[2023-06-08 00:35:26,092] [INFO] DFAST_QC pipeline started.
[2023-06-08 00:35:26,095] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 00:35:26,096] [INFO] DQC Reference Directory: /var/lib/cwl/stg662666a9-35bd-486f-97bc-2f9f4cd7189e/dqc_reference
[2023-06-08 00:35:27,427] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 00:35:27,428] [INFO] Task started: Prodigal
[2023-06-08 00:35:27,428] [INFO] Running command: gunzip -c /var/lib/cwl/stg00b06a50-117b-4371-859f-19b55086e921/GCA_945910515.1_SRR11489782_bin.75_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945910515.1_SRR11489782_bin.75_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945910515.1_SRR11489782_bin.75_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 00:35:34,193] [INFO] Task succeeded: Prodigal
[2023-06-08 00:35:34,193] [INFO] Task started: HMMsearch
[2023-06-08 00:35:34,193] [INFO] Running command: hmmsearch --tblout GCA_945910515.1_SRR11489782_bin.75_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg662666a9-35bd-486f-97bc-2f9f4cd7189e/dqc_reference/reference_markers.hmm GCA_945910515.1_SRR11489782_bin.75_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 00:35:34,464] [INFO] Task succeeded: HMMsearch
[2023-06-08 00:35:34,466] [INFO] Found 6/6 markers.
[2023-06-08 00:35:34,502] [INFO] Query marker FASTA was written to GCA_945910515.1_SRR11489782_bin.75_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 00:35:34,503] [INFO] Task started: Blastn
[2023-06-08 00:35:34,503] [INFO] Running command: blastn -query GCA_945910515.1_SRR11489782_bin.75_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg662666a9-35bd-486f-97bc-2f9f4cd7189e/dqc_reference/reference_markers.fasta -out GCA_945910515.1_SRR11489782_bin.75_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:35:35,119] [INFO] Task succeeded: Blastn
[2023-06-08 00:35:35,123] [INFO] Selected 7 target genomes.
[2023-06-08 00:35:35,123] [INFO] Target genome list was writen to GCA_945910515.1_SRR11489782_bin.75_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 00:35:35,124] [INFO] Task started: fastANI
[2023-06-08 00:35:35,124] [INFO] Running command: fastANI --query /var/lib/cwl/stg00b06a50-117b-4371-859f-19b55086e921/GCA_945910515.1_SRR11489782_bin.75_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945910515.1_SRR11489782_bin.75_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945910515.1_SRR11489782_bin.75_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 00:35:40,401] [INFO] Task succeeded: fastANI
[2023-06-08 00:35:40,402] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg662666a9-35bd-486f-97bc-2f9f4cd7189e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 00:35:40,402] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg662666a9-35bd-486f-97bc-2f9f4cd7189e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 00:35:40,409] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2023-06-08 00:35:40,409] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-08 00:35:40,409] [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
Megasphaera elsdenii	strain=DSM 20460	GCA_000283495.2	907	907	type	True	97.9559	667	810	95	conclusive
Megasphaera elsdenii	strain=ATCC 25940	GCA_003010495.1	907	907	type	True	97.9124	671	810	95	conclusive
Megasphaera massiliensis	strain=NP3	GCA_000455225.1	1232428	1232428	suspected-type	True	82.2783	502	810	95	below_threshold
Megasphaera stantonii	strain=AJH120	GCA_003030445.1	2144175	2144175	type	True	79.6202	331	810	95	below_threshold
Megasphaera stantonii	strain=AJH120	GCA_003367905.1	2144175	2144175	type	True	79.6121	338	810	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 00:35:40,412] [INFO] DFAST Taxonomy check result was written to GCA_945910515.1_SRR11489782_bin.75_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 00:35:40,412] [INFO] ===== Taxonomy check completed =====
[2023-06-08 00:35:40,413] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 00:35:40,413] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg662666a9-35bd-486f-97bc-2f9f4cd7189e/dqc_reference/checkm_data
[2023-06-08 00:35:40,414] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 00:35:40,446] [INFO] Task started: CheckM
[2023-06-08 00:35:40,446] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945910515.1_SRR11489782_bin.75_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945910515.1_SRR11489782_bin.75_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945910515.1_SRR11489782_bin.75_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 00:36:06,905] [INFO] Task succeeded: CheckM
[2023-06-08 00:36:06,906] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-08 00:36:06,938] [INFO] ===== Completeness check finished =====
[2023-06-08 00:36:06,939] [INFO] ===== Start GTDB Search =====
[2023-06-08 00:36:06,939] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945910515.1_SRR11489782_bin.75_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 00:36:06,940] [INFO] Task started: Blastn
[2023-06-08 00:36:06,940] [INFO] Running command: blastn -query GCA_945910515.1_SRR11489782_bin.75_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg662666a9-35bd-486f-97bc-2f9f4cd7189e/dqc_reference/reference_markers_gtdb.fasta -out GCA_945910515.1_SRR11489782_bin.75_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:36:07,835] [INFO] Task succeeded: Blastn
[2023-06-08 00:36:07,839] [INFO] Selected 7 target genomes.
[2023-06-08 00:36:07,839] [INFO] Target genome list was writen to GCA_945910515.1_SRR11489782_bin.75_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 00:36:07,840] [INFO] Task started: fastANI
[2023-06-08 00:36:07,840] [INFO] Running command: fastANI --query /var/lib/cwl/stg00b06a50-117b-4371-859f-19b55086e921/GCA_945910515.1_SRR11489782_bin.75_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945910515.1_SRR11489782_bin.75_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945910515.1_SRR11489782_bin.75_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 00:36:12,065] [INFO] Task succeeded: fastANI
[2023-06-08 00:36:12,079] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 00:36:12,079] [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
GCF_003010495.1	s__Megasphaera elsdenii	97.9124	671	810	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	98.27	97.55	0.90	0.81	29	conclusive
GCF_000417505.1	s__Megasphaera sp000417505	90.8762	640	810	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.18	97.65	0.90	0.81	11	-
GCA_902388315.1	s__Megasphaera sp902388315	90.269	472	810	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.43	99.12	0.87	0.82	3	-
GCA_900548635.1	s__Megasphaera sp900548635	88.1382	433	810	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.28	98.56	0.89	0.79	3	-
GCF_001546855.1	s__Megasphaera sp001546855	82.5592	488	810	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.96	99.94	0.97	0.94	9	-
GCA_900539295.1	s__Megasphaera sp900539295	82.5241	483	810	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002319965.1	s__Megasphaera sp002319965	82.3604	406	810	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	98.41	98.03	0.89	0.89	4	-
--------------------------------------------------------------------------------
[2023-06-08 00:36:12,081] [INFO] GTDB search result was written to GCA_945910515.1_SRR11489782_bin.75_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 00:36:12,082] [INFO] ===== GTDB Search completed =====
[2023-06-08 00:36:12,087] [INFO] DFAST_QC result json was written to GCA_945910515.1_SRR11489782_bin.75_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 00:36:12,087] [INFO] DFAST_QC completed!
[2023-06-08 00:36:12,087] [INFO] Total running time: 0h0m46s