[2023-06-17 14:42:57,841] [INFO] DFAST_QC pipeline started.
[2023-06-17 14:42:57,846] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 14:42:57,846] [INFO] DQC Reference Directory: /var/lib/cwl/stg85808598-044b-4ed4-9776-c9bb79f5f506/dqc_reference
[2023-06-17 14:42:59,323] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 14:42:59,324] [INFO] Task started: Prodigal
[2023-06-17 14:42:59,324] [INFO] Running command: gunzip -c /var/lib/cwl/stg2b9fcddb-58a3-4da6-ba30-84a62c777ef4/GCA_905210495.1_ERR321565-mag-bin.22_genomic.fna.gz | prodigal -d GCA_905210495.1_ERR321565-mag-bin.22_genomic.fna/cds.fna -a GCA_905210495.1_ERR321565-mag-bin.22_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 14:43:05,168] [INFO] Task succeeded: Prodigal
[2023-06-17 14:43:05,168] [INFO] Task started: HMMsearch
[2023-06-17 14:43:05,168] [INFO] Running command: hmmsearch --tblout GCA_905210495.1_ERR321565-mag-bin.22_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85808598-044b-4ed4-9776-c9bb79f5f506/dqc_reference/reference_markers.hmm GCA_905210495.1_ERR321565-mag-bin.22_genomic.fna/protein.faa > /dev/null
[2023-06-17 14:43:05,444] [INFO] Task succeeded: HMMsearch
[2023-06-17 14:43:05,446] [INFO] Found 6/6 markers.
[2023-06-17 14:43:05,481] [INFO] Query marker FASTA was written to GCA_905210495.1_ERR321565-mag-bin.22_genomic.fna/markers.fasta
[2023-06-17 14:43:05,481] [INFO] Task started: Blastn
[2023-06-17 14:43:05,482] [INFO] Running command: blastn -query GCA_905210495.1_ERR321565-mag-bin.22_genomic.fna/markers.fasta -db /var/lib/cwl/stg85808598-044b-4ed4-9776-c9bb79f5f506/dqc_reference/reference_markers.fasta -out GCA_905210495.1_ERR321565-mag-bin.22_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 14:43:06,247] [INFO] Task succeeded: Blastn
[2023-06-17 14:43:06,251] [INFO] Selected 31 target genomes.
[2023-06-17 14:43:06,251] [INFO] Target genome list was writen to GCA_905210495.1_ERR321565-mag-bin.22_genomic.fna/target_genomes.txt
[2023-06-17 14:43:06,277] [INFO] Task started: fastANI
[2023-06-17 14:43:06,278] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b9fcddb-58a3-4da6-ba30-84a62c777ef4/GCA_905210495.1_ERR321565-mag-bin.22_genomic.fna.gz --refList GCA_905210495.1_ERR321565-mag-bin.22_genomic.fna/target_genomes.txt --output GCA_905210495.1_ERR321565-mag-bin.22_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 14:43:27,846] [INFO] Task succeeded: fastANI
[2023-06-17 14:43:27,847] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85808598-044b-4ed4-9776-c9bb79f5f506/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 14:43:27,847] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85808598-044b-4ed4-9776-c9bb79f5f506/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 14:43:27,848] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 14:43:27,848] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 14:43:27,848] [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 14:43:27,850] [INFO] DFAST Taxonomy check result was written to GCA_905210495.1_ERR321565-mag-bin.22_genomic.fna/tc_result.tsv
[2023-06-17 14:43:27,851] [INFO] ===== Taxonomy check completed =====
[2023-06-17 14:43:27,851] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 14:43:27,851] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85808598-044b-4ed4-9776-c9bb79f5f506/dqc_reference/checkm_data
[2023-06-17 14:43:27,854] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 14:43:27,881] [INFO] Task started: CheckM
[2023-06-17 14:43:27,882] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905210495.1_ERR321565-mag-bin.22_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905210495.1_ERR321565-mag-bin.22_genomic.fna/checkm_input GCA_905210495.1_ERR321565-mag-bin.22_genomic.fna/checkm_result
[2023-06-17 14:43:51,048] [INFO] Task succeeded: CheckM
[2023-06-17 14:43:51,049] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.70%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 14:43:51,070] [INFO] ===== Completeness check finished =====
[2023-06-17 14:43:51,071] [INFO] ===== Start GTDB Search =====
[2023-06-17 14:43:51,071] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905210495.1_ERR321565-mag-bin.22_genomic.fna/markers.fasta)
[2023-06-17 14:43:51,071] [INFO] Task started: Blastn
[2023-06-17 14:43:51,072] [INFO] Running command: blastn -query GCA_905210495.1_ERR321565-mag-bin.22_genomic.fna/markers.fasta -db /var/lib/cwl/stg85808598-044b-4ed4-9776-c9bb79f5f506/dqc_reference/reference_markers_gtdb.fasta -out GCA_905210495.1_ERR321565-mag-bin.22_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 14:43:52,038] [INFO] Task succeeded: Blastn
[2023-06-17 14:43:52,042] [INFO] Selected 16 target genomes.
[2023-06-17 14:43:52,042] [INFO] Target genome list was writen to GCA_905210495.1_ERR321565-mag-bin.22_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 14:43:52,061] [INFO] Task started: fastANI
[2023-06-17 14:43:52,061] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b9fcddb-58a3-4da6-ba30-84a62c777ef4/GCA_905210495.1_ERR321565-mag-bin.22_genomic.fna.gz --refList GCA_905210495.1_ERR321565-mag-bin.22_genomic.fna/target_genomes_gtdb.txt --output GCA_905210495.1_ERR321565-mag-bin.22_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 14:43:59,675] [INFO] Task succeeded: fastANI
[2023-06-17 14:43:59,693] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 14:43:59,693] [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	98.6634	477	637	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	78.9654	217	637	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_900549955.1	s__Aphodomorpha sp900549955	78.4537	97	637	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_900550525.1	s__Aphodomorpha intestinavium	78.4263	110	637	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_902789675.1	s__UBA3792 sp902789675	78.0807	67	637	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	77.321	103	637	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	76.9157	67	637	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_017394605.1	s__CAG-1024 sp017394605	76.2867	53	637	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	-
--------------------------------------------------------------------------------
[2023-06-17 14:43:59,696] [INFO] GTDB search result was written to GCA_905210495.1_ERR321565-mag-bin.22_genomic.fna/result_gtdb.tsv
[2023-06-17 14:43:59,697] [INFO] ===== GTDB Search completed =====
[2023-06-17 14:43:59,700] [INFO] DFAST_QC result json was written to GCA_905210495.1_ERR321565-mag-bin.22_genomic.fna/dqc_result.json
[2023-06-17 14:43:59,701] [INFO] DFAST_QC completed!
[2023-06-17 14:43:59,701] [INFO] Total running time: 0h1m2s