[2023-06-29 21:52:51,409] [INFO] DFAST_QC pipeline started.
[2023-06-29 21:52:51,412] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 21:52:51,412] [INFO] DQC Reference Directory: /var/lib/cwl/stgb00f4757-87e0-4fb8-885f-5ed3ac167f34/dqc_reference
[2023-06-29 21:52:52,869] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 21:52:52,870] [INFO] Task started: Prodigal
[2023-06-29 21:52:52,871] [INFO] Running command: gunzip -c /var/lib/cwl/stg92ebe1ab-cdb7-4f6a-81d3-fb559f352dac/GCA_025463545.1_ASM2546354v1_genomic.fna.gz | prodigal -d GCA_025463545.1_ASM2546354v1_genomic.fna/cds.fna -a GCA_025463545.1_ASM2546354v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 21:52:57,432] [INFO] Task succeeded: Prodigal
[2023-06-29 21:52:57,432] [INFO] Task started: HMMsearch
[2023-06-29 21:52:57,432] [INFO] Running command: hmmsearch --tblout GCA_025463545.1_ASM2546354v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb00f4757-87e0-4fb8-885f-5ed3ac167f34/dqc_reference/reference_markers.hmm GCA_025463545.1_ASM2546354v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 21:52:57,610] [INFO] Task succeeded: HMMsearch
[2023-06-29 21:52:57,611] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg92ebe1ab-cdb7-4f6a-81d3-fb559f352dac/GCA_025463545.1_ASM2546354v1_genomic.fna.gz]
[2023-06-29 21:52:57,628] [INFO] Query marker FASTA was written to GCA_025463545.1_ASM2546354v1_genomic.fna/markers.fasta
[2023-06-29 21:52:57,629] [INFO] Task started: Blastn
[2023-06-29 21:52:57,629] [INFO] Running command: blastn -query GCA_025463545.1_ASM2546354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb00f4757-87e0-4fb8-885f-5ed3ac167f34/dqc_reference/reference_markers.fasta -out GCA_025463545.1_ASM2546354v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:52:58,344] [INFO] Task succeeded: Blastn
[2023-06-29 21:52:58,348] [INFO] Selected 8 target genomes.
[2023-06-29 21:52:58,348] [INFO] Target genome list was writen to GCA_025463545.1_ASM2546354v1_genomic.fna/target_genomes.txt
[2023-06-29 21:52:58,349] [INFO] Task started: fastANI
[2023-06-29 21:52:58,349] [INFO] Running command: fastANI --query /var/lib/cwl/stg92ebe1ab-cdb7-4f6a-81d3-fb559f352dac/GCA_025463545.1_ASM2546354v1_genomic.fna.gz --refList GCA_025463545.1_ASM2546354v1_genomic.fna/target_genomes.txt --output GCA_025463545.1_ASM2546354v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 21:53:02,918] [INFO] Task succeeded: fastANI
[2023-06-29 21:53:02,919] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb00f4757-87e0-4fb8-885f-5ed3ac167f34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 21:53:02,919] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb00f4757-87e0-4fb8-885f-5ed3ac167f34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 21:53:02,932] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 21:53:02,932] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 21:53:02,933] [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 psychrotolerans	strain=CGMCC 1.5382	GCA_004564325.1	386301	386301	type	True	80.4713	189	479	95	below_threshold
Cryobacterium arcticum	strain=SK-1	GCA_003185895.1	670052	670052	type	True	80.3546	196	479	95	below_threshold
Cryobacterium psychrotolerans	strain=CGMCC 1.5382	GCA_900101115.1	386301	386301	type	True	80.3415	193	479	95	below_threshold
Cryobacterium soli	strain=GCJ02	GCA_003611035.1	2220095	2220095	type	True	80.1798	195	479	95	below_threshold
Glaciibacter superstes	strain=DSM 21135	GCA_000421145.1	501023	501023	type	True	79.3388	216	479	95	below_threshold
Cryobacterium luteum	strain=CGMCC 1.11210	GCA_900110125.1	1424661	1424661	type	True	79.1694	169	479	95	below_threshold
Cryobacterium ruanii	strain=Sr36	GCA_004404055.1	1259197	1259197	type	True	79.0846	153	479	95	below_threshold
Cryobacterium luteum	strain=Hh15	GCA_004402515.1	1424661	1424661	type	True	78.9834	171	479	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 21:53:02,936] [INFO] DFAST Taxonomy check result was written to GCA_025463545.1_ASM2546354v1_genomic.fna/tc_result.tsv
[2023-06-29 21:53:02,936] [INFO] ===== Taxonomy check completed =====
[2023-06-29 21:53:02,937] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 21:53:02,937] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb00f4757-87e0-4fb8-885f-5ed3ac167f34/dqc_reference/checkm_data
[2023-06-29 21:53:02,940] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 21:53:02,959] [INFO] Task started: CheckM
[2023-06-29 21:53:02,959] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025463545.1_ASM2546354v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025463545.1_ASM2546354v1_genomic.fna/checkm_input GCA_025463545.1_ASM2546354v1_genomic.fna/checkm_result
[2023-06-29 21:53:22,603] [INFO] Task succeeded: CheckM
[2023-06-29 21:53:22,605] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 21:53:22,626] [INFO] ===== Completeness check finished =====
[2023-06-29 21:53:22,626] [INFO] ===== Start GTDB Search =====
[2023-06-29 21:53:22,627] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025463545.1_ASM2546354v1_genomic.fna/markers.fasta)
[2023-06-29 21:53:22,627] [INFO] Task started: Blastn
[2023-06-29 21:53:22,627] [INFO] Running command: blastn -query GCA_025463545.1_ASM2546354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb00f4757-87e0-4fb8-885f-5ed3ac167f34/dqc_reference/reference_markers_gtdb.fasta -out GCA_025463545.1_ASM2546354v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:53:23,501] [INFO] Task succeeded: Blastn
[2023-06-29 21:53:23,505] [INFO] Selected 8 target genomes.
[2023-06-29 21:53:23,506] [INFO] Target genome list was writen to GCA_025463545.1_ASM2546354v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 21:53:23,513] [INFO] Task started: fastANI
[2023-06-29 21:53:23,513] [INFO] Running command: fastANI --query /var/lib/cwl/stg92ebe1ab-cdb7-4f6a-81d3-fb559f352dac/GCA_025463545.1_ASM2546354v1_genomic.fna.gz --refList GCA_025463545.1_ASM2546354v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025463545.1_ASM2546354v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 21:53:28,333] [INFO] Task succeeded: fastANI
[2023-06-29 21:53:28,347] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 21:53:28,347] [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_015752155.1	s__Cryobacterium sp015752155	80.3629	204	479	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	80.3546	196	479	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004402595.1	s__Cryobacterium sp004402595	80.301	180	479	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	99.65	99.58	0.91	0.90	6	-
GCA_002404115.1	s__Cryobacterium sp002404115	80.2555	125	479	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	79.8184	199	479	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	79.7978	187	479	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004402235.1	s__Cryobacterium sp004402235	79.4356	180	479	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	99.29	99.21	0.93	0.91	7	-
GCF_900110125.1	s__Cryobacterium luteum	79.1148	171	479	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	99.76	99.53	0.96	0.95	3	-
--------------------------------------------------------------------------------
[2023-06-29 21:53:28,350] [INFO] GTDB search result was written to GCA_025463545.1_ASM2546354v1_genomic.fna/result_gtdb.tsv
[2023-06-29 21:53:28,350] [INFO] ===== GTDB Search completed =====
[2023-06-29 21:53:28,354] [INFO] DFAST_QC result json was written to GCA_025463545.1_ASM2546354v1_genomic.fna/dqc_result.json
[2023-06-29 21:53:28,354] [INFO] DFAST_QC completed!
[2023-06-29 21:53:28,354] [INFO] Total running time: 0h0m37s