[2024-01-25 19:06:05,815] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:06:05,816] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:06:05,817] [INFO] DQC Reference Directory: /var/lib/cwl/stg32ac1039-f655-49b3-a3c3-632ec35cca80/dqc_reference
[2024-01-25 19:06:06,962] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:06:06,963] [INFO] Task started: Prodigal
[2024-01-25 19:06:06,963] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ed127e4-174c-47b8-9607-1be57c5acac5/GCF_014653215.1_ASM1465321v1_genomic.fna.gz | prodigal -d GCF_014653215.1_ASM1465321v1_genomic.fna/cds.fna -a GCF_014653215.1_ASM1465321v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:06:14,630] [INFO] Task succeeded: Prodigal
[2024-01-25 19:06:14,631] [INFO] Task started: HMMsearch
[2024-01-25 19:06:14,631] [INFO] Running command: hmmsearch --tblout GCF_014653215.1_ASM1465321v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32ac1039-f655-49b3-a3c3-632ec35cca80/dqc_reference/reference_markers.hmm GCF_014653215.1_ASM1465321v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:06:14,896] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:06:14,897] [INFO] Found 6/6 markers.
[2024-01-25 19:06:14,925] [INFO] Query marker FASTA was written to GCF_014653215.1_ASM1465321v1_genomic.fna/markers.fasta
[2024-01-25 19:06:14,925] [INFO] Task started: Blastn
[2024-01-25 19:06:14,925] [INFO] Running command: blastn -query GCF_014653215.1_ASM1465321v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32ac1039-f655-49b3-a3c3-632ec35cca80/dqc_reference/reference_markers.fasta -out GCF_014653215.1_ASM1465321v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:06:16,115] [INFO] Task succeeded: Blastn
[2024-01-25 19:06:16,119] [INFO] Selected 29 target genomes.
[2024-01-25 19:06:16,119] [INFO] Target genome list was writen to GCF_014653215.1_ASM1465321v1_genomic.fna/target_genomes.txt
[2024-01-25 19:06:16,178] [INFO] Task started: fastANI
[2024-01-25 19:06:16,179] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ed127e4-174c-47b8-9607-1be57c5acac5/GCF_014653215.1_ASM1465321v1_genomic.fna.gz --refList GCF_014653215.1_ASM1465321v1_genomic.fna/target_genomes.txt --output GCF_014653215.1_ASM1465321v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:06:35,155] [INFO] Task succeeded: fastANI
[2024-01-25 19:06:35,156] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32ac1039-f655-49b3-a3c3-632ec35cca80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:06:35,156] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32ac1039-f655-49b3-a3c3-632ec35cca80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:06:35,172] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:06:35,172] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:06:35,173] [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
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	80.8363	497	1014	95	below_threshold
Protaetiibacter larvae	strain=KACC 19322	GCA_008365275.1	2592654	2592654	type	True	80.2802	468	1014	95	below_threshold
Chryseoglobus frigidaquae	strain=DSM 23889	GCA_009664385.2	424758	424758	type	True	79.3142	393	1014	95	below_threshold
Chryseoglobus frigidaquae	strain=DSM 23889	GCA_014200395.1	424758	424758	type	True	79.2838	399	1014	95	below_threshold
Agromyces tardus	strain=SJ-23	GCA_003710805.1	2583849	2583849	type	True	79.056	440	1014	95	below_threshold
Agromyces hippuratus	strain=DSM 8598	GCA_013410355.1	286438	286438	type	True	79.0404	424	1014	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.9944	439	1014	95	below_threshold
Agromyces fucosus	strain=CCUG 35506	GCA_004134865.1	41985	41985	type	True	78.9878	396	1014	95	below_threshold
Agromyces mediolanus	strain=JCM 3346	GCA_014648575.1	41986	41986	type	True	78.9789	393	1014	95	below_threshold
Agromyces ramosus	strain=DSM 43045	GCA_004216665.1	33879	33879	type	True	78.9363	412	1014	95	below_threshold
Rathayibacter festucae	strain=DSM 15932	GCA_004011135.1	110937	110937	type	True	78.8793	398	1014	95	below_threshold
Herbiconiux solani	strain=NBRC 106740	GCA_001571005.1	661329	661329	type	True	78.8623	394	1014	95	below_threshold
Galbitalea soli	strain=DSM 105515	GCA_013410525.1	1268042	1268042	type	True	78.8342	380	1014	95	below_threshold
Agromyces bracchium	strain=JCM 11433	GCA_009709675.1	88376	88376	type	True	78.7095	434	1014	95	below_threshold
Curtobacterium herbarum	strain=DSM 14013	GCA_016907335.1	150122	150122	suspected-type	True	78.6864	317	1014	95	below_threshold
Gryllotalpicola protaetiae	strain=2DFW10M-5	GCA_003627055.1	2419771	2419771	type	True	78.6321	340	1014	95	below_threshold
Frigoribacterium faeni	strain=NBRC 103066	GCA_007988805.1	145483	145483	type	True	78.6215	350	1014	95	below_threshold
Rathayibacter caricis	strain=DSM 15933	GCA_003044275.1	110936	110936	type	True	78.5679	366	1014	95	below_threshold
Agrococcus jenensis	strain=DSM 9580	GCA_003752465.1	46353	46353	type	True	78.484	359	1014	95	below_threshold
Curtobacterium herbarum	strain=LMG19917T	GCA_025000405.1	150122	150122	suspected-type	True	78.4659	317	1014	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	78.4498	351	1014	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	78.4479	364	1014	95	below_threshold
Microbacterium humi	strain=DSM 21799	GCA_900105715.1	640635	640635	type	True	78.4329	314	1014	95	below_threshold
Microbacterium lemovicicum	strain=Viu22	GCA_003991875.1	1072463	1072463	type	True	78.4237	371	1014	95	below_threshold
Microbacterium aurum	strain=DSM 8600	GCA_016907815.1	36805	36805	type	True	78.4175	337	1014	95	below_threshold
Microbacterium trichothecenolyticum	strain=DSM 8608	GCA_000956465.1	69370	69370	type	True	78.4153	361	1014	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	78.3476	382	1014	95	below_threshold
Microbacterium hatanonis	strain=JCM14558	GCA_008017415.1	404366	404366	type	True	78.2361	339	1014	95	below_threshold
Microbacterium flavum	strain=DSM 18909	GCA_018717645.1	415216	415216	type	True	78.0194	307	1014	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:06:35,174] [INFO] DFAST Taxonomy check result was written to GCF_014653215.1_ASM1465321v1_genomic.fna/tc_result.tsv
[2024-01-25 19:06:35,175] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:06:35,175] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:06:35,175] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32ac1039-f655-49b3-a3c3-632ec35cca80/dqc_reference/checkm_data
[2024-01-25 19:06:35,176] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:06:35,212] [INFO] Task started: CheckM
[2024-01-25 19:06:35,213] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014653215.1_ASM1465321v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014653215.1_ASM1465321v1_genomic.fna/checkm_input GCF_014653215.1_ASM1465321v1_genomic.fna/checkm_result
[2024-01-25 19:07:14,236] [INFO] Task succeeded: CheckM
[2024-01-25 19:07:14,237] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:07:14,258] [INFO] ===== Completeness check finished =====
[2024-01-25 19:07:14,258] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:07:14,259] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014653215.1_ASM1465321v1_genomic.fna/markers.fasta)
[2024-01-25 19:07:14,259] [INFO] Task started: Blastn
[2024-01-25 19:07:14,259] [INFO] Running command: blastn -query GCF_014653215.1_ASM1465321v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32ac1039-f655-49b3-a3c3-632ec35cca80/dqc_reference/reference_markers_gtdb.fasta -out GCF_014653215.1_ASM1465321v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:07:16,242] [INFO] Task succeeded: Blastn
[2024-01-25 19:07:16,246] [INFO] Selected 16 target genomes.
[2024-01-25 19:07:16,246] [INFO] Target genome list was writen to GCF_014653215.1_ASM1465321v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:07:16,260] [INFO] Task started: fastANI
[2024-01-25 19:07:16,261] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ed127e4-174c-47b8-9607-1be57c5acac5/GCF_014653215.1_ASM1465321v1_genomic.fna.gz --refList GCF_014653215.1_ASM1465321v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014653215.1_ASM1465321v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:07:26,306] [INFO] Task succeeded: fastANI
[2024-01-25 19:07:26,316] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:07:26,316] [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_014653215.1	s__Pseudolysinimonas yzui	100.0	1013	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudolysinimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003627075.1	s__Protaetiibacter intestinalis	80.8487	496	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014483895.1	s__Protaetiibacter sp014483895	80.5746	484	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003852775.1	s__Protaetiibacter sp003852775	80.3267	461	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308515.1	s__Pseudolysinimonas sp017308515	80.3075	505	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudolysinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008365275.1	s__Protaetiibacter larvae	80.2634	469	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898835.1	s__Protaetiibacter sp001898835	80.2467	482	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002325245.1	s__Pseudolysinimonas sp002325245	80.2442	454	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudolysinimonas	95.0	99.78	99.17	0.96	0.89	14	-
GCF_004216815.1	s__Protaetiibacter sp004216815	80.2423	516	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006517535.1	s__Schumannella sp006517535	80.1942	442	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Schumannella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479755.1	s__Pseudolysinimonas sp905479755	79.9662	428	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudolysinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425665.1	s__Yonghaparkia sp001425665	79.7911	396	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	99.25	99.25	0.97	0.97	2	-
GCF_008017545.1	s__Protaetiibacter sp008017545	79.7213	423	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014595885.1	s__Yonghaparkia alkaliphila_A	79.639	432	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017355965.1	s__JAFIQW01 sp017355965	79.4053	411	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__JAFIQW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011761235.1	s__Frigoribacterium faeni_A	78.9898	370	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:07:26,318] [INFO] GTDB search result was written to GCF_014653215.1_ASM1465321v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:07:26,318] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:07:26,322] [INFO] DFAST_QC result json was written to GCF_014653215.1_ASM1465321v1_genomic.fna/dqc_result.json
[2024-01-25 19:07:26,322] [INFO] DFAST_QC completed!
[2024-01-25 19:07:26,322] [INFO] Total running time: 0h1m21s