[2024-01-24 13:22:01,417] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:01,418] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:01,419] [INFO] DQC Reference Directory: /var/lib/cwl/stge12676ad-9542-46f1-8f68-38f35287ee32/dqc_reference
[2024-01-24 13:22:02,760] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:02,761] [INFO] Task started: Prodigal
[2024-01-24 13:22:02,761] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b607af6-3146-432e-b717-84a2d91b7ba5/GCF_003611035.1_ASM361103v1_genomic.fna.gz | prodigal -d GCF_003611035.1_ASM361103v1_genomic.fna/cds.fna -a GCF_003611035.1_ASM361103v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:17,244] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:17,244] [INFO] Task started: HMMsearch
[2024-01-24 13:22:17,245] [INFO] Running command: hmmsearch --tblout GCF_003611035.1_ASM361103v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge12676ad-9542-46f1-8f68-38f35287ee32/dqc_reference/reference_markers.hmm GCF_003611035.1_ASM361103v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:17,610] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:17,611] [INFO] Found 6/6 markers.
[2024-01-24 13:22:17,651] [INFO] Query marker FASTA was written to GCF_003611035.1_ASM361103v1_genomic.fna/markers.fasta
[2024-01-24 13:22:17,651] [INFO] Task started: Blastn
[2024-01-24 13:22:17,651] [INFO] Running command: blastn -query GCF_003611035.1_ASM361103v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge12676ad-9542-46f1-8f68-38f35287ee32/dqc_reference/reference_markers.fasta -out GCF_003611035.1_ASM361103v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:19,022] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:19,025] [INFO] Selected 15 target genomes.
[2024-01-24 13:22:19,025] [INFO] Target genome list was writen to GCF_003611035.1_ASM361103v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:19,057] [INFO] Task started: fastANI
[2024-01-24 13:22:19,057] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b607af6-3146-432e-b717-84a2d91b7ba5/GCF_003611035.1_ASM361103v1_genomic.fna.gz --refList GCF_003611035.1_ASM361103v1_genomic.fna/target_genomes.txt --output GCF_003611035.1_ASM361103v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:31,306] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:31,307] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge12676ad-9542-46f1-8f68-38f35287ee32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:31,307] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge12676ad-9542-46f1-8f68-38f35287ee32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:31,320] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:31,320] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:31,320] [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
Cryobacterium soli	strain=GCJ02	GCA_003611035.1	2220095	2220095	type	True	100.0	1460	1461	95	conclusive
Cryobacterium zongtaii	strain=TMN-42	GCA_002909375.1	1259217	1259217	type	True	86.2448	941	1461	95	below_threshold
Cryobacterium arcticum	strain=SK-1	GCA_003185895.1	670052	670052	type	True	86.0604	1007	1461	95	below_threshold
Cryobacterium psychrotolerans	strain=CGMCC 1.5382	GCA_900101115.1	386301	386301	type	True	81.3845	569	1461	95	below_threshold
Cryobacterium psychrotolerans	strain=CGMCC 1.5382	GCA_004564325.1	386301	386301	type	True	81.3242	572	1461	95	below_threshold
Cryobacterium breve	strain=TMT4-23	GCA_004402375.1	1259258	1259258	type	True	80.7824	609	1461	95	below_threshold
Cryobacterium tepidiphilum	strain=NEAU-85	GCA_003716325.1	2486026	2486026	type	True	80.6944	476	1461	95	below_threshold
Cryobacterium melibiosiphilum	strain=Hh39	GCA_003602235.1	995039	995039	type	True	80.63	631	1461	95	below_threshold
Cryobacterium luteum	strain=Hh15	GCA_004402515.1	1424661	1424661	type	True	80.1908	519	1461	95	below_threshold
Cryobacterium luteum	strain=CGMCC 1.11210	GCA_900110125.1	1424661	1424661	type	True	80.1865	526	1461	95	below_threshold
Cryobacterium levicorallinum	strain=GMCC 1.11211	GCA_900113585.1	995038	995038	type	True	80.1151	523	1461	95	below_threshold
Microterricola viridarii	strain=DSM 21772	GCA_900104895.1	412690	412690	type	True	80.0834	548	1461	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.9277	452	1461	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	78.7165	424	1461	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	78.4281	430	1461	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:31,322] [INFO] DFAST Taxonomy check result was written to GCF_003611035.1_ASM361103v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:31,322] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:31,322] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:31,323] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge12676ad-9542-46f1-8f68-38f35287ee32/dqc_reference/checkm_data
[2024-01-24 13:22:31,324] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:31,367] [INFO] Task started: CheckM
[2024-01-24 13:22:31,367] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003611035.1_ASM361103v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003611035.1_ASM361103v1_genomic.fna/checkm_input GCF_003611035.1_ASM361103v1_genomic.fna/checkm_result
[2024-01-24 13:23:18,793] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:18,795] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:18,816] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:18,817] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:18,817] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003611035.1_ASM361103v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:18,818] [INFO] Task started: Blastn
[2024-01-24 13:23:18,818] [INFO] Running command: blastn -query GCF_003611035.1_ASM361103v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge12676ad-9542-46f1-8f68-38f35287ee32/dqc_reference/reference_markers_gtdb.fasta -out GCF_003611035.1_ASM361103v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:20,832] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:20,835] [INFO] Selected 8 target genomes.
[2024-01-24 13:23:20,835] [INFO] Target genome list was writen to GCF_003611035.1_ASM361103v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:20,866] [INFO] Task started: fastANI
[2024-01-24 13:23:20,866] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b607af6-3146-432e-b717-84a2d91b7ba5/GCF_003611035.1_ASM361103v1_genomic.fna.gz --refList GCF_003611035.1_ASM361103v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003611035.1_ASM361103v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:29,302] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:29,314] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:29,314] [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_003611035.1	s__Cryobacterium soli	100.0	1460	1461	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001679725.1	s__Cryobacterium arcticum_A	93.2769	1201	1461	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	87.0762	1008	1461	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004210215.1	s__Cryobacterium sp004210215	86.5423	867	1461	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	86.5011	963	1461	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	86.2485	941	1461	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	86.0483	916	1461	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	86.0395	1009	1461	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:29,316] [INFO] GTDB search result was written to GCF_003611035.1_ASM361103v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:29,317] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:29,324] [INFO] DFAST_QC result json was written to GCF_003611035.1_ASM361103v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:29,324] [INFO] DFAST_QC completed!
[2024-01-24 13:23:29,324] [INFO] Total running time: 0h1m28s