[2023-06-30 21:10:01,700] [INFO] DFAST_QC pipeline started.
[2023-06-30 21:10:01,703] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 21:10:01,703] [INFO] DQC Reference Directory: /var/lib/cwl/stg72df8d2c-24d2-4ff4-b617-e1266c2e4564/dqc_reference
[2023-06-30 21:10:04,734] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 21:10:04,735] [INFO] Task started: Prodigal
[2023-06-30 21:10:04,736] [INFO] Running command: gunzip -c /var/lib/cwl/stg9d203602-d8e7-4e96-97ce-df67810d82f0/GCA_024403235.1_ASM2440323v1_genomic.fna.gz | prodigal -d GCA_024403235.1_ASM2440323v1_genomic.fna/cds.fna -a GCA_024403235.1_ASM2440323v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 21:10:10,008] [INFO] Task succeeded: Prodigal
[2023-06-30 21:10:10,009] [INFO] Task started: HMMsearch
[2023-06-30 21:10:10,009] [INFO] Running command: hmmsearch --tblout GCA_024403235.1_ASM2440323v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg72df8d2c-24d2-4ff4-b617-e1266c2e4564/dqc_reference/reference_markers.hmm GCA_024403235.1_ASM2440323v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 21:10:10,293] [INFO] Task succeeded: HMMsearch
[2023-06-30 21:10:10,294] [INFO] Found 6/6 markers.
[2023-06-30 21:10:10,334] [INFO] Query marker FASTA was written to GCA_024403235.1_ASM2440323v1_genomic.fna/markers.fasta
[2023-06-30 21:10:10,335] [INFO] Task started: Blastn
[2023-06-30 21:10:10,335] [INFO] Running command: blastn -query GCA_024403235.1_ASM2440323v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg72df8d2c-24d2-4ff4-b617-e1266c2e4564/dqc_reference/reference_markers.fasta -out GCA_024403235.1_ASM2440323v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 21:10:10,990] [INFO] Task succeeded: Blastn
[2023-06-30 21:10:10,995] [INFO] Selected 27 target genomes.
[2023-06-30 21:10:10,996] [INFO] Target genome list was writen to GCA_024403235.1_ASM2440323v1_genomic.fna/target_genomes.txt
[2023-06-30 21:10:11,002] [INFO] Task started: fastANI
[2023-06-30 21:10:11,003] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d203602-d8e7-4e96-97ce-df67810d82f0/GCA_024403235.1_ASM2440323v1_genomic.fna.gz --refList GCA_024403235.1_ASM2440323v1_genomic.fna/target_genomes.txt --output GCA_024403235.1_ASM2440323v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 21:10:28,286] [INFO] Task succeeded: fastANI
[2023-06-30 21:10:28,286] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg72df8d2c-24d2-4ff4-b617-e1266c2e4564/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 21:10:28,286] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg72df8d2c-24d2-4ff4-b617-e1266c2e4564/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 21:10:28,291] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 21:10:28,292] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 21:10:28,292] [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
Blautia hansenii	strain=DSM 20583	GCA_025147655.1	1322	1322	type	True	77.0315	50	756	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 21:10:28,294] [INFO] DFAST Taxonomy check result was written to GCA_024403235.1_ASM2440323v1_genomic.fna/tc_result.tsv
[2023-06-30 21:10:28,295] [INFO] ===== Taxonomy check completed =====
[2023-06-30 21:10:28,295] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 21:10:28,296] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg72df8d2c-24d2-4ff4-b617-e1266c2e4564/dqc_reference/checkm_data
[2023-06-30 21:10:28,298] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 21:10:28,336] [INFO] Task started: CheckM
[2023-06-30 21:10:28,337] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024403235.1_ASM2440323v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024403235.1_ASM2440323v1_genomic.fna/checkm_input GCA_024403235.1_ASM2440323v1_genomic.fna/checkm_result
[2023-06-30 21:10:51,795] [INFO] Task succeeded: CheckM
[2023-06-30 21:10:51,796] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.56%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 21:10:51,817] [INFO] ===== Completeness check finished =====
[2023-06-30 21:10:51,818] [INFO] ===== Start GTDB Search =====
[2023-06-30 21:10:51,819] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024403235.1_ASM2440323v1_genomic.fna/markers.fasta)
[2023-06-30 21:10:51,819] [INFO] Task started: Blastn
[2023-06-30 21:10:51,819] [INFO] Running command: blastn -query GCA_024403235.1_ASM2440323v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg72df8d2c-24d2-4ff4-b617-e1266c2e4564/dqc_reference/reference_markers_gtdb.fasta -out GCA_024403235.1_ASM2440323v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 21:10:52,904] [INFO] Task succeeded: Blastn
[2023-06-30 21:10:52,909] [INFO] Selected 27 target genomes.
[2023-06-30 21:10:52,909] [INFO] Target genome list was writen to GCA_024403235.1_ASM2440323v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 21:10:52,998] [INFO] Task started: fastANI
[2023-06-30 21:10:52,999] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d203602-d8e7-4e96-97ce-df67810d82f0/GCA_024403235.1_ASM2440323v1_genomic.fna.gz --refList GCA_024403235.1_ASM2440323v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024403235.1_ASM2440323v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 21:11:04,837] [INFO] Task succeeded: fastANI
[2023-06-30 21:11:04,857] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 21:11:04,857] [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
GCA_017555455.1	s__SFDP01 sp017555455	77.9623	113	756	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__SFDP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017623295.1	s__UBA3282 sp017623295	77.3892	85	756	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017436305.1	s__RGIG3040 sp017436305	77.3697	78	756	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RGIG3040	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017521195.1	s__SFDP01 sp017521195	77.3255	105	756	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__SFDP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017411305.1	s__CAG-95 sp017411305	77.2771	75	756	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017561085.1	s__CAG-95 sp017561085	77.2738	87	756	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017437065.1	s__RGIG3002 sp017437065	77.1775	82	756	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RGIG3002	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017558145.1	s__SFDP01 sp017558145	77.1135	105	756	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__SFDP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017522685.1	s__Acetatifactor sp017522685	76.89	64	756	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017520425.1	s__Acetatifactor sp017520425	76.8074	82	756	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017520155.1	s__SFDP01 sp017520155	76.663	97	756	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__SFDP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900753305.1	s__COE1 sp900753305	76.5648	53	756	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	99.96	99.96	0.93	0.93	2	-
GCA_017468395.1	s__SIG332 sp017468395	76.556	58	756	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__SIG332	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017482205.1	s__CAG-510 sp017482205	76.426	61	756	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-510	95.0	98.99	98.99	0.84	0.84	2	-
GCA_002490775.1	s__CAG-95 sp002490775	76.374	55	756	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900770785.1	s__SFDP01 sp900770785	76.2883	74	756	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__SFDP01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 21:11:04,860] [INFO] GTDB search result was written to GCA_024403235.1_ASM2440323v1_genomic.fna/result_gtdb.tsv
[2023-06-30 21:11:04,860] [INFO] ===== GTDB Search completed =====
[2023-06-30 21:11:04,864] [INFO] DFAST_QC result json was written to GCA_024403235.1_ASM2440323v1_genomic.fna/dqc_result.json
[2023-06-30 21:11:04,864] [INFO] DFAST_QC completed!
[2023-06-30 21:11:04,864] [INFO] Total running time: 0h1m3s