[2024-01-24 13:32:41,500] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:41,502] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:41,502] [INFO] DQC Reference Directory: /var/lib/cwl/stg2228d2bd-f840-4580-96ca-a4361b538be5/dqc_reference
[2024-01-24 13:32:42,675] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:42,676] [INFO] Task started: Prodigal
[2024-01-24 13:32:42,676] [INFO] Running command: gunzip -c /var/lib/cwl/stg9a64a2aa-4762-491d-8384-af8262fccb57/GCF_023062595.1_ASM2306259v1_genomic.fna.gz | prodigal -d GCF_023062595.1_ASM2306259v1_genomic.fna/cds.fna -a GCF_023062595.1_ASM2306259v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:56,689] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:56,690] [INFO] Task started: HMMsearch
[2024-01-24 13:32:56,690] [INFO] Running command: hmmsearch --tblout GCF_023062595.1_ASM2306259v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2228d2bd-f840-4580-96ca-a4361b538be5/dqc_reference/reference_markers.hmm GCF_023062595.1_ASM2306259v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:57,038] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:57,039] [INFO] Found 6/6 markers.
[2024-01-24 13:32:57,079] [INFO] Query marker FASTA was written to GCF_023062595.1_ASM2306259v1_genomic.fna/markers.fasta
[2024-01-24 13:32:57,079] [INFO] Task started: Blastn
[2024-01-24 13:32:57,079] [INFO] Running command: blastn -query GCF_023062595.1_ASM2306259v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2228d2bd-f840-4580-96ca-a4361b538be5/dqc_reference/reference_markers.fasta -out GCF_023062595.1_ASM2306259v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:57,897] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:57,900] [INFO] Selected 20 target genomes.
[2024-01-24 13:32:57,900] [INFO] Target genome list was writen to GCF_023062595.1_ASM2306259v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:57,906] [INFO] Task started: fastANI
[2024-01-24 13:32:57,906] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a64a2aa-4762-491d-8384-af8262fccb57/GCF_023062595.1_ASM2306259v1_genomic.fna.gz --refList GCF_023062595.1_ASM2306259v1_genomic.fna/target_genomes.txt --output GCF_023062595.1_ASM2306259v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:15,975] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:15,975] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2228d2bd-f840-4580-96ca-a4361b538be5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:15,976] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2228d2bd-f840-4580-96ca-a4361b538be5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:15,987] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:33:15,987] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:33:15,988] [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
Pseudarthrobacter sulfonivorans	strain=ALL	GCA_014712225.1	121292	121292	type	True	80.391	577	1652	95	below_threshold
Arthrobacter pascens	strain=DSM 20545	GCA_017052465.1	1677	1677	type	True	80.3131	653	1652	95	below_threshold
Arthrobacter ipis	strain=IA7	GCA_014694315.1	2716202	2716202	type	True	80.2502	603	1652	95	below_threshold
Arthrobacter globiformis	strain=NBRC 12137	GCA_000238915.2	1665	1665	type	True	80.2313	598	1652	95	below_threshold
Pseudarthrobacter psychrotolerans	strain=YJ56	GCA_009911795.1	2697569	2697569	type	True	80.1839	604	1652	95	below_threshold
Pseudarthrobacter siccitolerans	strain=4J27	GCA_001046895.1	861266	861266	type	True	80.085	593	1652	95	below_threshold
Pseudarthrobacter polychromogenes	strain=CGMCC 1.1927	GCA_014644495.1	1676	1676	type	True	80.0793	589	1652	95	below_threshold
Pseudarthrobacter phenanthrenivorans	strain=Sphe3	GCA_000189535.1	361575	361575	type	True	80.072	572	1652	95	below_threshold
Pseudarthrobacter scleromae	strain=CGMCC 1.3601	GCA_014644515.1	158897	158897	type	True	79.9355	576	1652	95	below_threshold
Pseudarthrobacter chlorophenolicus	strain=A6	GCA_900104315.1	85085	85085	type	True	79.8909	568	1652	95	below_threshold
Arthrobacter celericrescens	strain=NEAU-SA2	GCA_003614925.1	2320851	2320851	type	True	79.4414	537	1652	95	below_threshold
Arthrobacter cupressi	strain=DSM 24664	GCA_013409905.1	1045773	1045773	type	True	79.4039	511	1652	95	below_threshold
Paenarthrobacter histidinolovorans	strain=JCM 2520	GCA_014647595.1	43664	43664	type	True	79.3069	457	1652	95	below_threshold
Paenarthrobacter aurescens	strain=NBRC 12136	GCA_006538985.1	43663	43663	type	True	79.2121	435	1652	95	below_threshold
Paenarthrobacter ilicis	strain=DSM 20138	GCA_016907545.1	43665	43665	type	True	79.0998	432	1652	95	below_threshold
Arthrobacter pullicola	strain=Sa2BUA2	GCA_014836875.1	2762224	2762224	type	True	78.2968	213	1652	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	78.2222	205	1652	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_017353495.1	2816859	2816859	type	True	78.1779	205	1652	95	below_threshold
Arthrobacter gallicola	strain=Sa2CUA1	GCA_014836775.1	2762225	2762225	type	True	77.7737	229	1652	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	76.6093	94	1652	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:15,989] [INFO] DFAST Taxonomy check result was written to GCF_023062595.1_ASM2306259v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:15,989] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:15,990] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:15,990] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2228d2bd-f840-4580-96ca-a4361b538be5/dqc_reference/checkm_data
[2024-01-24 13:33:15,990] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:16,037] [INFO] Task started: CheckM
[2024-01-24 13:33:16,037] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023062595.1_ASM2306259v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023062595.1_ASM2306259v1_genomic.fna/checkm_input GCF_023062595.1_ASM2306259v1_genomic.fna/checkm_result
[2024-01-24 13:33:55,279] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:55,280] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:55,296] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:55,296] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:55,297] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023062595.1_ASM2306259v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:55,297] [INFO] Task started: Blastn
[2024-01-24 13:33:55,297] [INFO] Running command: blastn -query GCF_023062595.1_ASM2306259v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2228d2bd-f840-4580-96ca-a4361b538be5/dqc_reference/reference_markers_gtdb.fasta -out GCF_023062595.1_ASM2306259v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:56,520] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:56,523] [INFO] Selected 25 target genomes.
[2024-01-24 13:33:56,523] [INFO] Target genome list was writen to GCF_023062595.1_ASM2306259v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:56,566] [INFO] Task started: fastANI
[2024-01-24 13:33:56,566] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a64a2aa-4762-491d-8384-af8262fccb57/GCF_023062595.1_ASM2306259v1_genomic.fna.gz --refList GCF_023062595.1_ASM2306259v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023062595.1_ASM2306259v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:18,240] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:18,254] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:34:18,255] [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_004320525.1	s__Pseudarthrobacter sp004320525	80.7078	676	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001423745.1	s__Arthrobacter_I sp001423745	80.6911	686	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685965.1	s__Arthrobacter_I sp000685965	80.6383	686	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002929335.1	s__Arthrobacter_I sp002929335	80.6375	718	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	96.02	96.02	0.78	0.78	2	-
GCF_005280255.1	s__Arthrobacter_I sp005280255	80.5941	701	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000876655.1	s__Arthrobacter_I sp000876655	80.5905	658	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000196235.1	s__Arthrobacter_I sp000196235	80.5324	672	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	98.94	98.92	0.91	0.91	3	-
GCF_002008315.2	s__Arthrobacter sp002008315	80.5125	646	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017832975.1	s__Arthrobacter_I sp017832975	80.4066	682	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352915.1	s__Arthrobacter_I sp003352915	80.3694	556	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613755.1	s__Arthrobacter_I sp018613755	80.3674	696	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001750145.1	s__Arthrobacter_I sp001750145	80.3608	580	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613835.1	s__Arthrobacter sp018613835	80.3241	686	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002929275.1	s__Arthrobacter sp002929275	80.3048	657	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007679325.1	s__Arthrobacter_I sp007679325	80.3027	600	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374925.1	s__Arthrobacter_I sp000374925	80.1967	587	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	97.54	97.54	0.90	0.90	2	-
GCF_001512305.1	s__Arthrobacter_I sp001512305	80.1609	599	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013359735.1	s__Arthrobacter_I sp013359735	80.1601	568	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009928425.1	s__Arthrobacter_I sp009928425	80.1549	564	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018224015.1	s__Arthrobacter_I sp018224015	80.1366	557	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014764445.1	s__Pseudarthrobacter luteus_A	80.1036	589	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	97.74	97.74	0.82	0.82	2	-
GCF_902506095.1	s__Pseudarthrobacter sp902506095	80.0817	583	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168135.1	s__Arthrobacter_I sp900168135	80.0269	581	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	95.10	95.10	0.85	0.85	2	-
GCF_000374905.1	s__Pseudarthrobacter sp000374905	79.7779	579	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	98.45	96.91	0.92	0.90	5	-
GCF_003614925.1	s__Arthrobacter_G celericrescens	79.4411	537	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_G	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:18,256] [INFO] GTDB search result was written to GCF_023062595.1_ASM2306259v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:18,256] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:18,260] [INFO] DFAST_QC result json was written to GCF_023062595.1_ASM2306259v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:18,260] [INFO] DFAST_QC completed!
[2024-01-24 13:34:18,261] [INFO] Total running time: 0h1m37s