[2024-01-24 12:44:10,883] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:10,886] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:10,887] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd66d6c9-09c7-4e59-b9ea-ef02bd17df61/dqc_reference
[2024-01-24 12:44:12,298] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:12,299] [INFO] Task started: Prodigal
[2024-01-24 12:44:12,299] [INFO] Running command: gunzip -c /var/lib/cwl/stg494ebde3-908a-48bb-be9c-0e33fe1b9a75/GCF_021582895.2_ASM2158289v2_genomic.fna.gz | prodigal -d GCF_021582895.2_ASM2158289v2_genomic.fna/cds.fna -a GCF_021582895.2_ASM2158289v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:23,198] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:23,198] [INFO] Task started: HMMsearch
[2024-01-24 12:44:23,198] [INFO] Running command: hmmsearch --tblout GCF_021582895.2_ASM2158289v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd66d6c9-09c7-4e59-b9ea-ef02bd17df61/dqc_reference/reference_markers.hmm GCF_021582895.2_ASM2158289v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:23,484] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:23,485] [INFO] Found 6/6 markers.
[2024-01-24 12:44:23,518] [INFO] Query marker FASTA was written to GCF_021582895.2_ASM2158289v2_genomic.fna/markers.fasta
[2024-01-24 12:44:23,518] [INFO] Task started: Blastn
[2024-01-24 12:44:23,518] [INFO] Running command: blastn -query GCF_021582895.2_ASM2158289v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd66d6c9-09c7-4e59-b9ea-ef02bd17df61/dqc_reference/reference_markers.fasta -out GCF_021582895.2_ASM2158289v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:24,587] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:24,592] [INFO] Selected 24 target genomes.
[2024-01-24 12:44:24,592] [INFO] Target genome list was writen to GCF_021582895.2_ASM2158289v2_genomic.fna/target_genomes.txt
[2024-01-24 12:44:24,610] [INFO] Task started: fastANI
[2024-01-24 12:44:24,610] [INFO] Running command: fastANI --query /var/lib/cwl/stg494ebde3-908a-48bb-be9c-0e33fe1b9a75/GCF_021582895.2_ASM2158289v2_genomic.fna.gz --refList GCF_021582895.2_ASM2158289v2_genomic.fna/target_genomes.txt --output GCF_021582895.2_ASM2158289v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:42,236] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:42,237] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd66d6c9-09c7-4e59-b9ea-ef02bd17df61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:42,237] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd66d6c9-09c7-4e59-b9ea-ef02bd17df61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:42,254] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:44:42,255] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:44:42,255] [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 luticocti	strain=DSM 19459	GCA_000422405.1	451764	451764	type	True	82.9189	690	1189	95	below_threshold
Microbacterium protaetiae	strain=DFW100M-13	GCA_004135285.1	2509458	2509458	type	True	81.6565	723	1189	95	below_threshold
Microbacterium thalassium	strain=DSM 12511	GCA_014208045.1	362649	362649	type	True	80.0901	535	1189	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	80.0627	570	1189	95	below_threshold
Microbacterium invictum	strain=JCM 17023	GCA_015278285.1	515415	515415	type	True	79.969	527	1189	95	below_threshold
Microbacterium invictum	strain=DSM 19600	GCA_023155715.1	515415	515415	type	True	79.9407	528	1189	95	below_threshold
Microbacterium helvum	strain=NEAU-LLC	GCA_014779795.1	2773713	2773713	type	True	79.936	620	1189	95	below_threshold
Microbacterium hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	79.8485	536	1189	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	79.8172	576	1189	95	below_threshold
Microbacterium pullorum	strain=Sa4CUA7	GCA_014836535.1	2762236	2762236	type	True	79.7821	505	1189	95	below_threshold
Microbacterium flavescens	strain=JCM 3877	GCA_018588945.1	69366	69366	type	True	79.7656	552	1189	95	below_threshold
Microbacterium immunditiarum	strain=DSM 24662	GCA_013409785.1	337480	337480	type	True	79.7569	564	1189	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	79.7354	551	1189	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	79.6932	426	1189	95	below_threshold
Microbacterium trichothecenolyticum	strain=DSM 8608	GCA_000956465.1	69370	69370	type	True	79.6349	589	1189	95	below_threshold
Microbacterium sulfonylureivorans	strain=LAM7116	GCA_003999995.1	2486854	2486854	type	True	79.6105	543	1189	95	below_threshold
Microbacterium ulmi	strain=JCM 14282	GCA_013004565.1	179095	179095	type	True	79.5828	491	1189	95	below_threshold
Microbacterium aerolatum	strain=NBRC 103071	GCA_007988825.1	153731	153731	type	True	79.5707	472	1189	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	79.5606	486	1189	95	below_threshold
Microbacterium aerolatum	strain=CCM 4955	GCA_014635005.1	153731	153731	type	True	79.5543	487	1189	95	below_threshold
Microbacterium ulmi	strain=CECT 5976	GCA_011759705.1	179095	179095	type	True	79.5304	515	1189	95	below_threshold
Microbacterium resistens	strain=NBRC 103078	GCA_001552355.1	156977	156977	type	True	79.3457	426	1189	95	below_threshold
Microbacterium album	strain=CGMCC 1.15794	GCA_014643695.1	2053191	2053191	type	True	79.0698	402	1189	95	below_threshold
Microbacterium halophytorum	strain=YJYP 303	GCA_002970975.1	2067568	2067568	type	True	78.5038	381	1189	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:42,258] [INFO] DFAST Taxonomy check result was written to GCF_021582895.2_ASM2158289v2_genomic.fna/tc_result.tsv
[2024-01-24 12:44:42,259] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:42,259] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:42,259] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd66d6c9-09c7-4e59-b9ea-ef02bd17df61/dqc_reference/checkm_data
[2024-01-24 12:44:42,260] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:42,298] [INFO] Task started: CheckM
[2024-01-24 12:44:42,298] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021582895.2_ASM2158289v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021582895.2_ASM2158289v2_genomic.fna/checkm_input GCF_021582895.2_ASM2158289v2_genomic.fna/checkm_result
[2024-01-24 12:45:42,653] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:42,655] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.37%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:42,684] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:42,684] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:42,684] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021582895.2_ASM2158289v2_genomic.fna/markers.fasta)
[2024-01-24 12:45:42,685] [INFO] Task started: Blastn
[2024-01-24 12:45:42,685] [INFO] Running command: blastn -query GCF_021582895.2_ASM2158289v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd66d6c9-09c7-4e59-b9ea-ef02bd17df61/dqc_reference/reference_markers_gtdb.fasta -out GCF_021582895.2_ASM2158289v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:44,538] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:44,542] [INFO] Selected 25 target genomes.
[2024-01-24 12:45:44,543] [INFO] Target genome list was writen to GCF_021582895.2_ASM2158289v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:44,572] [INFO] Task started: fastANI
[2024-01-24 12:45:44,572] [INFO] Running command: fastANI --query /var/lib/cwl/stg494ebde3-908a-48bb-be9c-0e33fe1b9a75/GCF_021582895.2_ASM2158289v2_genomic.fna.gz --refList GCF_021582895.2_ASM2158289v2_genomic.fna/target_genomes_gtdb.txt --output GCF_021582895.2_ASM2158289v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:03,011] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:03,035] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:46:03,035] [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_000422405.1	s__Microbacterium luticocti	82.9287	688	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649635.1	s__Microbacterium sp009649635	82.6928	680	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135285.1	s__Microbacterium protaetiae	81.667	722	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015277855.1	s__Microbacterium sp015277855	80.0762	568	1189	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	80.054	538	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380605.1	s__Microbacterium sp000380605	80.0202	594	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422925.1	s__Microbacterium sp001422925	79.928	585	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004010105.1	s__Microbacterium sp004010105	79.9154	382	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017306415.1	s__Microbacterium sp001897105	79.895	587	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.03	95.75	0.95	0.85	5	-
GCF_003386735.1	s__Microbacterium trichothecenolyticum_A	79.8904	574	1189	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	79.8098	553	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003931875.1	s__Microbacterium sp003931875	79.8013	519	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409785.1	s__Microbacterium immunditiarum	79.7702	563	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012524205.1	s__Microbacterium sp012524205	79.7695	570	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002705755.3	s__Microbacterium esteraromaticum_A	79.7307	448	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.15	98.15	0.64	0.64	2	-
GCF_900292075.1	s__Microbacterium timonense	79.7021	576	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000956465.1	s__Microbacterium trichothecenolyticum	79.6573	586	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007988825.1	s__Microbacterium aerolatum	79.587	471	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003999995.1	s__Microbacterium sp003999995	79.5813	546	1189	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	79.5775	484	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010634855.1	s__Microbacterium sp010634855	79.5666	577	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.26	99.26	0.95	0.95	2	-
GCF_012847295.1	s__Microbacterium sp012847295	79.564	473	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900155915.1	s__Microbacterium sp900155915	79.4926	501	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552355.1	s__Microbacterium resistens	79.3067	429	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643695.1	s__Microbacterium album	79.0991	399	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:03,036] [INFO] GTDB search result was written to GCF_021582895.2_ASM2158289v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:03,037] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:03,042] [INFO] DFAST_QC result json was written to GCF_021582895.2_ASM2158289v2_genomic.fna/dqc_result.json
[2024-01-24 12:46:03,042] [INFO] DFAST_QC completed!
[2024-01-24 12:46:03,042] [INFO] Total running time: 0h1m52s