[2024-01-25 19:38:35,607] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:38:35,608] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:38:35,608] [INFO] DQC Reference Directory: /var/lib/cwl/stgb55cf918-8832-48e7-9354-8861ed82c47c/dqc_reference
[2024-01-25 19:38:36,758] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:38:36,759] [INFO] Task started: Prodigal
[2024-01-25 19:38:36,759] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e6f6edf-c63d-4791-8783-3af8448c2173/GCF_900240295.1_PRJEB23091_genomic.fna.gz | prodigal -d GCF_900240295.1_PRJEB23091_genomic.fna/cds.fna -a GCF_900240295.1_PRJEB23091_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:38:42,161] [INFO] Task succeeded: Prodigal
[2024-01-25 19:38:42,161] [INFO] Task started: HMMsearch
[2024-01-25 19:38:42,161] [INFO] Running command: hmmsearch --tblout GCF_900240295.1_PRJEB23091_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb55cf918-8832-48e7-9354-8861ed82c47c/dqc_reference/reference_markers.hmm GCF_900240295.1_PRJEB23091_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:38:42,340] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:38:42,341] [INFO] Found 6/6 markers.
[2024-01-25 19:38:42,362] [INFO] Query marker FASTA was written to GCF_900240295.1_PRJEB23091_genomic.fna/markers.fasta
[2024-01-25 19:38:42,363] [INFO] Task started: Blastn
[2024-01-25 19:38:42,363] [INFO] Running command: blastn -query GCF_900240295.1_PRJEB23091_genomic.fna/markers.fasta -db /var/lib/cwl/stgb55cf918-8832-48e7-9354-8861ed82c47c/dqc_reference/reference_markers.fasta -out GCF_900240295.1_PRJEB23091_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:38:42,908] [INFO] Task succeeded: Blastn
[2024-01-25 19:38:42,911] [INFO] Selected 17 target genomes.
[2024-01-25 19:38:42,911] [INFO] Target genome list was writen to GCF_900240295.1_PRJEB23091_genomic.fna/target_genomes.txt
[2024-01-25 19:38:42,916] [INFO] Task started: fastANI
[2024-01-25 19:38:42,917] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e6f6edf-c63d-4791-8783-3af8448c2173/GCF_900240295.1_PRJEB23091_genomic.fna.gz --refList GCF_900240295.1_PRJEB23091_genomic.fna/target_genomes.txt --output GCF_900240295.1_PRJEB23091_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:38:50,073] [INFO] Task succeeded: fastANI
[2024-01-25 19:38:50,074] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb55cf918-8832-48e7-9354-8861ed82c47c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:38:50,074] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb55cf918-8832-48e7-9354-8861ed82c47c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:38:50,081] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:38:50,081] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:38:50,081] [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 vaginalis' Bordigoni et al. 2020	strain=Marseille-P4857	GCA_900240295.1	2045301	2045301	type	True	100.0	725	726	95	conclusive
Megasphaera massiliensis	strain=NP3	GCA_000455225.1	1232428	1232428	suspected-type	True	78.2882	143	726	95	below_threshold
Megasphaera stantonii	strain=AJH120	GCA_003367905.1	2144175	2144175	type	True	77.8492	132	726	95	below_threshold
Megasphaera stantonii	strain=AJH120	GCA_003030445.1	2144175	2144175	type	True	77.8452	132	726	95	below_threshold
Megasphaera elsdenii	strain=ATCC 25940	GCA_003010495.1	907	907	type	True	77.5512	130	726	95	below_threshold
Megasphaera elsdenii	strain=DSM 20460	GCA_000283495.2	907	907	type	True	77.5095	128	726	95	below_threshold
Megasphaera lornae	strain=UPII 199-6	GCA_000214495.2	1000568	1000568	type	True	77.2519	75	726	95	below_threshold
Megasphaera cerevisiae	strain=DSM 20462	GCA_900167325.1	39029	39029	type	True	77.1595	107	726	95	below_threshold
Megasphaera cerevisiae	strain=DSM 20462	GCA_001045675.1	39029	39029	type	True	77.1464	104	726	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:38:50,085] [INFO] DFAST Taxonomy check result was written to GCF_900240295.1_PRJEB23091_genomic.fna/tc_result.tsv
[2024-01-25 19:38:50,086] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:38:50,086] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:38:50,086] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb55cf918-8832-48e7-9354-8861ed82c47c/dqc_reference/checkm_data
[2024-01-25 19:38:50,087] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:38:50,111] [INFO] Task started: CheckM
[2024-01-25 19:38:50,111] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900240295.1_PRJEB23091_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900240295.1_PRJEB23091_genomic.fna/checkm_input GCF_900240295.1_PRJEB23091_genomic.fna/checkm_result
[2024-01-25 19:39:10,532] [INFO] Task succeeded: CheckM
[2024-01-25 19:39:10,534] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:39:10,549] [INFO] ===== Completeness check finished =====
[2024-01-25 19:39:10,549] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:39:10,549] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900240295.1_PRJEB23091_genomic.fna/markers.fasta)
[2024-01-25 19:39:10,549] [INFO] Task started: Blastn
[2024-01-25 19:39:10,550] [INFO] Running command: blastn -query GCF_900240295.1_PRJEB23091_genomic.fna/markers.fasta -db /var/lib/cwl/stgb55cf918-8832-48e7-9354-8861ed82c47c/dqc_reference/reference_markers_gtdb.fasta -out GCF_900240295.1_PRJEB23091_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:39:11,334] [INFO] Task succeeded: Blastn
[2024-01-25 19:39:11,337] [INFO] Selected 18 target genomes.
[2024-01-25 19:39:11,337] [INFO] Target genome list was writen to GCF_900240295.1_PRJEB23091_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:39:11,353] [INFO] Task started: fastANI
[2024-01-25 19:39:11,353] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e6f6edf-c63d-4791-8783-3af8448c2173/GCF_900240295.1_PRJEB23091_genomic.fna.gz --refList GCF_900240295.1_PRJEB23091_genomic.fna/target_genomes_gtdb.txt --output GCF_900240295.1_PRJEB23091_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:39:18,362] [INFO] Task succeeded: fastANI
[2024-01-25 19:39:18,370] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:39:18,371] [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_900240295.1	s__Anaeroglobus vaginalis	100.0	725	726	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Anaeroglobus	95.0	99.10	99.10	0.91	0.91	2	conclusive
GCF_003467125.1	s__Caecibacter sp003467125	79.366	127	726	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Caecibacter	95.0	98.80	97.67	0.92	0.89	5	-
GCF_003367905.1	s__Megasphaera stantonii	77.8422	133	726	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	97.46	96.44	0.91	0.87	8	-
GCA_900095875.1	s__Caecibacter massiliensis	77.7973	131	726	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Caecibacter	95.0	98.76	97.64	0.92	0.86	18	-
GCA_902388315.1	s__Megasphaera sp902388315	77.7552	115	726	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.43	99.12	0.87	0.82	3	-
GCF_003010495.1	s__Megasphaera elsdenii	77.5512	130	726	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	98.27	97.55	0.90	0.81	29	-
GCF_000417505.1	s__Megasphaera sp000417505	77.4893	127	726	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.18	97.65	0.90	0.81	11	-
GCF_001546855.1	s__Megasphaera sp001546855	77.4804	109	726	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.96	99.94	0.97	0.94	9	-
GCF_001045675.1	s__Megasphaera cerevisiae	77.1674	103	726	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.73	99.50	0.95	0.92	3	-
GCA_900539295.1	s__Megasphaera sp900539295	77.1112	126	726	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_900540735.1	s__Megasphaera sp900540735	77.0326	83	726	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.96	99.96	0.96	0.96	2	-
GCA_900548635.1	s__Megasphaera sp900548635	76.8496	110	726	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.28	98.56	0.89	0.79	3	-
GCA_900554215.1	s__Megasphaera sp900554215	76.7434	92	726	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	95.76	95.76	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:39:18,372] [INFO] GTDB search result was written to GCF_900240295.1_PRJEB23091_genomic.fna/result_gtdb.tsv
[2024-01-25 19:39:18,373] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:39:18,376] [INFO] DFAST_QC result json was written to GCF_900240295.1_PRJEB23091_genomic.fna/dqc_result.json
[2024-01-25 19:39:18,376] [INFO] DFAST_QC completed!
[2024-01-25 19:39:18,376] [INFO] Total running time: 0h0m43s