[2024-01-25 19:24:45,020] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:24:45,022] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:24:45,022] [INFO] DQC Reference Directory: /var/lib/cwl/stg3b20344e-a5b4-4d65-bd2a-e2e6c63622ab/dqc_reference
[2024-01-25 19:24:48,895] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:24:48,897] [INFO] Task started: Prodigal
[2024-01-25 19:24:48,897] [INFO] Running command: gunzip -c /var/lib/cwl/stg9d81d805-9e07-4fb7-89f4-f410024bed30/GCF_014137985.1_ASM1413798v1_genomic.fna.gz | prodigal -d GCF_014137985.1_ASM1413798v1_genomic.fna/cds.fna -a GCF_014137985.1_ASM1413798v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:24:57,202] [INFO] Task succeeded: Prodigal
[2024-01-25 19:24:57,203] [INFO] Task started: HMMsearch
[2024-01-25 19:24:57,203] [INFO] Running command: hmmsearch --tblout GCF_014137985.1_ASM1413798v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3b20344e-a5b4-4d65-bd2a-e2e6c63622ab/dqc_reference/reference_markers.hmm GCF_014137985.1_ASM1413798v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:24:57,442] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:24:57,443] [INFO] Found 6/6 markers.
[2024-01-25 19:24:57,483] [INFO] Query marker FASTA was written to GCF_014137985.1_ASM1413798v1_genomic.fna/markers.fasta
[2024-01-25 19:24:57,483] [INFO] Task started: Blastn
[2024-01-25 19:24:57,483] [INFO] Running command: blastn -query GCF_014137985.1_ASM1413798v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b20344e-a5b4-4d65-bd2a-e2e6c63622ab/dqc_reference/reference_markers.fasta -out GCF_014137985.1_ASM1413798v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:24:59,219] [INFO] Task succeeded: Blastn
[2024-01-25 19:24:59,222] [INFO] Selected 12 target genomes.
[2024-01-25 19:24:59,222] [INFO] Target genome list was writen to GCF_014137985.1_ASM1413798v1_genomic.fna/target_genomes.txt
[2024-01-25 19:24:59,413] [INFO] Task started: fastANI
[2024-01-25 19:24:59,413] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d81d805-9e07-4fb7-89f4-f410024bed30/GCF_014137985.1_ASM1413798v1_genomic.fna.gz --refList GCF_014137985.1_ASM1413798v1_genomic.fna/target_genomes.txt --output GCF_014137985.1_ASM1413798v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:25:06,386] [INFO] Task succeeded: fastANI
[2024-01-25 19:25:06,386] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3b20344e-a5b4-4d65-bd2a-e2e6c63622ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:25:06,386] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3b20344e-a5b4-4d65-bd2a-e2e6c63622ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:25:06,448] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:25:06,448] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:25:06,448] [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 halimionae	strain=DSM 27576	GCA_014137985.1	1526413	1526413	type	True	100.0	971	972	95	conclusive
Microbacterium halimionae	strain=CECT 8593	GCA_011761265.1	1526413	1526413	type	True	99.9982	967	972	95	conclusive
Microbacterium endophyticum	strain=DSM 27099	GCA_011047135.1	1526412	1526412	type	True	85.7865	730	972	95	below_threshold
Microbacterium endophyticum	strain=DSM 27099	GCA_014191465.1	1526412	1526412	type	True	85.7582	723	972	95	below_threshold
Microbacterium endophyticum	strain=CECT 8354	GCA_011761445.1	1526412	1526412	type	True	85.714	734	972	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	78.0145	255	972	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	77.9558	164	972	95	below_threshold
Microbacterium invictum	strain=JCM 17023	GCA_015278285.1	515415	515415	type	True	77.8313	222	972	95	below_threshold
Microbacterium ginsengiterrae	strain=DSM 24823	GCA_014205075.1	546115	546115	type	True	77.8185	162	972	95	below_threshold
Microbacterium invictum	strain=DSM 19600	GCA_023155715.1	515415	515415	type	True	77.8093	225	972	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	77.7616	244	972	95	below_threshold
Microbacterium ginsengiterrae	strain=JCM 15516	GCA_015278215.1	546115	546115	type	True	77.507	162	972	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:25:06,449] [INFO] DFAST Taxonomy check result was written to GCF_014137985.1_ASM1413798v1_genomic.fna/tc_result.tsv
[2024-01-25 19:25:06,450] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:25:06,450] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:25:06,450] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3b20344e-a5b4-4d65-bd2a-e2e6c63622ab/dqc_reference/checkm_data
[2024-01-25 19:25:06,457] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:25:06,492] [INFO] Task started: CheckM
[2024-01-25 19:25:06,492] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014137985.1_ASM1413798v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014137985.1_ASM1413798v1_genomic.fna/checkm_input GCF_014137985.1_ASM1413798v1_genomic.fna/checkm_result
[2024-01-25 19:25:37,888] [INFO] Task succeeded: CheckM
[2024-01-25 19:25:37,890] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:25:37,922] [INFO] ===== Completeness check finished =====
[2024-01-25 19:25:37,922] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:25:37,923] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014137985.1_ASM1413798v1_genomic.fna/markers.fasta)
[2024-01-25 19:25:37,923] [INFO] Task started: Blastn
[2024-01-25 19:25:37,923] [INFO] Running command: blastn -query GCF_014137985.1_ASM1413798v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b20344e-a5b4-4d65-bd2a-e2e6c63622ab/dqc_reference/reference_markers_gtdb.fasta -out GCF_014137985.1_ASM1413798v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:25:39,129] [INFO] Task succeeded: Blastn
[2024-01-25 19:25:39,132] [INFO] Selected 23 target genomes.
[2024-01-25 19:25:39,132] [INFO] Target genome list was writen to GCF_014137985.1_ASM1413798v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:25:39,180] [INFO] Task started: fastANI
[2024-01-25 19:25:39,180] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d81d805-9e07-4fb7-89f4-f410024bed30/GCF_014137985.1_ASM1413798v1_genomic.fna.gz --refList GCF_014137985.1_ASM1413798v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014137985.1_ASM1413798v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:25:53,269] [INFO] Task succeeded: fastANI
[2024-01-25 19:25:53,306] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:25:53,307] [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_011761265.1	s__Microbacterium halimionae	99.9982	967	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_011047135.1	s__Microbacterium endophyticum	85.7865	730	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	0.99	3	-
GCF_000799385.1	s__Microbacterium sp000799385	78.222	248	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248655.1	s__Microbacterium sp003248655	78.1672	211	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715145.1	s__Microbacterium sp006715145	78.1393	224	972	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	78.0176	262	972	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	77.9912	278	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003095395.1	s__Microbacterium sp003095395	77.9764	237	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001456955.1	s__Microbacterium enclense	77.9608	238	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.78	97.57	0.95	0.89	3	-
GCF_014201255.1	s__Microbacterium sp014201255	77.9561	195	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012847295.1	s__Microbacterium sp012847295	77.9053	219	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017968845.1	s__Microbacterium sp017968845	77.8602	162	972	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	77.8596	255	972	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	77.8204	222	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900078385.1	s__Microbacterium sp900078385	77.8172	229	972	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	77.817	162	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.21	98.43	0.95	0.89	3	-
GCF_018588945.1	s__Microbacterium flavescens	77.8118	250	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014837165.1	s__Microbacterium sp014837165	77.7788	242	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907815.1	s__Microbacterium aurum	77.7654	228	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.09	96.17	0.91	0.83	3	-
GCF_003850245.1	s__Microbacterium sp003850245	77.7559	201	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873155.1	s__Microbacterium sp014873155	77.7351	245	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011046485.1	s__Microbacterium sp011046485	77.7306	250	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001476285.1	s__Microbacterium testaceum_B	77.6716	235	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.43	98.38	0.88	0.88	4	-
--------------------------------------------------------------------------------
[2024-01-25 19:25:53,308] [INFO] GTDB search result was written to GCF_014137985.1_ASM1413798v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:25:53,309] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:25:53,312] [INFO] DFAST_QC result json was written to GCF_014137985.1_ASM1413798v1_genomic.fna/dqc_result.json
[2024-01-25 19:25:53,312] [INFO] DFAST_QC completed!
[2024-01-25 19:25:53,312] [INFO] Total running time: 0h1m8s