[2024-01-25 18:16:20,726] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:16:20,728] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:16:20,728] [INFO] DQC Reference Directory: /var/lib/cwl/stgf564b583-0d92-41a9-88aa-823d1692ac33/dqc_reference
[2024-01-25 18:16:21,846] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:16:21,846] [INFO] Task started: Prodigal
[2024-01-25 18:16:21,846] [INFO] Running command: gunzip -c /var/lib/cwl/stg7269f303-82d5-4925-a3fd-6c80379c8b45/GCF_000421145.1_ASM42114v1_genomic.fna.gz | prodigal -d GCF_000421145.1_ASM42114v1_genomic.fna/cds.fna -a GCF_000421145.1_ASM42114v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:16:34,994] [INFO] Task succeeded: Prodigal
[2024-01-25 18:16:34,994] [INFO] Task started: HMMsearch
[2024-01-25 18:16:34,994] [INFO] Running command: hmmsearch --tblout GCF_000421145.1_ASM42114v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf564b583-0d92-41a9-88aa-823d1692ac33/dqc_reference/reference_markers.hmm GCF_000421145.1_ASM42114v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:16:35,244] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:16:35,247] [INFO] Found 6/6 markers.
[2024-01-25 18:16:35,287] [INFO] Query marker FASTA was written to GCF_000421145.1_ASM42114v1_genomic.fna/markers.fasta
[2024-01-25 18:16:35,288] [INFO] Task started: Blastn
[2024-01-25 18:16:35,288] [INFO] Running command: blastn -query GCF_000421145.1_ASM42114v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf564b583-0d92-41a9-88aa-823d1692ac33/dqc_reference/reference_markers.fasta -out GCF_000421145.1_ASM42114v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:16:36,256] [INFO] Task succeeded: Blastn
[2024-01-25 18:16:36,259] [INFO] Selected 15 target genomes.
[2024-01-25 18:16:36,259] [INFO] Target genome list was writen to GCF_000421145.1_ASM42114v1_genomic.fna/target_genomes.txt
[2024-01-25 18:16:36,269] [INFO] Task started: fastANI
[2024-01-25 18:16:36,269] [INFO] Running command: fastANI --query /var/lib/cwl/stg7269f303-82d5-4925-a3fd-6c80379c8b45/GCF_000421145.1_ASM42114v1_genomic.fna.gz --refList GCF_000421145.1_ASM42114v1_genomic.fna/target_genomes.txt --output GCF_000421145.1_ASM42114v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:16:47,904] [INFO] Task succeeded: fastANI
[2024-01-25 18:16:47,904] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf564b583-0d92-41a9-88aa-823d1692ac33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:16:47,905] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf564b583-0d92-41a9-88aa-823d1692ac33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:16:47,914] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:16:47,914] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:16:47,914] [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
Glaciibacter superstes	strain=DSM 21135	GCA_000421145.1	501023	501023	type	True	100.0	1583	1586	95	conclusive
Cryobacterium tepidiphilum	strain=NEAU-85	GCA_003716325.1	2486026	2486026	type	True	79.6682	444	1586	95	below_threshold
Cryobacterium psychrotolerans	strain=CGMCC 1.5382	GCA_900101115.1	386301	386301	type	True	79.6306	464	1586	95	below_threshold
Cryobacterium psychrotolerans	strain=CGMCC 1.5382	GCA_004564325.1	386301	386301	type	True	79.5998	473	1586	95	below_threshold
Cryobacterium soli	strain=GCJ02	GCA_003611035.1	2220095	2220095	type	True	79.3483	499	1586	95	below_threshold
Cryobacterium arcticum	strain=SK-1	GCA_003185895.1	670052	670052	type	True	79.2758	484	1586	95	below_threshold
Cryobacterium zongtaii	strain=TMN-42	GCA_002909375.1	1259217	1259217	type	True	79.0451	456	1586	95	below_threshold
Cryobacterium melibiosiphilum	strain=Hh39	GCA_003602235.1	995039	995039	type	True	78.9311	438	1586	95	below_threshold
Microterricola pindariensis	strain=PON 10	GCA_002936985.1	478010	478010	type	True	78.81	419	1586	95	below_threshold
Cryobacterium levicorallinum	strain=GMCC 1.11211	GCA_900113585.1	995038	995038	type	True	78.6475	367	1586	95	below_threshold
Cryobacterium flavum	strain=CGMCC 1.11215	GCA_900103805.1	1424659	1424659	type	True	78.596	405	1586	95	below_threshold
Cryobacterium flavum	strain=Hh8	GCA_004402625.1	1424659	1424659	type	True	78.5772	405	1586	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	77.994	390	1586	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	77.9349	389	1586	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	77.906	398	1586	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:16:47,915] [INFO] DFAST Taxonomy check result was written to GCF_000421145.1_ASM42114v1_genomic.fna/tc_result.tsv
[2024-01-25 18:16:47,917] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:16:47,917] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:16:47,917] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf564b583-0d92-41a9-88aa-823d1692ac33/dqc_reference/checkm_data
[2024-01-25 18:16:47,918] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:16:47,964] [INFO] Task started: CheckM
[2024-01-25 18:16:47,964] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000421145.1_ASM42114v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000421145.1_ASM42114v1_genomic.fna/checkm_input GCF_000421145.1_ASM42114v1_genomic.fna/checkm_result
[2024-01-25 18:17:28,841] [INFO] Task succeeded: CheckM
[2024-01-25 18:17:28,842] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:17:28,857] [INFO] ===== Completeness check finished =====
[2024-01-25 18:17:28,857] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:17:28,858] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000421145.1_ASM42114v1_genomic.fna/markers.fasta)
[2024-01-25 18:17:28,858] [INFO] Task started: Blastn
[2024-01-25 18:17:28,858] [INFO] Running command: blastn -query GCF_000421145.1_ASM42114v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf564b583-0d92-41a9-88aa-823d1692ac33/dqc_reference/reference_markers_gtdb.fasta -out GCF_000421145.1_ASM42114v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:17:30,470] [INFO] Task succeeded: Blastn
[2024-01-25 18:17:30,473] [INFO] Selected 18 target genomes.
[2024-01-25 18:17:30,473] [INFO] Target genome list was writen to GCF_000421145.1_ASM42114v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:17:30,488] [INFO] Task started: fastANI
[2024-01-25 18:17:30,488] [INFO] Running command: fastANI --query /var/lib/cwl/stg7269f303-82d5-4925-a3fd-6c80379c8b45/GCF_000421145.1_ASM42114v1_genomic.fna.gz --refList GCF_000421145.1_ASM42114v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000421145.1_ASM42114v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:17:43,434] [INFO] Task succeeded: fastANI
[2024-01-25 18:17:43,445] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:17:43,445] [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_000421145.1	s__Glaciibacter superstes	100.0	1583	1586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Glaciibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004402595.1	s__Cryobacterium sp004402595	79.771	428	1586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	99.65	99.58	0.91	0.90	6	-
GCF_004403515.1	s__Cryobacterium sp004403515	79.7361	442	1586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004402215.1	s__Cryobacterium sp004402215	79.7223	487	1586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004402495.1	s__Cryobacterium sp004402495	79.6804	462	1586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	98.47	98.47	0.92	0.92	2	-
GCF_900101115.1	s__Cryobacterium psychrotolerans	79.6754	460	1586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	99.25	98.21	0.94	0.88	4	-
GCF_003716325.1	s__Cryobacterium_C tepidiphilum	79.6541	446	1586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001679725.1	s__Cryobacterium arcticum_A	79.5311	486	1586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015752155.1	s__Cryobacterium sp015752155	79.4961	497	1586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004403395.1	s__Cryobacterium sp004403395	79.3482	429	1586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002929555.1	s__Cryobacterium sp002929555	79.298	469	1586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004403065.1	s__Cryobacterium sp004403065	79.2813	426	1586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003185895.1	s__Cryobacterium arcticum	79.2772	485	1586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004403945.1	s__Cryobacterium sp004403945	79.2052	485	1586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004402485.1	s__Cryobacterium sp004402485	79.0943	451	1586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002909375.1	s__Cryobacterium zongtaii	79.0649	454	1586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	97.98	96.32	0.90	0.86	11	-
GCF_004402695.1	s__Cryobacterium sp004402695	79.0348	468	1586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014376815.1	s__Cryobacterium sp014376815	78.6445	381	1586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:17:43,447] [INFO] GTDB search result was written to GCF_000421145.1_ASM42114v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:17:43,447] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:17:43,450] [INFO] DFAST_QC result json was written to GCF_000421145.1_ASM42114v1_genomic.fna/dqc_result.json
[2024-01-25 18:17:43,450] [INFO] DFAST_QC completed!
[2024-01-25 18:17:43,450] [INFO] Total running time: 0h1m23s