[2023-06-18 17:32:28,630] [INFO] DFAST_QC pipeline started.
[2023-06-18 17:32:28,632] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 17:32:28,632] [INFO] DQC Reference Directory: /var/lib/cwl/stge37aa91f-9328-47d9-bb90-1cb393cbedd9/dqc_reference
[2023-06-18 17:32:29,780] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 17:32:29,781] [INFO] Task started: Prodigal
[2023-06-18 17:32:29,781] [INFO] Running command: gunzip -c /var/lib/cwl/stg2f5a0e8d-c34f-4e85-87dd-ee441958d1a6/GCA_018367555.1_ASM1836755v1_genomic.fna.gz | prodigal -d GCA_018367555.1_ASM1836755v1_genomic.fna/cds.fna -a GCA_018367555.1_ASM1836755v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 17:32:33,723] [INFO] Task succeeded: Prodigal
[2023-06-18 17:32:33,723] [INFO] Task started: HMMsearch
[2023-06-18 17:32:33,723] [INFO] Running command: hmmsearch --tblout GCA_018367555.1_ASM1836755v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge37aa91f-9328-47d9-bb90-1cb393cbedd9/dqc_reference/reference_markers.hmm GCA_018367555.1_ASM1836755v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 17:32:33,891] [INFO] Task succeeded: HMMsearch
[2023-06-18 17:32:33,892] [INFO] Found 6/6 markers.
[2023-06-18 17:32:33,915] [INFO] Query marker FASTA was written to GCA_018367555.1_ASM1836755v1_genomic.fna/markers.fasta
[2023-06-18 17:32:33,915] [INFO] Task started: Blastn
[2023-06-18 17:32:33,916] [INFO] Running command: blastn -query GCA_018367555.1_ASM1836755v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge37aa91f-9328-47d9-bb90-1cb393cbedd9/dqc_reference/reference_markers.fasta -out GCA_018367555.1_ASM1836755v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:32:34,479] [INFO] Task succeeded: Blastn
[2023-06-18 17:32:34,485] [INFO] Selected 14 target genomes.
[2023-06-18 17:32:34,485] [INFO] Target genome list was writen to GCA_018367555.1_ASM1836755v1_genomic.fna/target_genomes.txt
[2023-06-18 17:32:34,487] [INFO] Task started: fastANI
[2023-06-18 17:32:34,487] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f5a0e8d-c34f-4e85-87dd-ee441958d1a6/GCA_018367555.1_ASM1836755v1_genomic.fna.gz --refList GCA_018367555.1_ASM1836755v1_genomic.fna/target_genomes.txt --output GCA_018367555.1_ASM1836755v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 17:32:39,457] [INFO] Task succeeded: fastANI
[2023-06-18 17:32:39,458] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge37aa91f-9328-47d9-bb90-1cb393cbedd9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 17:32:39,458] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge37aa91f-9328-47d9-bb90-1cb393cbedd9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 17:32:39,466] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 17:32:39,467] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 17:32:39,467] [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	77.7733	155	542	95	below_threshold
Megasphaera massiliensis	strain=NP3	GCA_000455225.1	1232428	1232428	suspected-type	True	77.6221	63	542	95	below_threshold
'Megasphaera vaginalis' Bordigoni et al. 2020	strain=Marseille-P4857	GCA_900240295.1	2045301	2045301	type	True	77.2783	81	542	95	below_threshold
Megasphaera stantonii	strain=AJH120	GCA_003367905.1	2144175	2144175	type	True	77.0446	62	542	95	below_threshold
Megasphaera stantonii	strain=AJH120	GCA_003030445.1	2144175	2144175	type	True	77.0129	62	542	95	below_threshold
Megasphaera elsdenii	strain=DSM 20460	GCA_000283495.2	907	907	type	True	76.9987	56	542	95	below_threshold
Megasphaera elsdenii	strain=ATCC 25940	GCA_003010495.1	907	907	type	True	76.9933	58	542	95	below_threshold
Megasphaera lornae	strain=UPII 199-6	GCA_000214495.2	1000568	1000568	type	True	76.7051	61	542	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 17:32:39,470] [INFO] DFAST Taxonomy check result was written to GCA_018367555.1_ASM1836755v1_genomic.fna/tc_result.tsv
[2023-06-18 17:32:39,471] [INFO] ===== Taxonomy check completed =====
[2023-06-18 17:32:39,471] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 17:32:39,471] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge37aa91f-9328-47d9-bb90-1cb393cbedd9/dqc_reference/checkm_data
[2023-06-18 17:32:39,472] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 17:32:39,492] [INFO] Task started: CheckM
[2023-06-18 17:32:39,493] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018367555.1_ASM1836755v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018367555.1_ASM1836755v1_genomic.fna/checkm_input GCA_018367555.1_ASM1836755v1_genomic.fna/checkm_result
[2023-06-18 17:32:57,356] [INFO] Task succeeded: CheckM
[2023-06-18 17:32:57,357] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 17:32:57,381] [INFO] ===== Completeness check finished =====
[2023-06-18 17:32:57,382] [INFO] ===== Start GTDB Search =====
[2023-06-18 17:32:57,382] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018367555.1_ASM1836755v1_genomic.fna/markers.fasta)
[2023-06-18 17:32:57,382] [INFO] Task started: Blastn
[2023-06-18 17:32:57,382] [INFO] Running command: blastn -query GCA_018367555.1_ASM1836755v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge37aa91f-9328-47d9-bb90-1cb393cbedd9/dqc_reference/reference_markers_gtdb.fasta -out GCA_018367555.1_ASM1836755v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:32:58,164] [INFO] Task succeeded: Blastn
[2023-06-18 17:32:58,170] [INFO] Selected 20 target genomes.
[2023-06-18 17:32:58,170] [INFO] Target genome list was writen to GCA_018367555.1_ASM1836755v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 17:32:58,206] [INFO] Task started: fastANI
[2023-06-18 17:32:58,206] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f5a0e8d-c34f-4e85-87dd-ee441958d1a6/GCA_018367555.1_ASM1836755v1_genomic.fna.gz --refList GCA_018367555.1_ASM1836755v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018367555.1_ASM1836755v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 17:33:04,799] [INFO] Task succeeded: fastANI
[2023-06-18 17:33:04,809] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 17:33:04,810] [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_000165735.1	s__Anaeroglobus micronuciformis	97.8073	508	542	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Anaeroglobus	95.0	97.87	97.00	0.95	0.90	14	conclusive
GCF_900095855.1	s__Anaeroglobus massiliensis	77.7708	155	542	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Anaeroglobus	95.0	99.40	98.79	0.98	0.97	3	-
GCF_000455225.1	s__Megasphaera massiliensis	77.6221	63	542	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_003467125.1	s__Caecibacter sp003467125	77.6014	51	542	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Caecibacter	95.0	98.80	97.67	0.92	0.89	5	-
GCA_002319965.1	s__Megasphaera sp002319965	77.3861	51	542	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	98.41	98.03	0.89	0.89	4	-
GCF_900240295.1	s__Anaeroglobus vaginalis	77.2783	81	542	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Anaeroglobus	95.0	99.10	99.10	0.91	0.91	2	-
GCF_001546855.1	s__Megasphaera sp001546855	77.2164	58	542	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_003367905.1	s__Megasphaera stantonii	77.0886	61	542	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	97.46	96.44	0.91	0.87	8	-
GCF_003010495.1	s__Megasphaera elsdenii	76.9933	58	542	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_000214495.1	s__Megasphaera lornae	76.7051	61	542	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.01	98.81	0.95	0.94	5	-
--------------------------------------------------------------------------------
[2023-06-18 17:33:04,813] [INFO] GTDB search result was written to GCA_018367555.1_ASM1836755v1_genomic.fna/result_gtdb.tsv
[2023-06-18 17:33:04,814] [INFO] ===== GTDB Search completed =====
[2023-06-18 17:33:04,817] [INFO] DFAST_QC result json was written to GCA_018367555.1_ASM1836755v1_genomic.fna/dqc_result.json
[2023-06-18 17:33:04,817] [INFO] DFAST_QC completed!
[2023-06-18 17:33:04,817] [INFO] Total running time: 0h0m36s