[2024-01-25 18:44:35,597] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:44:35,603] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:44:35,603] [INFO] DQC Reference Directory: /var/lib/cwl/stg5743facb-cb62-418b-b375-5fee6b1d7433/dqc_reference
[2024-01-25 18:44:36,768] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:44:36,769] [INFO] Task started: Prodigal
[2024-01-25 18:44:36,769] [INFO] Running command: gunzip -c /var/lib/cwl/stge56d3e5f-823a-4924-b9c8-100a5116f7e5/GCF_000422405.1_ASM42240v1_genomic.fna.gz | prodigal -d GCF_000422405.1_ASM42240v1_genomic.fna/cds.fna -a GCF_000422405.1_ASM42240v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:44:45,494] [INFO] Task succeeded: Prodigal
[2024-01-25 18:44:45,494] [INFO] Task started: HMMsearch
[2024-01-25 18:44:45,494] [INFO] Running command: hmmsearch --tblout GCF_000422405.1_ASM42240v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5743facb-cb62-418b-b375-5fee6b1d7433/dqc_reference/reference_markers.hmm GCF_000422405.1_ASM42240v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:44:45,695] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:44:45,697] [INFO] Found 6/6 markers.
[2024-01-25 18:44:45,728] [INFO] Query marker FASTA was written to GCF_000422405.1_ASM42240v1_genomic.fna/markers.fasta
[2024-01-25 18:44:45,729] [INFO] Task started: Blastn
[2024-01-25 18:44:45,729] [INFO] Running command: blastn -query GCF_000422405.1_ASM42240v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5743facb-cb62-418b-b375-5fee6b1d7433/dqc_reference/reference_markers.fasta -out GCF_000422405.1_ASM42240v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:46,891] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:46,894] [INFO] Selected 22 target genomes.
[2024-01-25 18:44:46,895] [INFO] Target genome list was writen to GCF_000422405.1_ASM42240v1_genomic.fna/target_genomes.txt
[2024-01-25 18:44:46,909] [INFO] Task started: fastANI
[2024-01-25 18:44:46,909] [INFO] Running command: fastANI --query /var/lib/cwl/stge56d3e5f-823a-4924-b9c8-100a5116f7e5/GCF_000422405.1_ASM42240v1_genomic.fna.gz --refList GCF_000422405.1_ASM42240v1_genomic.fna/target_genomes.txt --output GCF_000422405.1_ASM42240v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:45:02,999] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:03,000] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5743facb-cb62-418b-b375-5fee6b1d7433/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:45:03,000] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5743facb-cb62-418b-b375-5fee6b1d7433/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:45:03,013] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:45:03,013] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:45:03,014] [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 luticocti	strain=DSM 19459	GCA_000422405.1	451764	451764	type	True	100.0	1023	1026	95	conclusive
Microbacterium protaetiae	strain=DFW100M-13	GCA_004135285.1	2509458	2509458	type	True	82.2858	632	1026	95	below_threshold
Microbacterium pullorum	strain=Sa4CUA7	GCA_014836535.1	2762236	2762236	type	True	80.6316	497	1026	95	below_threshold
Microbacterium thalassium	strain=DSM 12511	GCA_014208045.1	362649	362649	type	True	80.5705	505	1026	95	below_threshold
Microbacterium invictum	strain=JCM 17023	GCA_015278285.1	515415	515415	type	True	80.5358	505	1026	95	below_threshold
Microbacterium telephonicum	strain=S2T63	GCA_003651225.1	1714841	1714841	type	True	80.4698	510	1026	95	below_threshold
Microbacterium helvum	strain=NEAU-LLC	GCA_014779795.1	2773713	2773713	type	True	80.4663	574	1026	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	80.4522	503	1026	95	below_threshold
Microbacterium hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	80.4256	527	1026	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	80.4166	567	1026	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	80.396	511	1026	95	below_threshold
Microbacterium invictum	strain=DSM 19600	GCA_023155715.1	515415	515415	type	True	80.377	527	1026	95	below_threshold
Microbacterium ureisolvens	strain=CFH S00084	GCA_015278315.1	2781186	2781186	type	True	80.2952	544	1026	95	below_threshold
Microbacterium mangrovi	strain=MUSC 115	GCA_000802305.1	1348253	1348253	type	True	80.246	532	1026	95	below_threshold
Microbacterium flavescens	strain=JCM 3877	GCA_018588945.1	69366	69366	type	True	80.2331	502	1026	95	below_threshold
Microbacterium saccharophilum	strain=NBRC 108778	GCA_007992455.1	1213358	1213358	type	True	80.1209	481	1026	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	80.0327	546	1026	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_001689915.1	904291	904291	type	True	79.8251	427	1026	95	below_threshold
Microbacterium aerolatum	strain=NBRC 103071	GCA_007988825.1	153731	153731	type	True	79.7722	436	1026	95	below_threshold
Microbacterium aerolatum	strain=CCM 4955	GCA_014635005.1	153731	153731	type	True	79.648	450	1026	95	below_threshold
Microbacterium marinilacus	strain=YM11-607	GCA_019753765.1	415209	415209	type	True	79.4818	429	1026	95	below_threshold
Microbacterium gorillae	strain=G3	GCA_000826185.2	1231063	1231063	type	True	79.1646	391	1026	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:45:03,016] [INFO] DFAST Taxonomy check result was written to GCF_000422405.1_ASM42240v1_genomic.fna/tc_result.tsv
[2024-01-25 18:45:03,017] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:45:03,017] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:45:03,017] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5743facb-cb62-418b-b375-5fee6b1d7433/dqc_reference/checkm_data
[2024-01-25 18:45:03,018] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:45:03,050] [INFO] Task started: CheckM
[2024-01-25 18:45:03,050] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000422405.1_ASM42240v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000422405.1_ASM42240v1_genomic.fna/checkm_input GCF_000422405.1_ASM42240v1_genomic.fna/checkm_result
[2024-01-25 18:46:02,086] [INFO] Task succeeded: CheckM
[2024-01-25 18:46:02,087] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:46:02,102] [INFO] ===== Completeness check finished =====
[2024-01-25 18:46:02,102] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:46:02,104] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000422405.1_ASM42240v1_genomic.fna/markers.fasta)
[2024-01-25 18:46:02,104] [INFO] Task started: Blastn
[2024-01-25 18:46:02,104] [INFO] Running command: blastn -query GCF_000422405.1_ASM42240v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5743facb-cb62-418b-b375-5fee6b1d7433/dqc_reference/reference_markers_gtdb.fasta -out GCF_000422405.1_ASM42240v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:46:04,012] [INFO] Task succeeded: Blastn
[2024-01-25 18:46:04,015] [INFO] Selected 20 target genomes.
[2024-01-25 18:46:04,015] [INFO] Target genome list was writen to GCF_000422405.1_ASM42240v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:46:04,042] [INFO] Task started: fastANI
[2024-01-25 18:46:04,042] [INFO] Running command: fastANI --query /var/lib/cwl/stge56d3e5f-823a-4924-b9c8-100a5116f7e5/GCF_000422405.1_ASM42240v1_genomic.fna.gz --refList GCF_000422405.1_ASM42240v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000422405.1_ASM42240v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:46:19,222] [INFO] Task succeeded: fastANI
[2024-01-25 18:46:19,234] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:46:19,235] [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_000422405.1	s__Microbacterium luticocti	100.0	1023	1026	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_009649635.1	s__Microbacterium sp009649635	82.8342	623	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135285.1	s__Microbacterium protaetiae	82.2681	634	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004010105.1	s__Microbacterium sp004010105	80.6316	371	1026	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	80.6187	499	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014208045.1	s__Microbacterium thalassium	80.5951	503	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380605.1	s__Microbacterium sp000380605	80.5659	562	1026	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	80.4892	518	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003651225.1	s__Microbacterium telephonicum	80.4873	508	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013282805.1	s__Microbacterium hominis_B	80.4365	515	1026	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	80.431	529	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000802305.1	s__Microbacterium mangrovi	80.3165	526	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386735.1	s__Microbacterium trichothecenolyticum_A	80.2666	552	1026	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	80.2222	504	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001314225.1	s__Microbacterium sp001314225	80.1466	499	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427525.1	s__Microbacterium sp001427525	80.0636	511	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005502885.1	s__Microbacterium sp005502885	79.9383	495	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428485.1	s__Microbacterium sp001428485	79.9329	500	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002837415.1	s__Microbacterium sp002837415	79.8582	423	1026	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	79.749	438	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:46:19,236] [INFO] GTDB search result was written to GCF_000422405.1_ASM42240v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:46:19,237] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:46:19,240] [INFO] DFAST_QC result json was written to GCF_000422405.1_ASM42240v1_genomic.fna/dqc_result.json
[2024-01-25 18:46:19,241] [INFO] DFAST_QC completed!
[2024-01-25 18:46:19,241] [INFO] Total running time: 0h1m44s