[2023-06-08 20:36:33,804] [INFO] DFAST_QC pipeline started.
[2023-06-08 20:36:33,810] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 20:36:33,811] [INFO] DQC Reference Directory: /var/lib/cwl/stg092591cf-e501-4ffd-b4e3-e0b67ea3b0f1/dqc_reference
[2023-06-08 20:36:35,198] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 20:36:35,199] [INFO] Task started: Prodigal
[2023-06-08 20:36:35,199] [INFO] Running command: gunzip -c /var/lib/cwl/stga6303bf4-32f6-4c3a-837c-2626e2559349/GCA_902835295.1_MGYG-HGUT-04777_genomic.fna.gz | prodigal -d GCA_902835295.1_MGYG-HGUT-04777_genomic.fna/cds.fna -a GCA_902835295.1_MGYG-HGUT-04777_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 20:36:38,630] [INFO] Task succeeded: Prodigal
[2023-06-08 20:36:38,631] [INFO] Task started: HMMsearch
[2023-06-08 20:36:38,631] [INFO] Running command: hmmsearch --tblout GCA_902835295.1_MGYG-HGUT-04777_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg092591cf-e501-4ffd-b4e3-e0b67ea3b0f1/dqc_reference/reference_markers.hmm GCA_902835295.1_MGYG-HGUT-04777_genomic.fna/protein.faa > /dev/null
[2023-06-08 20:36:38,859] [INFO] Task succeeded: HMMsearch
[2023-06-08 20:36:38,860] [WARNING] Found 2/6 markers. [/var/lib/cwl/stga6303bf4-32f6-4c3a-837c-2626e2559349/GCA_902835295.1_MGYG-HGUT-04777_genomic.fna.gz]
[2023-06-08 20:36:38,907] [INFO] Query marker FASTA was written to GCA_902835295.1_MGYG-HGUT-04777_genomic.fna/markers.fasta
[2023-06-08 20:36:38,907] [INFO] Task started: Blastn
[2023-06-08 20:36:38,908] [INFO] Running command: blastn -query GCA_902835295.1_MGYG-HGUT-04777_genomic.fna/markers.fasta -db /var/lib/cwl/stg092591cf-e501-4ffd-b4e3-e0b67ea3b0f1/dqc_reference/reference_markers.fasta -out GCA_902835295.1_MGYG-HGUT-04777_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:36:39,422] [INFO] Task succeeded: Blastn
[2023-06-08 20:36:39,430] [INFO] Selected 13 target genomes.
[2023-06-08 20:36:39,430] [INFO] Target genome list was writen to GCA_902835295.1_MGYG-HGUT-04777_genomic.fna/target_genomes.txt
[2023-06-08 20:36:39,432] [INFO] Task started: fastANI
[2023-06-08 20:36:39,432] [INFO] Running command: fastANI --query /var/lib/cwl/stga6303bf4-32f6-4c3a-837c-2626e2559349/GCA_902835295.1_MGYG-HGUT-04777_genomic.fna.gz --refList GCA_902835295.1_MGYG-HGUT-04777_genomic.fna/target_genomes.txt --output GCA_902835295.1_MGYG-HGUT-04777_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 20:36:44,175] [INFO] Task succeeded: fastANI
[2023-06-08 20:36:44,176] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg092591cf-e501-4ffd-b4e3-e0b67ea3b0f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 20:36:44,176] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg092591cf-e501-4ffd-b4e3-e0b67ea3b0f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 20:36:44,181] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 20:36:44,181] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 20:36:44,181] [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
Collinsella aerofaciens	strain=NCTC11838	GCA_900461335.1	74426	74426	type	True	92.8952	107	123	95	below_threshold
Collinsella aerofaciens	strain=JCM 10188	GCA_010509075.1	74426	74426	type	True	92.8256	107	123	95	below_threshold
Collinsella aerofaciens	strain=ATCC 25986	GCA_000169035.1	74426	74426	type	True	92.7873	109	123	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 20:36:44,184] [INFO] DFAST Taxonomy check result was written to GCA_902835295.1_MGYG-HGUT-04777_genomic.fna/tc_result.tsv
[2023-06-08 20:36:44,185] [INFO] ===== Taxonomy check completed =====
[2023-06-08 20:36:44,185] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 20:36:44,185] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg092591cf-e501-4ffd-b4e3-e0b67ea3b0f1/dqc_reference/checkm_data
[2023-06-08 20:36:44,186] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 20:36:44,213] [INFO] Task started: CheckM
[2023-06-08 20:36:44,213] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902835295.1_MGYG-HGUT-04777_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902835295.1_MGYG-HGUT-04777_genomic.fna/checkm_input GCA_902835295.1_MGYG-HGUT-04777_genomic.fna/checkm_result
[2023-06-08 20:37:02,835] [INFO] Task succeeded: CheckM
[2023-06-08 20:37:02,837] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.18%
Contamintation: 7.97%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 20:37:02,864] [INFO] ===== Completeness check finished =====
[2023-06-08 20:37:02,865] [INFO] ===== Start GTDB Search =====
[2023-06-08 20:37:02,865] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902835295.1_MGYG-HGUT-04777_genomic.fna/markers.fasta)
[2023-06-08 20:37:02,865] [INFO] Task started: Blastn
[2023-06-08 20:37:02,866] [INFO] Running command: blastn -query GCA_902835295.1_MGYG-HGUT-04777_genomic.fna/markers.fasta -db /var/lib/cwl/stg092591cf-e501-4ffd-b4e3-e0b67ea3b0f1/dqc_reference/reference_markers_gtdb.fasta -out GCA_902835295.1_MGYG-HGUT-04777_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:37:03,442] [INFO] Task succeeded: Blastn
[2023-06-08 20:37:03,446] [INFO] Selected 15 target genomes.
[2023-06-08 20:37:03,447] [INFO] Target genome list was writen to GCA_902835295.1_MGYG-HGUT-04777_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 20:37:03,455] [INFO] Task started: fastANI
[2023-06-08 20:37:03,455] [INFO] Running command: fastANI --query /var/lib/cwl/stga6303bf4-32f6-4c3a-837c-2626e2559349/GCA_902835295.1_MGYG-HGUT-04777_genomic.fna.gz --refList GCA_902835295.1_MGYG-HGUT-04777_genomic.fna/target_genomes_gtdb.txt --output GCA_902835295.1_MGYG-HGUT-04777_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 20:37:07,748] [INFO] Task succeeded: fastANI
[2023-06-08 20:37:07,761] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 20:37:07,762] [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_905215065.1	s__Collinsella sp905215065	94.8929	111	123	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1686	95.36	95.20	0.87	0.82	13	-
GCA_902835305.1	s__Collinsella sp902835305	94.7046	108	123	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.56	95.13	0.93	0.87	3	-
GCA_900541645.1	s__Collinsella sp900541645	94.5107	105	123	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.32	95.32	0.85	0.85	2	-
GCF_003469205.1	s__Collinsella sp003469205	94.4293	113	123	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.74	95.06	0.88	0.84	17	-
GCF_003458415.1	s__Collinsella sp003458415	94.3233	112	123	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.71	95.33	0.90	0.87	8	-
GCA_905197665.1	s__Collinsella sp900556445	94.3091	106	123	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.037	96.72	95.07	0.91	0.87	4	-
GCA_905214525.1	s__Collinsella sp905214525	94.1892	113	123	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.3232	N/A	N/A	N/A	N/A	1	-
GCA_900762345.1	s__Collinsella sp900762345	94.1487	100	123	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902405995.1	s__Collinsella sp902405995	93.6865	110	123	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1886	96.57	95.30	0.89	0.86	5	-
GCA_900768435.1	s__Collinsella sp900768435	93.129	100	123	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018381235.1	s__Collinsella sp018381235	93.0934	113	123	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0673	N/A	N/A	N/A	N/A	1	-
GCA_900755685.1	s__Collinsella sp900755685	93.0111	105	123	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1616	97.58	95.18	0.89	0.84	3	-
GCA_900545055.1	s__Collinsella sp900545055	92.8155	98	123	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550355.1	s__Collinsella sp900550355	92.4237	100	123	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.039	N/A	N/A	N/A	N/A	1	-
GCA_900542155.1	s__Collinsella sp900542155	92.2501	108	123	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-08 20:37:07,764] [INFO] GTDB search result was written to GCA_902835295.1_MGYG-HGUT-04777_genomic.fna/result_gtdb.tsv
[2023-06-08 20:37:07,765] [INFO] ===== GTDB Search completed =====
[2023-06-08 20:37:07,768] [INFO] DFAST_QC result json was written to GCA_902835295.1_MGYG-HGUT-04777_genomic.fna/dqc_result.json
[2023-06-08 20:37:07,769] [INFO] DFAST_QC completed!
[2023-06-08 20:37:07,769] [INFO] Total running time: 0h0m34s