[2024-01-24 12:44:43,999] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:44,005] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:44,006] [INFO] DQC Reference Directory: /var/lib/cwl/stge560057e-7c63-4e77-8af6-fa27ddaac1a9/dqc_reference
[2024-01-24 12:44:45,355] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:45,355] [INFO] Task started: Prodigal
[2024-01-24 12:44:45,356] [INFO] Running command: gunzip -c /var/lib/cwl/stg48f9535f-0e9d-4130-a313-e5d751852765/GCF_016907775.1_ASM1690777v1_genomic.fna.gz | prodigal -d GCF_016907775.1_ASM1690777v1_genomic.fna/cds.fna -a GCF_016907775.1_ASM1690777v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:52,617] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:52,617] [INFO] Task started: HMMsearch
[2024-01-24 12:44:52,618] [INFO] Running command: hmmsearch --tblout GCF_016907775.1_ASM1690777v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge560057e-7c63-4e77-8af6-fa27ddaac1a9/dqc_reference/reference_markers.hmm GCF_016907775.1_ASM1690777v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:52,933] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:52,934] [INFO] Found 6/6 markers.
[2024-01-24 12:44:52,959] [INFO] Query marker FASTA was written to GCF_016907775.1_ASM1690777v1_genomic.fna/markers.fasta
[2024-01-24 12:44:52,960] [INFO] Task started: Blastn
[2024-01-24 12:44:52,960] [INFO] Running command: blastn -query GCF_016907775.1_ASM1690777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge560057e-7c63-4e77-8af6-fa27ddaac1a9/dqc_reference/reference_markers.fasta -out GCF_016907775.1_ASM1690777v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:53,782] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:53,786] [INFO] Selected 27 target genomes.
[2024-01-24 12:44:53,786] [INFO] Target genome list was writen to GCF_016907775.1_ASM1690777v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:53,823] [INFO] Task started: fastANI
[2024-01-24 12:44:53,824] [INFO] Running command: fastANI --query /var/lib/cwl/stg48f9535f-0e9d-4130-a313-e5d751852765/GCF_016907775.1_ASM1690777v1_genomic.fna.gz --refList GCF_016907775.1_ASM1690777v1_genomic.fna/target_genomes.txt --output GCF_016907775.1_ASM1690777v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:14,636] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:14,637] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge560057e-7c63-4e77-8af6-fa27ddaac1a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:14,637] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge560057e-7c63-4e77-8af6-fa27ddaac1a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:14,653] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:14,653] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:14,654] [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
Pseudoglutamicibacter cumminsii	strain=DSM 10493	GCA_016907775.1	156979	156979	type	True	100.0	753	753	95	conclusive
Arthrobacter psychrochitiniphilus	strain=DSM 23143	GCA_013408645.1	291045	291045	type	True	78.7976	50	753	95	below_threshold
Zhihengliuella flava	strain=DSM 26152	GCA_015751895.1	1285193	1285193	type	True	78.2885	72	753	95	below_threshold
Glutamicibacter halophytocola	strain=KLBMP 5180	GCA_001302565.1	1933880	1933880	type	True	77.8727	84	753	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	77.8704	87	753	95	below_threshold
Glutamicibacter uratoxydans	strain=NBRC 15515	GCA_006539925.1	43667	43667	type	True	77.5998	90	753	95	below_threshold
Citricoccus muralis	strain=DSM 14442	GCA_003386075.1	169134	169134	type	True	77.5725	87	753	95	below_threshold
Galactobacter valiniphilus	strain=JZ R-35	GCA_003575975.1	2676122	2676122	type	True	77.4236	136	753	95	below_threshold
Glutamicibacter nicotianae	strain=NBRC 14234	GCA_006539525.1	37929	37929	type	True	77.3127	90	753	95	below_threshold
Galactobacter caseinivorans	strain=JZ R-183	GCA_003640665.1	2676123	2676123	type	True	77.1131	94	753	95	below_threshold
Citricoccus zhacaiensis	strain=CGMCC 1.7064	GCA_014645315.1	489142	489142	type	True	77.0083	83	753	95	below_threshold
Glutamicibacter mysorens	strain=NBRC 103060	GCA_001552115.1	257984	257984	type	True	77.0051	97	753	95	below_threshold
Arthrobacter crusticola	strain=SLN-3	GCA_004357995.1	2547960	2547960	type	True	76.6181	77	753	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	76.5359	57	753	95	below_threshold
Tersicoccus solisilvae	strain=CGMCC 1.15480	GCA_014643255.1	1882339	1882339	type	True	76.4482	75	753	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	76.13	59	753	95	below_threshold
Tersicoccus phoenicis	strain=DSM 30849	GCA_001968835.1	554083	554083	type	True	76.1027	73	753	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	76.0167	60	753	95	below_threshold
Lentzea alba	strain=NEAU-D13	GCA_011067745.1	2714351	2714351	type	True	75.3071	54	753	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:14,656] [INFO] DFAST Taxonomy check result was written to GCF_016907775.1_ASM1690777v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:14,656] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:14,656] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:14,657] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge560057e-7c63-4e77-8af6-fa27ddaac1a9/dqc_reference/checkm_data
[2024-01-24 12:45:14,658] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:14,686] [INFO] Task started: CheckM
[2024-01-24 12:45:14,686] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016907775.1_ASM1690777v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016907775.1_ASM1690777v1_genomic.fna/checkm_input GCF_016907775.1_ASM1690777v1_genomic.fna/checkm_result
[2024-01-24 12:45:41,694] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:41,696] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:41,729] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:41,729] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:41,730] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016907775.1_ASM1690777v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:41,731] [INFO] Task started: Blastn
[2024-01-24 12:45:41,731] [INFO] Running command: blastn -query GCF_016907775.1_ASM1690777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge560057e-7c63-4e77-8af6-fa27ddaac1a9/dqc_reference/reference_markers_gtdb.fasta -out GCF_016907775.1_ASM1690777v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:42,841] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:42,848] [INFO] Selected 14 target genomes.
[2024-01-24 12:45:42,848] [INFO] Target genome list was writen to GCF_016907775.1_ASM1690777v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:42,875] [INFO] Task started: fastANI
[2024-01-24 12:45:42,876] [INFO] Running command: fastANI --query /var/lib/cwl/stg48f9535f-0e9d-4130-a313-e5d751852765/GCF_016907775.1_ASM1690777v1_genomic.fna.gz --refList GCF_016907775.1_ASM1690777v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016907775.1_ASM1690777v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:52,011] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:52,030] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:52,031] [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_016907775.1	s__Pseudoglutamicibacter cumminsii	100.0	752	753	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudoglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003143995.1	s__Pseudoglutamicibacter cumminsii_A	94.3936	647	753	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudoglutamicibacter	95.0	96.00	96.00	0.92	0.92	2	-
GCF_000758985.1	s__Pseudoglutamicibacter albus_A	85.0017	563	753	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudoglutamicibacter	95.0	98.46	98.42	0.96	0.96	3	-
GCF_001302565.1	s__Glutamicibacter halophytocola	78.0154	86	753	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.28	98.01	0.91	0.89	4	-
GCF_003575975.1	s__Galactobacter valiniphilus	77.4236	136	753	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Galactobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007786235.1	s__Paenarthrobacter nitroguajacolicus_A	77.2477	68	753	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003640665.1	s__Galactobacter caseinivorans	77.1131	94	753	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Galactobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002975405.1	s__Glutamicibacter sp002975405	77.109	86	753	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.44	96.03	0.93	0.84	6	-
GCF_002157505.1	s__Arthrobacter_D agilis_D	77.1002	80	753	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900016675.1	s__Arthrobacter_B saudimassiliensis	77.0402	99	753	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004357995.1	s__Arthrobacter_D crusticola	76.6181	77	753	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011067745.1	s__Lentzea alba	75.3071	54	753	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:52,034] [INFO] GTDB search result was written to GCF_016907775.1_ASM1690777v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:52,035] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:52,047] [INFO] DFAST_QC result json was written to GCF_016907775.1_ASM1690777v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:52,048] [INFO] DFAST_QC completed!
[2024-01-24 12:45:52,048] [INFO] Total running time: 0h1m8s