CCM 4955	GCA_014635005.1	153731	153731	type	True	79.2188	414	1263	95	below_threshold
Microbacterium azadirachtae	strain=DSM 23848	GCA_000956545.1	582680	582680	type	True	78.7664	440	1263	95	below_threshold
Microbacterium rhizomatis	strain=JCM 30598	GCA_008710745.1	1631477	1631477	type	True	78.7157	443	1263	95	below_threshold
Microbacterium marinilacus	strain=YM11-607	GCA_019753765.1	415209	415209	type	True	78.566	420	1263	95	below_threshold
Microbacterium album	strain=CGMCC 1.15794	GCA_014643695.1	2053191	2053191	type	True	78.5278	369	1263	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:04:36,860] [INFO] DFAST Taxonomy check result was written to GCF_004135285.1_ASM413528v1_genomic.fna/tc_result.tsv
[2024-01-24 11:04:36,861] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:04:36,861] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:04:36,861] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga5c92a66-6af4-40a0-858d-2ba857c72a6d/dqc_reference/checkm_data
[2024-01-24 11:04:36,862] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:04:36,904] [INFO] Task started: CheckM
[2024-01-24 11:04:36,905] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004135285.1_ASM413528v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004135285.1_ASM413528v1_genomic.fna/checkm_input GCF_004135285.1_ASM413528v1_genomic.fna/checkm_result
[2024-01-24 11:05:27,993] [INFO] Task succeeded: CheckM
[2024-01-24 11:05:27,994] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:05:28,016] [INFO] ===== Completeness check finished =====
[2024-01-24 11:05:28,016] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:05:28,017] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004135285.1_ASM413528v1_genomic.fna/markers.fasta)
[2024-01-24 11:05:28,017] [INFO] Task started: Blastn
[2024-01-24 11:05:28,017] [INFO] Running command: blastn -query GCF_004135285.1_ASM413528v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5c92a66-6af4-40a0-858d-2ba857c72a6d/dqc_reference/reference_markers_gtdb.fasta -out GCF_004135285.1_ASM413528v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:29,966] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:29,971] [INFO] Selected 20 target genomes.
[2024-01-24 11:05:29,971] [INFO] Target genome list was writen to GCF_004135285.1_ASM413528v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:05:29,988] [INFO] Task started: fastANI
[2024-01-24 11:05:29,988] [INFO] Running command: fastANI --query /var/lib/cwl/stg96ff7d78-ec7a-4f27-91c5-658f47d444b9/GCF_004135285.1_ASM413528v1_genomic.fna.gz --refList GCF_004135285.1_ASM413528v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004135285.1_ASM413528v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:05:43,832] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:43,851] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:05:43,851] [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_004135285.1	s__Microbacterium protaetiae	100.0	1263	1263	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_000422405.1	s__Microbacterium luticocti	82.0163	652	1263	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649635.1	s__Microbacterium sp009649635	81.1095	597	1263	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006783905.1	s__Microbacterium kyungheense	79.7451	534	1263	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836535.1	s__Microbacterium sp014836535	79.6382	465	1263	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898315.1	s__Microbacterium sp001898315	79.6094	465	1263	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.98	99.98	0.99	0.99	3	-
GCF_014779795.1	s__Microbacterium helvum	79.5299	568	1263	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075375.1	s__Microbacterium testaceum_E	79.5023	406	1263	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	96.83	96.83	0.84	0.84	2	-
GCF_000956535.1	s__Microbacterium ginsengisoli	79.4923	413	1263	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.60	98.14	0.85	0.83	9	-
GCF_010634855.1	s__Microbacterium sp010634855	79.484	504	1263	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.26	99.26	0.95	0.95	2	-
GCF_018588945.1	s__Microbacterium flavescens	79.453	480	1263	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000802305.1	s__Microbacterium mangrovi	79.4148	498	1263	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409745.1	s__Microbacterium pseudoresistens	79.4053	388	1263	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017831975.1	s__Microbacterium terrae	79.4019	517	1263	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_009758255.1	s__Microbacterium sp009758255	79.3541	443	1263	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015278315.1	s__Microbacterium ureisolvens	79.3408	549	1263	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.97	99.97	1.00	1.00	2	-
GCF_903645325.1	s__Microbacterium sp903645325	79.2639	402	1263	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	79.2531	410	1263	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCA_002837415.1	s__Microbacterium sp002837415	78.9742	390	1263	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008710745.1	s__Microbacterium rhizomatis	78.6983	445	1263	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 11:05:43,852] [INFO] GTDB search result was written to GCF_004135285.1_ASM413528v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:05:43,853] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:05:43,858] [INFO] DFAST_QC result json was written to GCF_004135285.1_ASM413528v1_genomic.fna/dqc_result.json
[2024-01-24 11:05:43,858] [INFO] DFAST_QC completed!
[2024-01-24 11:05:43,858] [INFO] Total running time: 0h1m41s