[2024-01-24 15:18:26,346] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:26,348] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:26,348] [INFO] DQC Reference Directory: /var/lib/cwl/stg5372e7ff-f38d-4d59-87be-0a9d575e91f1/dqc_reference
[2024-01-24 15:18:27,688] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:27,689] [INFO] Task started: Prodigal
[2024-01-24 15:18:27,689] [INFO] Running command: gunzip -c /var/lib/cwl/stg19578af5-97c9-4f06-a281-b4c2437ba2f5/GCF_902375645.1_MGYG-HGUT-01515_genomic.fna.gz | prodigal -d GCF_902375645.1_MGYG-HGUT-01515_genomic.fna/cds.fna -a GCF_902375645.1_MGYG-HGUT-01515_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:31,351] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:31,352] [INFO] Task started: HMMsearch
[2024-01-24 15:18:31,352] [INFO] Running command: hmmsearch --tblout GCF_902375645.1_MGYG-HGUT-01515_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5372e7ff-f38d-4d59-87be-0a9d575e91f1/dqc_reference/reference_markers.hmm GCF_902375645.1_MGYG-HGUT-01515_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:31,645] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:31,646] [INFO] Found 6/6 markers.
[2024-01-24 15:18:31,670] [INFO] Query marker FASTA was written to GCF_902375645.1_MGYG-HGUT-01515_genomic.fna/markers.fasta
[2024-01-24 15:18:31,671] [INFO] Task started: Blastn
[2024-01-24 15:18:31,671] [INFO] Running command: blastn -query GCF_902375645.1_MGYG-HGUT-01515_genomic.fna/markers.fasta -db /var/lib/cwl/stg5372e7ff-f38d-4d59-87be-0a9d575e91f1/dqc_reference/reference_markers.fasta -out GCF_902375645.1_MGYG-HGUT-01515_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:32,785] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:32,791] [INFO] Selected 15 target genomes.
[2024-01-24 15:18:32,792] [INFO] Target genome list was writen to GCF_902375645.1_MGYG-HGUT-01515_genomic.fna/target_genomes.txt
[2024-01-24 15:18:32,880] [INFO] Task started: fastANI
[2024-01-24 15:18:32,881] [INFO] Running command: fastANI --query /var/lib/cwl/stg19578af5-97c9-4f06-a281-b4c2437ba2f5/GCF_902375645.1_MGYG-HGUT-01515_genomic.fna.gz --refList GCF_902375645.1_MGYG-HGUT-01515_genomic.fna/target_genomes.txt --output GCF_902375645.1_MGYG-HGUT-01515_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:39,991] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:39,991] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5372e7ff-f38d-4d59-87be-0a9d575e91f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:39,991] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5372e7ff-f38d-4d59-87be-0a9d575e91f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:39,998] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:18:39,998] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:39,998] [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
Lagierella massiliensis	strain=Marseille-P2012	GCA_902375645.1	1689303	1689303	type	True	100.0	605	609	95	conclusive
Lagierella massiliensis	strain=SIT14	GCA_001407835.1	1689303	1689303	type	True	100.0	604	609	95	conclusive
Finegoldia magna	strain=FDAARGOS_1593	GCA_020731325.1	1260	1260	suspected-type	True	79.6967	66	609	95	below_threshold
Finegoldia magna	strain=DSM 20470	GCA_003182075.1	1260	1260	suspected-type	True	78.736	56	609	95	below_threshold
Miniphocaeibacter halophilus	strain=AMB_01	GCA_016458825.1	2931922	2931922	type	True	77.751	77	609	95	below_threshold
Miniphocaeibacter massiliensis	strain=Marseille-P4678	GCA_900232905.1	2041841	2041841	type	True	77.1155	70	609	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:40,000] [INFO] DFAST Taxonomy check result was written to GCF_902375645.1_MGYG-HGUT-01515_genomic.fna/tc_result.tsv
[2024-01-24 15:18:40,000] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:40,001] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:40,001] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5372e7ff-f38d-4d59-87be-0a9d575e91f1/dqc_reference/checkm_data
[2024-01-24 15:18:40,002] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:40,024] [INFO] Task started: CheckM
[2024-01-24 15:18:40,024] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902375645.1_MGYG-HGUT-01515_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902375645.1_MGYG-HGUT-01515_genomic.fna/checkm_input GCF_902375645.1_MGYG-HGUT-01515_genomic.fna/checkm_result
[2024-01-24 15:18:58,782] [INFO] Task succeeded: CheckM
[2024-01-24 15:18:58,783] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:18:58,804] [INFO] ===== Completeness check finished =====
[2024-01-24 15:18:58,804] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:18:58,805] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902375645.1_MGYG-HGUT-01515_genomic.fna/markers.fasta)
[2024-01-24 15:18:58,805] [INFO] Task started: Blastn
[2024-01-24 15:18:58,805] [INFO] Running command: blastn -query GCF_902375645.1_MGYG-HGUT-01515_genomic.fna/markers.fasta -db /var/lib/cwl/stg5372e7ff-f38d-4d59-87be-0a9d575e91f1/dqc_reference/reference_markers_gtdb.fasta -out GCF_902375645.1_MGYG-HGUT-01515_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:59,646] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:59,649] [INFO] Selected 19 target genomes.
[2024-01-24 15:18:59,649] [INFO] Target genome list was writen to GCF_902375645.1_MGYG-HGUT-01515_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:18:59,664] [INFO] Task started: fastANI
[2024-01-24 15:18:59,665] [INFO] Running command: fastANI --query /var/lib/cwl/stg19578af5-97c9-4f06-a281-b4c2437ba2f5/GCF_902375645.1_MGYG-HGUT-01515_genomic.fna.gz --refList GCF_902375645.1_MGYG-HGUT-01515_genomic.fna/target_genomes_gtdb.txt --output GCF_902375645.1_MGYG-HGUT-01515_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:07,123] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:07,130] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:07,131] [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_001407835.1	s__Lagierella massiliensis	100.0	604	609	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Lagierella	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_000159695.1	s__Finegoldia magna_F	79.2361	67	609	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Finegoldia	95.0	95.41	95.07	0.87	0.83	5	-
GCA_910589545.1	s__Finegoldia sp910589545	78.4697	55	609	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Finegoldia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016458825.1	s__Miniphocibacter sp016458825	77.9384	77	609	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Miniphocibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900766215.1	s__Finegoldia sp900766215	77.3839	51	609	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Finegoldia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900232905.1	s__Miniphocibacter massiliensis	77.1341	71	609	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Miniphocibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012841535.1	s__Miniphocibacter sp012841535	76.8464	79	609	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Miniphocibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:07,135] [INFO] GTDB search result was written to GCF_902375645.1_MGYG-HGUT-01515_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:07,135] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:07,138] [INFO] DFAST_QC result json was written to GCF_902375645.1_MGYG-HGUT-01515_genomic.fna/dqc_result.json
[2024-01-24 15:19:07,138] [INFO] DFAST_QC completed!
[2024-01-24 15:19:07,138] [INFO] Total running time: 0h0m41s