[2023-06-17 16:58:50,536] [INFO] DFAST_QC pipeline started.
[2023-06-17 16:58:50,538] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 16:58:50,538] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f15a47f-784a-40d8-b853-dbfaff38aa78/dqc_reference
[2023-06-17 16:58:51,760] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 16:58:51,761] [INFO] Task started: Prodigal
[2023-06-17 16:58:51,761] [INFO] Running command: gunzip -c /var/lib/cwl/stgb329f01c-ce59-4739-b23b-437777c06852/GCA_028722025.1_ASM2872202v1_genomic.fna.gz | prodigal -d GCA_028722025.1_ASM2872202v1_genomic.fna/cds.fna -a GCA_028722025.1_ASM2872202v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 16:58:57,066] [INFO] Task succeeded: Prodigal
[2023-06-17 16:58:57,067] [INFO] Task started: HMMsearch
[2023-06-17 16:58:57,067] [INFO] Running command: hmmsearch --tblout GCA_028722025.1_ASM2872202v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f15a47f-784a-40d8-b853-dbfaff38aa78/dqc_reference/reference_markers.hmm GCA_028722025.1_ASM2872202v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 16:58:57,289] [INFO] Task succeeded: HMMsearch
[2023-06-17 16:58:57,290] [INFO] Found 6/6 markers.
[2023-06-17 16:58:57,312] [INFO] Query marker FASTA was written to GCA_028722025.1_ASM2872202v1_genomic.fna/markers.fasta
[2023-06-17 16:58:57,312] [INFO] Task started: Blastn
[2023-06-17 16:58:57,312] [INFO] Running command: blastn -query GCA_028722025.1_ASM2872202v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f15a47f-784a-40d8-b853-dbfaff38aa78/dqc_reference/reference_markers.fasta -out GCA_028722025.1_ASM2872202v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 16:58:58,046] [INFO] Task succeeded: Blastn
[2023-06-17 16:58:58,052] [INFO] Selected 31 target genomes.
[2023-06-17 16:58:58,052] [INFO] Target genome list was writen to GCA_028722025.1_ASM2872202v1_genomic.fna/target_genomes.txt
[2023-06-17 16:58:58,060] [INFO] Task started: fastANI
[2023-06-17 16:58:58,060] [INFO] Running command: fastANI --query /var/lib/cwl/stgb329f01c-ce59-4739-b23b-437777c06852/GCA_028722025.1_ASM2872202v1_genomic.fna.gz --refList GCA_028722025.1_ASM2872202v1_genomic.fna/target_genomes.txt --output GCA_028722025.1_ASM2872202v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 16:59:18,692] [INFO] Task succeeded: fastANI
[2023-06-17 16:59:18,693] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f15a47f-784a-40d8-b853-dbfaff38aa78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 16:59:18,694] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f15a47f-784a-40d8-b853-dbfaff38aa78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 16:59:18,696] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 16:59:18,696] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 16:59:18,697] [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
--------------------------------------------------------------------------------
[2023-06-17 16:59:18,699] [INFO] DFAST Taxonomy check result was written to GCA_028722025.1_ASM2872202v1_genomic.fna/tc_result.tsv
[2023-06-17 16:59:18,700] [INFO] ===== Taxonomy check completed =====
[2023-06-17 16:59:18,700] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 16:59:18,701] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f15a47f-784a-40d8-b853-dbfaff38aa78/dqc_reference/checkm_data
[2023-06-17 16:59:18,705] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 16:59:18,726] [INFO] Task started: CheckM
[2023-06-17 16:59:18,726] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028722025.1_ASM2872202v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028722025.1_ASM2872202v1_genomic.fna/checkm_input GCA_028722025.1_ASM2872202v1_genomic.fna/checkm_result
[2023-06-17 16:59:40,341] [INFO] Task succeeded: CheckM
[2023-06-17 16:59:40,343] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 16:59:40,364] [INFO] ===== Completeness check finished =====
[2023-06-17 16:59:40,365] [INFO] ===== Start GTDB Search =====
[2023-06-17 16:59:40,365] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028722025.1_ASM2872202v1_genomic.fna/markers.fasta)
[2023-06-17 16:59:40,365] [INFO] Task started: Blastn
[2023-06-17 16:59:40,366] [INFO] Running command: blastn -query GCA_028722025.1_ASM2872202v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f15a47f-784a-40d8-b853-dbfaff38aa78/dqc_reference/reference_markers_gtdb.fasta -out GCA_028722025.1_ASM2872202v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 16:59:41,662] [INFO] Task succeeded: Blastn
[2023-06-17 16:59:41,667] [INFO] Selected 17 target genomes.
[2023-06-17 16:59:41,667] [INFO] Target genome list was writen to GCA_028722025.1_ASM2872202v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 16:59:41,679] [INFO] Task started: fastANI
[2023-06-17 16:59:41,679] [INFO] Running command: fastANI --query /var/lib/cwl/stgb329f01c-ce59-4739-b23b-437777c06852/GCA_028722025.1_ASM2872202v1_genomic.fna.gz --refList GCA_028722025.1_ASM2872202v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028722025.1_ASM2872202v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 16:59:49,348] [INFO] Task succeeded: fastANI
[2023-06-17 16:59:49,360] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 16:59:49,361] [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_000432015.1	s__CAG-1024 sp000432015	98.6167	470	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__CAG-1024	95.0	98.73	98.71	0.87	0.85	5	conclusive
GCA_004554165.1	s__CAG-1024 sp004554165	79.5154	221	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__CAG-1024	95.0	98.83	98.73	0.93	0.90	3	-
GCA_900550525.1	s__Aphodomorpha intestinavium	78.4186	117	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__Aphodomorpha	95.0	98.57	98.50	0.86	0.85	3	-
GCA_900549955.1	s__Aphodomorpha sp900549955	78.134	103	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__Aphodomorpha	95.0	100.00	100.00	0.93	0.93	2	-
GCA_902789675.1	s__UBA3792 sp902789675	77.9918	67	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__UBA3792	95.0	96.13	96.13	0.86	0.86	2	-
GCA_012517905.1	s__UBA7703 sp012517905	77.5612	106	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__UBA7703	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017429985.1	s__CAG-1024 sp017429985	77.4021	66	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__CAG-1024	95.0	98.78	98.78	0.87	0.87	2	-
GCA_900546845.1	s__UBA1685 sp900546845	76.9851	51	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__UBA1685	95.0	97.42	97.42	0.86	0.86	2	-
GCA_017394605.1	s__CAG-1024 sp017394605	76.892	52	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__CAG-1024	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017388175.1	s__UBA3792 sp017388175	76.6803	55	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__UBA3792	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 16:59:49,363] [INFO] GTDB search result was written to GCA_028722025.1_ASM2872202v1_genomic.fna/result_gtdb.tsv
[2023-06-17 16:59:49,363] [INFO] ===== GTDB Search completed =====
[2023-06-17 16:59:49,366] [INFO] DFAST_QC result json was written to GCA_028722025.1_ASM2872202v1_genomic.fna/dqc_result.json
[2023-06-17 16:59:49,366] [INFO] DFAST_QC completed!
[2023-06-17 16:59:49,366] [INFO] Total running time: 0h0m59s