[2024-01-24 13:32:56,680] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:56,681] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:56,681] [INFO] DQC Reference Directory: /var/lib/cwl/stgc5d145e4-292b-4917-876c-0b5f1dce0312/dqc_reference
[2024-01-24 13:32:57,925] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:57,926] [INFO] Task started: Prodigal
[2024-01-24 13:32:57,926] [INFO] Running command: gunzip -c /var/lib/cwl/stg6de0f6f6-d02c-4c64-b36c-bb6a6ed69018/GCF_002909375.1_ASM290937v1_genomic.fna.gz | prodigal -d GCF_002909375.1_ASM290937v1_genomic.fna/cds.fna -a GCF_002909375.1_ASM290937v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:10,120] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:10,120] [INFO] Task started: HMMsearch
[2024-01-24 13:33:10,121] [INFO] Running command: hmmsearch --tblout GCF_002909375.1_ASM290937v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc5d145e4-292b-4917-876c-0b5f1dce0312/dqc_reference/reference_markers.hmm GCF_002909375.1_ASM290937v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:10,387] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:10,389] [INFO] Found 6/6 markers.
[2024-01-24 13:33:10,425] [INFO] Query marker FASTA was written to GCF_002909375.1_ASM290937v1_genomic.fna/markers.fasta
[2024-01-24 13:33:10,425] [INFO] Task started: Blastn
[2024-01-24 13:33:10,425] [INFO] Running command: blastn -query GCF_002909375.1_ASM290937v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5d145e4-292b-4917-876c-0b5f1dce0312/dqc_reference/reference_markers.fasta -out GCF_002909375.1_ASM290937v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:11,602] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:11,606] [INFO] Selected 14 target genomes.
[2024-01-24 13:33:11,607] [INFO] Target genome list was writen to GCF_002909375.1_ASM290937v1_genomic.fna/target_genomes.txt
[2024-01-24 13:33:11,640] [INFO] Task started: fastANI
[2024-01-24 13:33:11,640] [INFO] Running command: fastANI --query /var/lib/cwl/stg6de0f6f6-d02c-4c64-b36c-bb6a6ed69018/GCF_002909375.1_ASM290937v1_genomic.fna.gz --refList GCF_002909375.1_ASM290937v1_genomic.fna/target_genomes.txt --output GCF_002909375.1_ASM290937v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:23,400] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:23,401] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc5d145e4-292b-4917-876c-0b5f1dce0312/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:23,402] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc5d145e4-292b-4917-876c-0b5f1dce0312/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:23,416] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:23,416] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:23,416] [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 zongtaii	strain=TMN-42	GCA_002909375.1	1259217	1259217	type	True	100.0	1331	1332	95	conclusive
Cryobacterium soli	strain=GCJ02	GCA_003611035.1	2220095	2220095	type	True	86.3088	947	1332	95	below_threshold
Cryobacterium arcticum	strain=SK-1	GCA_003185895.1	670052	670052	type	True	85.9413	961	1332	95	below_threshold
Cryobacterium psychrotolerans	strain=CGMCC 1.5382	GCA_004564325.1	386301	386301	type	True	81.2495	547	1332	95	below_threshold
Cryobacterium psychrotolerans	strain=CGMCC 1.5382	GCA_900101115.1	386301	386301	type	True	81.1742	549	1332	95	below_threshold
Cryobacterium breve	strain=TMT4-23	GCA_004402375.1	1259258	1259258	type	True	80.8937	588	1332	95	below_threshold
Cryobacterium melibiosiphilum	strain=Hh39	GCA_003602235.1	995039	995039	type	True	80.7568	600	1332	95	below_threshold
Cryobacterium tepidiphilum	strain=NEAU-85	GCA_003716325.1	2486026	2486026	type	True	80.2985	454	1332	95	below_threshold
Cryobacterium flavum	strain=Hh8	GCA_004402625.1	1424659	1424659	type	True	80.1057	522	1332	95	below_threshold
Cryobacterium levicorallinum	strain=GMCC 1.11211	GCA_900113585.1	995038	995038	type	True	80.0962	490	1332	95	below_threshold
Cryobacterium flavum	strain=CGMCC 1.11215	GCA_900103805.1	1424659	1424659	type	True	80.079	522	1332	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.7316	420	1332	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	78.4715	398	1332	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	78.3825	386	1332	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:23,418] [INFO] DFAST Taxonomy check result was written to GCF_002909375.1_ASM290937v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:23,418] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:23,419] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:23,419] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc5d145e4-292b-4917-876c-0b5f1dce0312/dqc_reference/checkm_data
[2024-01-24 13:33:23,420] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:23,464] [INFO] Task started: CheckM
[2024-01-24 13:33:23,464] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002909375.1_ASM290937v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002909375.1_ASM290937v1_genomic.fna/checkm_input GCF_002909375.1_ASM290937v1_genomic.fna/checkm_result
[2024-01-24 13:34:01,832] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:01,833] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:01,858] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:01,858] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:01,858] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002909375.1_ASM290937v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:01,859] [INFO] Task started: Blastn
[2024-01-24 13:34:01,859] [INFO] Running command: blastn -query GCF_002909375.1_ASM290937v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5d145e4-292b-4917-876c-0b5f1dce0312/dqc_reference/reference_markers_gtdb.fasta -out GCF_002909375.1_ASM290937v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:03,721] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:03,725] [INFO] Selected 8 target genomes.
[2024-01-24 13:34:03,725] [INFO] Target genome list was writen to GCF_002909375.1_ASM290937v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:03,733] [INFO] Task started: fastANI
[2024-01-24 13:34:03,733] [INFO] Running command: fastANI --query /var/lib/cwl/stg6de0f6f6-d02c-4c64-b36c-bb6a6ed69018/GCF_002909375.1_ASM290937v1_genomic.fna.gz --refList GCF_002909375.1_ASM290937v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002909375.1_ASM290937v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:12,575] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:12,589] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:12,589] [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_002909375.1	s__Cryobacterium zongtaii	100.0	1331	1332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	97.98	96.32	0.90	0.86	11	conclusive
GCF_002929555.1	s__Cryobacterium sp002929555	92.0398	1084	1332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004402695.1	s__Cryobacterium sp004402695	90.642	985	1332	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	88.3076	1011	1332	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	87.9518	904	1332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001679725.1	s__Cryobacterium arcticum_A	86.4002	971	1332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003611035.1	s__Cryobacterium soli	86.2736	951	1332	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	85.93	962	1332	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 13:34:12,591] [INFO] GTDB search result was written to GCF_002909375.1_ASM290937v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:12,592] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:12,595] [INFO] DFAST_QC result json was written to GCF_002909375.1_ASM290937v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:12,595] [INFO] DFAST_QC completed!
[2024-01-24 13:34:12,595] [INFO] Total running time: 0h1m16s