[2024-01-24 13:32:25,352] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:25,353] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:25,353] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb35bf32-b518-4085-86fc-a4b70bbce409/dqc_reference
[2024-01-24 13:32:26,693] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:26,694] [INFO] Task started: Prodigal
[2024-01-24 13:32:26,694] [INFO] Running command: gunzip -c /var/lib/cwl/stg5793ff75-95ce-479c-8638-087be87d19af/GCF_000826185.2_Microbacterium_massiliensis_G3_genomic.fna.gz | prodigal -d GCF_000826185.2_Microbacterium_massiliensis_G3_genomic.fna/cds.fna -a GCF_000826185.2_Microbacterium_massiliensis_G3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:37,816] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:37,816] [INFO] Task started: HMMsearch
[2024-01-24 13:32:37,816] [INFO] Running command: hmmsearch --tblout GCF_000826185.2_Microbacterium_massiliensis_G3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb35bf32-b518-4085-86fc-a4b70bbce409/dqc_reference/reference_markers.hmm GCF_000826185.2_Microbacterium_massiliensis_G3_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:38,088] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:38,090] [INFO] Found 6/6 markers.
[2024-01-24 13:32:38,123] [INFO] Query marker FASTA was written to GCF_000826185.2_Microbacterium_massiliensis_G3_genomic.fna/markers.fasta
[2024-01-24 13:32:38,123] [INFO] Task started: Blastn
[2024-01-24 13:32:38,123] [INFO] Running command: blastn -query GCF_000826185.2_Microbacterium_massiliensis_G3_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb35bf32-b518-4085-86fc-a4b70bbce409/dqc_reference/reference_markers.fasta -out GCF_000826185.2_Microbacterium_massiliensis_G3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:39,449] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:39,452] [INFO] Selected 24 target genomes.
[2024-01-24 13:32:39,452] [INFO] Target genome list was writen to GCF_000826185.2_Microbacterium_massiliensis_G3_genomic.fna/target_genomes.txt
[2024-01-24 13:32:39,473] [INFO] Task started: fastANI
[2024-01-24 13:32:39,473] [INFO] Running command: fastANI --query /var/lib/cwl/stg5793ff75-95ce-479c-8638-087be87d19af/GCF_000826185.2_Microbacterium_massiliensis_G3_genomic.fna.gz --refList GCF_000826185.2_Microbacterium_massiliensis_G3_genomic.fna/target_genomes.txt --output GCF_000826185.2_Microbacterium_massiliensis_G3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:55,628] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:55,629] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb35bf32-b518-4085-86fc-a4b70bbce409/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:55,629] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb35bf32-b518-4085-86fc-a4b70bbce409/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:55,655] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:55,655] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:55,656] [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 gorillae	strain=G3	GCA_000826185.2	1231063	1231063	type	True	100.0	1220	1224	95	conclusive
Microbacterium thalassium	strain=DSM 12511	GCA_014208045.1	362649	362649	type	True	79.6894	410	1224	95	below_threshold
Microbacterium paraoxydans	strain=DSM 15019	GCA_900105335.1	199592	199592	suspected-type	True	79.6442	432	1224	95	below_threshold
Microbacterium pullorum	strain=Sa4CUA7	GCA_014836535.1	2762236	2762236	type	True	79.626	377	1224	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	79.5666	403	1224	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	79.5655	428	1224	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	79.4966	382	1224	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_004564075.1	904291	904291	type	True	79.4338	381	1224	95	below_threshold
Microbacterium algeriense	strain=G1	GCA_008868005.1	2615184	2615184	type	True	79.4028	432	1224	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_002741995.1	904291	904291	type	True	79.3742	364	1224	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_001689915.1	904291	904291	type	True	79.3739	364	1224	95	below_threshold
Microbacterium marinum	strain=DSM 24947	GCA_014204835.1	421115	421115	type	True	79.3509	355	1224	95	below_threshold
Microbacterium azadirachtae	strain=DSM 23848	GCA_000956545.1	582680	582680	type	True	79.2998	444	1224	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	79.2986	381	1224	95	below_threshold
Microbacterium invictum	strain=DSM 19600	GCA_023155715.1	515415	515415	type	True	79.2968	395	1224	95	below_threshold
Microbacterium enclense	strain=NIO-1002	GCA_001456955.1	993073	993073	type	True	79.2886	373	1224	95	below_threshold
Microbacterium invictum	strain=JCM 17023	GCA_015278285.1	515415	515415	type	True	79.2666	388	1224	95	below_threshold
Microbacterium enclense	strain=NIO-1002	GCA_900096885.1	993073	993073	type	True	79.2632	375	1224	95	below_threshold
Microbacterium helvum	strain=NEAU-LLC	GCA_014779795.1	2773713	2773713	type	True	79.2223	449	1224	95	below_threshold
Microbacterium resistens	strain=NBRC 103078	GCA_001552355.1	156977	156977	type	True	79.1744	409	1224	95	below_threshold
Agromyces aurantiacus	strain=DSM 14598	GCA_016907355.1	165814	165814	type	True	78.2902	355	1224	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_900104685.1	589382	589382	type	True	78.1496	335	1224	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	78.1176	330	1224	95	below_threshold
Agromyces flavus	strain=CCM 7623	GCA_014635805.1	589382	589382	type	True	78.0929	329	1224	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:55,660] [INFO] DFAST Taxonomy check result was written to GCF_000826185.2_Microbacterium_massiliensis_G3_genomic.fna/tc_result.tsv
[2024-01-24 13:32:55,661] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:55,661] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:55,661] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb35bf32-b518-4085-86fc-a4b70bbce409/dqc_reference/checkm_data
[2024-01-24 13:32:55,663] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:55,719] [INFO] Task started: CheckM
[2024-01-24 13:32:55,719] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000826185.2_Microbacterium_massiliensis_G3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000826185.2_Microbacterium_massiliensis_G3_genomic.fna/checkm_input GCF_000826185.2_Microbacterium_massiliensis_G3_genomic.fna/checkm_result
[2024-01-24 13:34:03,976] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:03,977] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:03,994] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:03,994] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:03,994] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000826185.2_Microbacterium_massiliensis_G3_genomic.fna/markers.fasta)
[2024-01-24 13:34:03,995] [INFO] Task started: Blastn
[2024-01-24 13:34:03,995] [INFO] Running command: blastn -query GCF_000826185.2_Microbacterium_massiliensis_G3_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb35bf32-b518-4085-86fc-a4b70bbce409/dqc_reference/reference_markers_gtdb.fasta -out GCF_000826185.2_Microbacterium_massiliensis_G3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:06,227] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:06,231] [INFO] Selected 25 target genomes.
[2024-01-24 13:34:06,232] [INFO] Target genome list was writen to GCF_000826185.2_Microbacterium_massiliensis_G3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:06,254] [INFO] Task started: fastANI
[2024-01-24 13:34:06,254] [INFO] Running command: fastANI --query /var/lib/cwl/stg5793ff75-95ce-479c-8638-087be87d19af/GCF_000826185.2_Microbacterium_massiliensis_G3_genomic.fna.gz --refList GCF_000826185.2_Microbacterium_massiliensis_G3_genomic.fna/target_genomes_gtdb.txt --output GCF_000826185.2_Microbacterium_massiliensis_G3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:23,790] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:23,816] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:23,816] [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_000826185.2	s__Microbacterium gorillae	100.0	1221	1224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018268435.1	s__Microbacterium sp018268435	79.8297	385	1224	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	79.7258	450	1224	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	79.6953	373	1224	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	79.693	407	1224	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	79.6849	447	1224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003387575.1	s__Microbacterium sp003387575	79.5767	427	1224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015040615.1	s__Microbacterium sp015040615	79.5514	443	1224	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	79.5461	416	1224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCA_017306305.1	s__Microbacterium sp017306305	79.5016	421	1224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.93	98.76	0.92	0.91	3	-
GCF_004564075.1	s__Microbacterium sediminis	79.4599	379	1224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.95	99.95	1.00	1.00	3	-
GCF_001262495.1	s__Microbacterium sp001262495	79.4051	409	1224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426925.1	s__Microbacterium sp001426925	79.3721	401	1224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.86	98.86	0.90	0.90	2	-
GCF_001644225.1	s__Microbacterium oleivorans_A	79.3601	382	1224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007679045.1	s__Microbacterium sp007679045	79.3526	397	1224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.00	99.00	0.94	0.94	2	-
GCF_014204835.1	s__Microbacterium marinum	79.324	357	1224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	96.15	96.15	0.88	0.88	2	-
GCF_000956545.1	s__Microbacterium azadirachtae	79.31	443	1224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.29	96.06	0.91	0.89	5	-
GCF_018224615.1	s__Microbacterium paraoxydans_B	79.2749	412	1224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870695.1	s__Microbacterium sp016870695	79.2726	285	1224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779795.1	s__Microbacterium helvum	79.2648	445	1224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000956505.1	s__Microbacterium azadirachtae_A	79.1873	459	1224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	96.57	96.57	0.89	0.89	2	-
GCF_001552355.1	s__Microbacterium resistens	79.1735	409	1224	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	78.6814	329	1224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907355.1	s__Agromyces aurantiacus	78.2457	351	1224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104685.1	s__Agromyces flavus	78.1632	334	1224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:23,822] [INFO] GTDB search result was written to GCF_000826185.2_Microbacterium_massiliensis_G3_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:23,823] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:23,828] [INFO] DFAST_QC result json was written to GCF_000826185.2_Microbacterium_massiliensis_G3_genomic.fna/dqc_result.json
[2024-01-24 13:34:23,828] [INFO] DFAST_QC completed!
[2024-01-24 13:34:23,828] [INFO] Total running time: 0h1m58s