[2024-01-24 13:57:42,626] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:42,634] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:42,634] [INFO] DQC Reference Directory: /var/lib/cwl/stg61393840-d2ca-4f2e-8df6-ed1463649b0d/dqc_reference
[2024-01-24 13:57:44,014] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:44,015] [INFO] Task started: Prodigal
[2024-01-24 13:57:44,015] [INFO] Running command: gunzip -c /var/lib/cwl/stgadaa0879-28cc-41c2-81b8-6d70f2d3984e/GCF_004403415.1_ASM440341v1_genomic.fna.gz | prodigal -d GCF_004403415.1_ASM440341v1_genomic.fna/cds.fna -a GCF_004403415.1_ASM440341v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:54,307] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:54,307] [INFO] Task started: HMMsearch
[2024-01-24 13:57:54,308] [INFO] Running command: hmmsearch --tblout GCF_004403415.1_ASM440341v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg61393840-d2ca-4f2e-8df6-ed1463649b0d/dqc_reference/reference_markers.hmm GCF_004403415.1_ASM440341v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:54,602] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:54,604] [INFO] Found 6/6 markers.
[2024-01-24 13:57:54,635] [INFO] Query marker FASTA was written to GCF_004403415.1_ASM440341v1_genomic.fna/markers.fasta
[2024-01-24 13:57:54,635] [INFO] Task started: Blastn
[2024-01-24 13:57:54,635] [INFO] Running command: blastn -query GCF_004403415.1_ASM440341v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61393840-d2ca-4f2e-8df6-ed1463649b0d/dqc_reference/reference_markers.fasta -out GCF_004403415.1_ASM440341v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:55,750] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:55,763] [INFO] Selected 14 target genomes.
[2024-01-24 13:57:55,764] [INFO] Target genome list was writen to GCF_004403415.1_ASM440341v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:55,770] [INFO] Task started: fastANI
[2024-01-24 13:57:55,770] [INFO] Running command: fastANI --query /var/lib/cwl/stgadaa0879-28cc-41c2-81b8-6d70f2d3984e/GCF_004403415.1_ASM440341v1_genomic.fna.gz --refList GCF_004403415.1_ASM440341v1_genomic.fna/target_genomes.txt --output GCF_004403415.1_ASM440341v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:06,660] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:06,661] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg61393840-d2ca-4f2e-8df6-ed1463649b0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:06,661] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg61393840-d2ca-4f2e-8df6-ed1463649b0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:06,674] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:58:06,674] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:58:06,674] [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 breve	strain=TMT4-23	GCA_004402375.1	1259258	1259258	type	True	86.8501	856	1143	95	below_threshold
Cryobacterium psychrotolerans	strain=CGMCC 1.5382	GCA_900101115.1	386301	386301	type	True	81.6459	587	1143	95	below_threshold
Cryobacterium psychrotolerans	strain=CGMCC 1.5382	GCA_004564325.1	386301	386301	type	True	81.6283	583	1143	95	below_threshold
Cryobacterium zongtaii	strain=TMN-42	GCA_002909375.1	1259217	1259217	type	True	81.3236	564	1143	95	below_threshold
Cryobacterium soli	strain=GCJ02	GCA_003611035.1	2220095	2220095	type	True	81.2401	574	1143	95	below_threshold
Cryobacterium arcticum	strain=SK-1	GCA_003185895.1	670052	670052	type	True	81.1456	581	1143	95	below_threshold
Cryobacterium melibiosiphilum	strain=Hh39	GCA_003602235.1	995039	995039	type	True	80.5889	559	1143	95	below_threshold
Cryobacterium levicorallinum	strain=NBRC 107883	GCA_007992355.1	995038	995038	type	True	80.1683	498	1143	95	below_threshold
Cryobacterium levicorallinum	strain=GMCC 1.11211	GCA_900113585.1	995038	995038	type	True	80.0887	503	1143	95	below_threshold
Cryobacterium levicorallinum	strain=Hh34	GCA_004402405.1	995038	995038	type	True	80.0025	508	1143	95	below_threshold
Cryobacterium psychrophilum	strain=DSM 4854	GCA_004365915.1	41988	41988	type	True	79.7136	478	1143	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	78.2358	349	1143	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.2288	402	1143	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	78.1626	358	1143	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:06,676] [INFO] DFAST Taxonomy check result was written to GCF_004403415.1_ASM440341v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:06,677] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:06,677] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:06,677] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg61393840-d2ca-4f2e-8df6-ed1463649b0d/dqc_reference/checkm_data
[2024-01-24 13:58:06,679] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:06,716] [INFO] Task started: CheckM
[2024-01-24 13:58:06,717] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004403415.1_ASM440341v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004403415.1_ASM440341v1_genomic.fna/checkm_input GCF_004403415.1_ASM440341v1_genomic.fna/checkm_result
[2024-01-24 13:58:42,321] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:42,325] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:42,352] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:42,352] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:42,353] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004403415.1_ASM440341v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:42,353] [INFO] Task started: Blastn
[2024-01-24 13:58:42,353] [INFO] Running command: blastn -query GCF_004403415.1_ASM440341v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61393840-d2ca-4f2e-8df6-ed1463649b0d/dqc_reference/reference_markers_gtdb.fasta -out GCF_004403415.1_ASM440341v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:44,152] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:44,159] [INFO] Selected 6 target genomes.
[2024-01-24 13:58:44,160] [INFO] Target genome list was writen to GCF_004403415.1_ASM440341v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:44,166] [INFO] Task started: fastANI
[2024-01-24 13:58:44,167] [INFO] Running command: fastANI --query /var/lib/cwl/stgadaa0879-28cc-41c2-81b8-6d70f2d3984e/GCF_004403415.1_ASM440341v1_genomic.fna.gz --refList GCF_004403415.1_ASM440341v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004403415.1_ASM440341v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:49,746] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:49,756] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:49,757] [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_002929845.1	s__Cryobacterium sp002929845	98.8139	996	1143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	97.90	95.88	0.91	0.88	15	conclusive
GCF_004403465.1	s__Cryobacterium sp004403465	90.0996	900	1143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	99.40	99.40	0.93	0.93	2	-
GCF_004403395.1	s__Cryobacterium sp004403395	89.9309	857	1143	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	87.7578	840	1143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004402375.1	s__Cryobacterium breve	86.8646	855	1143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004402595.1	s__Cryobacterium sp004402595	84.9398	794	1143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	99.65	99.58	0.91	0.90	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:49,759] [INFO] GTDB search result was written to GCF_004403415.1_ASM440341v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:49,759] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:49,764] [INFO] DFAST_QC result json was written to GCF_004403415.1_ASM440341v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:49,764] [INFO] DFAST_QC completed!
[2024-01-24 13:58:49,765] [INFO] Total running time: 0h1m7s