[2024-01-24 11:19:54,637] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:19:54,639] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:19:54,639] [INFO] DQC Reference Directory: /var/lib/cwl/stg121e1bfd-2771-421d-96f6-9cd04a8acbc5/dqc_reference
[2024-01-24 11:19:56,020] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:19:56,022] [INFO] Task started: Prodigal
[2024-01-24 11:19:56,022] [INFO] Running command: gunzip -c /var/lib/cwl/stg07ddea5a-a606-4092-86a9-2f7efd723f27/GCF_014836535.1_ASM1483653v1_genomic.fna.gz | prodigal -d GCF_014836535.1_ASM1483653v1_genomic.fna/cds.fna -a GCF_014836535.1_ASM1483653v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:05,404] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:05,404] [INFO] Task started: HMMsearch
[2024-01-24 11:20:05,404] [INFO] Running command: hmmsearch --tblout GCF_014836535.1_ASM1483653v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg121e1bfd-2771-421d-96f6-9cd04a8acbc5/dqc_reference/reference_markers.hmm GCF_014836535.1_ASM1483653v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:05,693] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:05,694] [INFO] Found 6/6 markers.
[2024-01-24 11:20:05,723] [INFO] Query marker FASTA was written to GCF_014836535.1_ASM1483653v1_genomic.fna/markers.fasta
[2024-01-24 11:20:05,723] [INFO] Task started: Blastn
[2024-01-24 11:20:05,723] [INFO] Running command: blastn -query GCF_014836535.1_ASM1483653v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg121e1bfd-2771-421d-96f6-9cd04a8acbc5/dqc_reference/reference_markers.fasta -out GCF_014836535.1_ASM1483653v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:06,944] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:06,948] [INFO] Selected 23 target genomes.
[2024-01-24 11:20:06,948] [INFO] Target genome list was writen to GCF_014836535.1_ASM1483653v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:06,956] [INFO] Task started: fastANI
[2024-01-24 11:20:06,956] [INFO] Running command: fastANI --query /var/lib/cwl/stg07ddea5a-a606-4092-86a9-2f7efd723f27/GCF_014836535.1_ASM1483653v1_genomic.fna.gz --refList GCF_014836535.1_ASM1483653v1_genomic.fna/target_genomes.txt --output GCF_014836535.1_ASM1483653v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:23,216] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:23,217] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg121e1bfd-2771-421d-96f6-9cd04a8acbc5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:23,217] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg121e1bfd-2771-421d-96f6-9cd04a8acbc5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:23,234] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:20:23,234] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:23,235] [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 pullorum	strain=Sa4CUA7	GCA_014836535.1	2762236	2762236	type	True	100.0	1025	1028	95	conclusive
Microbacterium saccharophilum	strain=K-1	GCA_008017435.1	1213358	1213358	type	True	81.7457	560	1028	95	below_threshold
Microbacterium telephonicum	strain=S2T63	GCA_003651225.1	1714841	1714841	type	True	81.6537	572	1028	95	below_threshold
Microbacterium saccharophilum	strain=NBRC 108778	GCA_007992455.1	1213358	1213358	type	True	81.6531	560	1028	95	below_threshold
Microbacterium lacticum	strain=JCM 1379	GCA_014646835.1	33885	33885	type	True	81.4775	519	1028	95	below_threshold
Microbacterium lacticum	strain=NBRC 14135	GCA_006539445.1	33885	33885	type	True	81.4477	522	1028	95	below_threshold
Microbacterium thalassium	strain=DSM 12511	GCA_014208045.1	362649	362649	type	True	81.3518	558	1028	95	below_threshold
Microbacterium lacticum	strain=DSM 20427	GCA_006716815.1	33885	33885	type	True	81.3463	540	1028	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	81.1001	579	1028	95	below_threshold
Microbacterium helvum	strain=NEAU-LLC	GCA_014779795.1	2773713	2773713	type	True	81.0441	595	1028	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	81.0284	567	1028	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	80.9926	569	1028	95	below_threshold
Microbacterium wangchenii	strain=dk512	GCA_004564355.1	2541726	2541726	type	True	80.951	542	1028	95	below_threshold
Microbacterium flavescens	strain=JCM 3877	GCA_018588945.1	69366	69366	type	True	80.9425	555	1028	95	below_threshold
Microbacterium lushaniae	strain=L-031	GCA_008727775.1	2614639	2614639	type	True	80.9279	530	1028	95	below_threshold
Microbacterium kyungheense	strain=DSM 105492	GCA_006783905.1	1263636	1263636	type	True	80.8502	608	1028	95	below_threshold
Microbacterium luticocti	strain=DSM 19459	GCA_000422405.1	451764	451764	type	True	80.7679	492	1028	95	below_threshold
Microbacterium sulfonylureivorans	strain=LAM7116	GCA_003999995.1	2486854	2486854	type	True	80.7217	580	1028	95	below_threshold
Microbacterium timonense	strain=Marseille-P5731	GCA_900292075.1	2086576	2086576	type	True	80.5434	542	1028	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	80.4258	588	1028	95	below_threshold
Microbacterium caowuchunii	strain=ST-M6	GCA_008727755.1	2614638	2614638	type	True	80.217	497	1028	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	79.9207	455	1028	95	below_threshold
Microbacterium marinilacus	strain=YM11-607	GCA_019753765.1	415209	415209	type	True	79.5308	458	1028	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:23,236] [INFO] DFAST Taxonomy check result was written to GCF_014836535.1_ASM1483653v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:23,237] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:23,237] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:23,237] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg121e1bfd-2771-421d-96f6-9cd04a8acbc5/dqc_reference/checkm_data
[2024-01-24 11:20:23,238] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:23,311] [INFO] Task started: CheckM
[2024-01-24 11:20:23,312] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014836535.1_ASM1483653v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014836535.1_ASM1483653v1_genomic.fna/checkm_input GCF_014836535.1_ASM1483653v1_genomic.fna/checkm_result
[2024-01-24 11:21:05,980] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:05,982] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:06,002] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:06,002] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:06,003] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014836535.1_ASM1483653v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:06,003] [INFO] Task started: Blastn
[2024-01-24 11:21:06,003] [INFO] Running command: blastn -query GCF_014836535.1_ASM1483653v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg121e1bfd-2771-421d-96f6-9cd04a8acbc5/dqc_reference/reference_markers_gtdb.fasta -out GCF_014836535.1_ASM1483653v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:07,935] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:07,940] [INFO] Selected 24 target genomes.
[2024-01-24 11:21:07,940] [INFO] Target genome list was writen to GCF_014836535.1_ASM1483653v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:07,959] [INFO] Task started: fastANI
[2024-01-24 11:21:07,959] [INFO] Running command: fastANI --query /var/lib/cwl/stg07ddea5a-a606-4092-86a9-2f7efd723f27/GCF_014836535.1_ASM1483653v1_genomic.fna.gz --refList GCF_014836535.1_ASM1483653v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014836535.1_ASM1483653v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:25,613] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:25,643] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:25,643] [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_014836535.1	s__Microbacterium sp014836535	100.0	1025	1028	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_007992455.1	s__Microbacterium saccharophilum	81.6282	562	1028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.54	98.03	0.93	0.90	5	-
GCF_003651225.1	s__Microbacterium telephonicum	81.6159	575	1028	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	81.4724	575	1028	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	81.3525	558	1028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716815.1	s__Microbacterium lacticum	81.3105	543	1028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.05	97.16	0.92	0.78	4	-
GCF_017876655.1	s__Microbacterium imperiale	81.2663	532	1028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427145.1	s__Microbacterium sp001427145	81.0699	554	1028	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	81.0668	617	1028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001422925.1	s__Microbacterium sp001422925	81.0269	600	1028	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	80.9549	554	1028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004564355.1	s__Microbacterium wangchenii	80.9392	543	1028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.29	98.90	0.96	0.95	3	-
GCF_004010105.1	s__Microbacterium sp004010105	80.8905	391	1028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009858275.1	s__Microbacterium sp009858275	80.8233	579	1028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003999995.1	s__Microbacterium sp003999995	80.7336	579	1028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422405.1	s__Microbacterium luticocti	80.6761	500	1028	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	80.5573	494	1028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900292075.1	s__Microbacterium timonense	80.5215	544	1028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015278355.1	s__Microbacterium yannicii_B	80.4721	599	1028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102175.1	s__Microbacterium sp900102175	80.4689	535	1028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907635.1	s__Microbacterium insulae	80.4459	539	1028	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	80.2782	488	1028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015235415.1	s__Microbacterium paludicola_A	80.1989	440	1028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009735645.1	s__Microbacterium oryzae	79.9207	455	1028	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 11:21:25,647] [INFO] GTDB search result was written to GCF_014836535.1_ASM1483653v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:25,648] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:25,655] [INFO] DFAST_QC result json was written to GCF_014836535.1_ASM1483653v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:25,655] [INFO] DFAST_QC completed!
[2024-01-24 11:21:25,655] [INFO] Total running time: 0h1m31s