[2023-06-16 19:10:13,935] [INFO] DFAST_QC pipeline started.
[2023-06-16 19:10:13,940] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 19:10:13,941] [INFO] DQC Reference Directory: /var/lib/cwl/stgd798d3bc-8bb9-4d6d-b4a1-2eaf43f1a4e4/dqc_reference
[2023-06-16 19:10:15,101] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 19:10:15,102] [INFO] Task started: Prodigal
[2023-06-16 19:10:15,102] [INFO] Running command: gunzip -c /var/lib/cwl/stgc140f27e-947f-4996-a64f-76eae84661e5/GCA_905200175.1_SRR5580102-mag-bin.18_genomic.fna.gz | prodigal -d GCA_905200175.1_SRR5580102-mag-bin.18_genomic.fna/cds.fna -a GCA_905200175.1_SRR5580102-mag-bin.18_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 19:10:21,186] [INFO] Task succeeded: Prodigal
[2023-06-16 19:10:21,186] [INFO] Task started: HMMsearch
[2023-06-16 19:10:21,187] [INFO] Running command: hmmsearch --tblout GCA_905200175.1_SRR5580102-mag-bin.18_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd798d3bc-8bb9-4d6d-b4a1-2eaf43f1a4e4/dqc_reference/reference_markers.hmm GCA_905200175.1_SRR5580102-mag-bin.18_genomic.fna/protein.faa > /dev/null
[2023-06-16 19:10:21,359] [INFO] Task succeeded: HMMsearch
[2023-06-16 19:10:21,364] [INFO] Found 6/6 markers.
[2023-06-16 19:10:21,387] [INFO] Query marker FASTA was written to GCA_905200175.1_SRR5580102-mag-bin.18_genomic.fna/markers.fasta
[2023-06-16 19:10:21,387] [INFO] Task started: Blastn
[2023-06-16 19:10:21,387] [INFO] Running command: blastn -query GCA_905200175.1_SRR5580102-mag-bin.18_genomic.fna/markers.fasta -db /var/lib/cwl/stgd798d3bc-8bb9-4d6d-b4a1-2eaf43f1a4e4/dqc_reference/reference_markers.fasta -out GCA_905200175.1_SRR5580102-mag-bin.18_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:10:22,025] [INFO] Task succeeded: Blastn
[2023-06-16 19:10:22,029] [INFO] Selected 26 target genomes.
[2023-06-16 19:10:22,029] [INFO] Target genome list was writen to GCA_905200175.1_SRR5580102-mag-bin.18_genomic.fna/target_genomes.txt
[2023-06-16 19:10:22,063] [INFO] Task started: fastANI
[2023-06-16 19:10:22,063] [INFO] Running command: fastANI --query /var/lib/cwl/stgc140f27e-947f-4996-a64f-76eae84661e5/GCA_905200175.1_SRR5580102-mag-bin.18_genomic.fna.gz --refList GCA_905200175.1_SRR5580102-mag-bin.18_genomic.fna/target_genomes.txt --output GCA_905200175.1_SRR5580102-mag-bin.18_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 19:10:36,945] [INFO] Task succeeded: fastANI
[2023-06-16 19:10:36,945] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd798d3bc-8bb9-4d6d-b4a1-2eaf43f1a4e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 19:10:36,945] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd798d3bc-8bb9-4d6d-b4a1-2eaf43f1a4e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 19:10:36,947] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 19:10:36,947] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-16 19:10:36,947] [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
--------------------------------------------------------------------------------
[2023-06-16 19:10:36,949] [INFO] DFAST Taxonomy check result was written to GCA_905200175.1_SRR5580102-mag-bin.18_genomic.fna/tc_result.tsv
[2023-06-16 19:10:36,949] [INFO] ===== Taxonomy check completed =====
[2023-06-16 19:10:36,949] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 19:10:36,949] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd798d3bc-8bb9-4d6d-b4a1-2eaf43f1a4e4/dqc_reference/checkm_data
[2023-06-16 19:10:36,952] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 19:10:36,982] [INFO] Task started: CheckM
[2023-06-16 19:10:36,982] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905200175.1_SRR5580102-mag-bin.18_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905200175.1_SRR5580102-mag-bin.18_genomic.fna/checkm_input GCA_905200175.1_SRR5580102-mag-bin.18_genomic.fna/checkm_result
[2023-06-16 19:10:59,076] [INFO] Task succeeded: CheckM
[2023-06-16 19:10:59,077] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.29%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 19:10:59,093] [INFO] ===== Completeness check finished =====
[2023-06-16 19:10:59,093] [INFO] ===== Start GTDB Search =====
[2023-06-16 19:10:59,094] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905200175.1_SRR5580102-mag-bin.18_genomic.fna/markers.fasta)
[2023-06-16 19:10:59,094] [INFO] Task started: Blastn
[2023-06-16 19:10:59,094] [INFO] Running command: blastn -query GCA_905200175.1_SRR5580102-mag-bin.18_genomic.fna/markers.fasta -db /var/lib/cwl/stgd798d3bc-8bb9-4d6d-b4a1-2eaf43f1a4e4/dqc_reference/reference_markers_gtdb.fasta -out GCA_905200175.1_SRR5580102-mag-bin.18_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:11:00,282] [INFO] Task succeeded: Blastn
[2023-06-16 19:11:00,285] [INFO] Selected 17 target genomes.
[2023-06-16 19:11:00,285] [INFO] Target genome list was writen to GCA_905200175.1_SRR5580102-mag-bin.18_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 19:11:00,313] [INFO] Task started: fastANI
[2023-06-16 19:11:00,313] [INFO] Running command: fastANI --query /var/lib/cwl/stgc140f27e-947f-4996-a64f-76eae84661e5/GCA_905200175.1_SRR5580102-mag-bin.18_genomic.fna.gz --refList GCA_905200175.1_SRR5580102-mag-bin.18_genomic.fna/target_genomes_gtdb.txt --output GCA_905200175.1_SRR5580102-mag-bin.18_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 19:11:07,952] [INFO] Task succeeded: fastANI
[2023-06-16 19:11:07,963] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 19:11:07,963] [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_900553295.1	s__Egerieenecus merdigallinarum	97.8455	509	642	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Egerieenecus	95.0	98.56	97.85	0.79	0.78	4	conclusive
GCA_900553315.1	s__Egerieenecus sp900553315	79.1043	166	642	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Egerieenecus	95.0	97.57	97.57	0.79	0.79	2	-
GCA_017463245.1	s__UBA11524 sp017463245	78.7835	168	642	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017936765.1	s__UBA11524 sp017936765	78.457	166	642	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	96.73	96.73	0.86	0.86	2	-
GCA_017938695.1	s__UBA11524 sp017938695	78.2705	179	642	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015056415.1	s__UBA11524 sp015056415	78.2157	144	642	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900769075.1	s__UBA11524 sp900769075	78.2087	123	642	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016295665.1	s__HGM11604 sp016295665	78.1916	134	642	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__HGM11604	95.0	98.69	98.69	0.84	0.84	2	-
GCA_902790495.1	s__RUG11272 sp902790495	78.095	109	642	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG11272	95.0	96.98	96.98	0.84	0.84	2	-
GCA_902767565.1	s__RUG11272 sp902767565	77.9509	71	642	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG11272	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017513475.1	s__UBA11524 sp017513475	77.7804	109	642	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017481825.1	s__UBA11524 sp017481825	77.6861	114	642	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017519405.1	s__RUG11272 sp017519405	77.6121	86	642	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG11272	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015056325.1	s__UBA11524 sp015056325	77.5595	115	642	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015056155.1	s__UBA11524 sp015056155	77.3559	108	642	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017399225.1	s__UBA11524 sp017399225	77.2744	127	642	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017569285.1	s__GCA-900199385 sp017569285	77.0804	63	642	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__GCA-900199385	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 19:11:07,965] [INFO] GTDB search result was written to GCA_905200175.1_SRR5580102-mag-bin.18_genomic.fna/result_gtdb.tsv
[2023-06-16 19:11:07,965] [INFO] ===== GTDB Search completed =====
[2023-06-16 19:11:07,968] [INFO] DFAST_QC result json was written to GCA_905200175.1_SRR5580102-mag-bin.18_genomic.fna/dqc_result.json
[2023-06-16 19:11:07,968] [INFO] DFAST_QC completed!
[2023-06-16 19:11:07,968] [INFO] Total running time: 0h0m54s