[2024-01-24 11:27:19,331] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:27:19,333] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:27:19,333] [INFO] DQC Reference Directory: /var/lib/cwl/stg21e4f300-1715-4e5d-9f0e-3de1ed5ed002/dqc_reference
[2024-01-24 11:27:21,855] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:27:21,855] [INFO] Task started: Prodigal
[2024-01-24 11:27:21,856] [INFO] Running command: gunzip -c /var/lib/cwl/stgba1598e5-a64b-4364-848a-e7466f3a4014/GCF_900095855.1_PRJEB15308_genomic.fna.gz | prodigal -d GCF_900095855.1_PRJEB15308_genomic.fna/cds.fna -a GCF_900095855.1_PRJEB15308_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:26,562] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:26,563] [INFO] Task started: HMMsearch
[2024-01-24 11:27:26,563] [INFO] Running command: hmmsearch --tblout GCF_900095855.1_PRJEB15308_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg21e4f300-1715-4e5d-9f0e-3de1ed5ed002/dqc_reference/reference_markers.hmm GCF_900095855.1_PRJEB15308_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:26,788] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:26,790] [INFO] Found 6/6 markers.
[2024-01-24 11:27:26,809] [INFO] Query marker FASTA was written to GCF_900095855.1_PRJEB15308_genomic.fna/markers.fasta
[2024-01-24 11:27:26,810] [INFO] Task started: Blastn
[2024-01-24 11:27:26,810] [INFO] Running command: blastn -query GCF_900095855.1_PRJEB15308_genomic.fna/markers.fasta -db /var/lib/cwl/stg21e4f300-1715-4e5d-9f0e-3de1ed5ed002/dqc_reference/reference_markers.fasta -out GCF_900095855.1_PRJEB15308_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:27,403] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:27,407] [INFO] Selected 18 target genomes.
[2024-01-24 11:27:27,408] [INFO] Target genome list was writen to GCF_900095855.1_PRJEB15308_genomic.fna/target_genomes.txt
[2024-01-24 11:27:27,455] [INFO] Task started: fastANI
[2024-01-24 11:27:27,456] [INFO] Running command: fastANI --query /var/lib/cwl/stgba1598e5-a64b-4364-848a-e7466f3a4014/GCF_900095855.1_PRJEB15308_genomic.fna.gz --refList GCF_900095855.1_PRJEB15308_genomic.fna/target_genomes.txt --output GCF_900095855.1_PRJEB15308_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:36,576] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:36,576] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg21e4f300-1715-4e5d-9f0e-3de1ed5ed002/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:36,577] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg21e4f300-1715-4e5d-9f0e-3de1ed5ed002/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:36,583] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:36,584] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:36,584] [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
Colibacter massiliensis	strain=Marseille-P2911	GCA_900095855.1	1852379	1852379	type	True	100.0	571	571	95	conclusive
Megasphaera elsdenii	strain=ATCC 25940	GCA_003010495.1	907	907	type	True	77.5706	104	571	95	below_threshold
Megasphaera elsdenii	strain=DSM 20460	GCA_000283495.2	907	907	type	True	77.5445	108	571	95	below_threshold
Megasphaera massiliensis	strain=NP3	GCA_000455225.1	1232428	1232428	suspected-type	True	77.4273	100	571	95	below_threshold
Megasphaera cerevisiae	strain=DSM 20462	GCA_001045675.1	39029	39029	type	True	77.192	79	571	95	below_threshold
Megasphaera cerevisiae	strain=DSM 20462	GCA_900167325.1	39029	39029	type	True	77.1726	77	571	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:36,585] [INFO] DFAST Taxonomy check result was written to GCF_900095855.1_PRJEB15308_genomic.fna/tc_result.tsv
[2024-01-24 11:27:36,586] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:36,586] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:36,586] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg21e4f300-1715-4e5d-9f0e-3de1ed5ed002/dqc_reference/checkm_data
[2024-01-24 11:27:36,588] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:36,607] [INFO] Task started: CheckM
[2024-01-24 11:27:36,607] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900095855.1_PRJEB15308_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900095855.1_PRJEB15308_genomic.fna/checkm_input GCF_900095855.1_PRJEB15308_genomic.fna/checkm_result
[2024-01-24 11:27:56,813] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:56,814] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:56,831] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:56,831] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:56,832] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900095855.1_PRJEB15308_genomic.fna/markers.fasta)
[2024-01-24 11:27:56,832] [INFO] Task started: Blastn
[2024-01-24 11:27:56,832] [INFO] Running command: blastn -query GCF_900095855.1_PRJEB15308_genomic.fna/markers.fasta -db /var/lib/cwl/stg21e4f300-1715-4e5d-9f0e-3de1ed5ed002/dqc_reference/reference_markers_gtdb.fasta -out GCF_900095855.1_PRJEB15308_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:57,675] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:57,680] [INFO] Selected 21 target genomes.
[2024-01-24 11:27:57,680] [INFO] Target genome list was writen to GCF_900095855.1_PRJEB15308_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:57,713] [INFO] Task started: fastANI
[2024-01-24 11:27:57,713] [INFO] Running command: fastANI --query /var/lib/cwl/stgba1598e5-a64b-4364-848a-e7466f3a4014/GCF_900095855.1_PRJEB15308_genomic.fna.gz --refList GCF_900095855.1_PRJEB15308_genomic.fna/target_genomes_gtdb.txt --output GCF_900095855.1_PRJEB15308_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:06,286] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:06,300] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:06,300] [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_900095855.1	s__Anaeroglobus massiliensis	100.0	571	571	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Anaeroglobus	95.0	99.40	98.79	0.98	0.97	3	conclusive
GCF_000165735.1	s__Anaeroglobus micronuciformis	78.2589	161	571	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Anaeroglobus	95.0	97.87	97.00	0.95	0.90	14	-
GCF_000239275.1	s__Anaeroglobus geminatus	78.0891	221	571	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Anaeroglobus	95.0	98.83	98.46	0.93	0.92	3	-
GCF_003010495.1	s__Megasphaera elsdenii	77.7105	105	571	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_000455225.1	s__Megasphaera massiliensis	77.4273	100	571	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	98.41	96.06	0.94	0.88	8	-
GCF_014269395.1	s__Caecibacter hominis	77.2367	75	571	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Caecibacter	95.0	99.84	99.81	0.96	0.95	4	-
GCF_000417505.1	s__Megasphaera sp000417505	77.0905	109	571	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_900539295.1	s__Megasphaera sp900539295	76.9694	98	571	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_900548635.1	s__Megasphaera sp900548635	76.8708	91	571	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	76.827	83	571	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	95.76	95.76	0.83	0.83	2	-
GCA_902388315.1	s__Megasphaera sp902388315	76.7019	92	571	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_002431345.1	s__Megasphaera sp002431345	76.6908	62	571	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.44	99.22	0.90	0.87	5	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:06,302] [INFO] GTDB search result was written to GCF_900095855.1_PRJEB15308_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:06,302] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:06,305] [INFO] DFAST_QC result json was written to GCF_900095855.1_PRJEB15308_genomic.fna/dqc_result.json
[2024-01-24 11:28:06,306] [INFO] DFAST_QC completed!
[2024-01-24 11:28:06,306] [INFO] Total running time: 0h0m47s