[2024-01-24 15:02:37,314] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:37,315] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:37,316] [INFO] DQC Reference Directory: /var/lib/cwl/stg90310288-2584-4cf5-b0fb-7e3fdbae0e44/dqc_reference
[2024-01-24 15:02:38,751] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:38,752] [INFO] Task started: Prodigal
[2024-01-24 15:02:38,753] [INFO] Running command: gunzip -c /var/lib/cwl/stg5eacceca-a6da-4303-ada8-45da776d4c57/GCF_014287795.1_ASM1428779v1_genomic.fna.gz | prodigal -d GCF_014287795.1_ASM1428779v1_genomic.fna/cds.fna -a GCF_014287795.1_ASM1428779v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:47,624] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:47,625] [INFO] Task started: HMMsearch
[2024-01-24 15:02:47,625] [INFO] Running command: hmmsearch --tblout GCF_014287795.1_ASM1428779v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90310288-2584-4cf5-b0fb-7e3fdbae0e44/dqc_reference/reference_markers.hmm GCF_014287795.1_ASM1428779v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:47,926] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:47,936] [INFO] Found 6/6 markers.
[2024-01-24 15:02:47,993] [INFO] Query marker FASTA was written to GCF_014287795.1_ASM1428779v1_genomic.fna/markers.fasta
[2024-01-24 15:02:47,994] [INFO] Task started: Blastn
[2024-01-24 15:02:47,994] [INFO] Running command: blastn -query GCF_014287795.1_ASM1428779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90310288-2584-4cf5-b0fb-7e3fdbae0e44/dqc_reference/reference_markers.fasta -out GCF_014287795.1_ASM1428779v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:48,633] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:48,637] [INFO] Selected 15 target genomes.
[2024-01-24 15:02:48,637] [INFO] Target genome list was writen to GCF_014287795.1_ASM1428779v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:48,651] [INFO] Task started: fastANI
[2024-01-24 15:02:48,651] [INFO] Running command: fastANI --query /var/lib/cwl/stg5eacceca-a6da-4303-ada8-45da776d4c57/GCF_014287795.1_ASM1428779v1_genomic.fna.gz --refList GCF_014287795.1_ASM1428779v1_genomic.fna/target_genomes.txt --output GCF_014287795.1_ASM1428779v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:57,240] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:57,240] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90310288-2584-4cf5-b0fb-7e3fdbae0e44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:57,240] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90310288-2584-4cf5-b0fb-7e3fdbae0e44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:57,248] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:02:57,248] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:02:57,248] [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
Christensenella minuta	strain=DSM 22607	GCA_001652705.1	626937	626937	type	True	83.9181	579	1002	95	below_threshold
Christensenella minuta	strain=DSM 22607	GCA_003628755.1	626937	626937	type	True	83.7943	599	1002	95	below_threshold
Christensenella minuta	strain=DSM 22607	GCA_001571425.1	626937	626937	type	True	83.7419	584	1002	95	below_threshold
Christensenella minuta	strain=DSM 22607	GCA_001678855.1	626937	626937	type	True	83.6872	591	1002	95	below_threshold
Christensenella intestinihominis	strain=AF73-05CM02	GCA_001678845.1	1851429	1851429	type	True	81.2683	529	1002	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:57,250] [INFO] DFAST Taxonomy check result was written to GCF_014287795.1_ASM1428779v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:57,251] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:57,251] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:57,252] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90310288-2584-4cf5-b0fb-7e3fdbae0e44/dqc_reference/checkm_data
[2024-01-24 15:02:57,255] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:57,290] [INFO] Task started: CheckM
[2024-01-24 15:02:57,291] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014287795.1_ASM1428779v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014287795.1_ASM1428779v1_genomic.fna/checkm_input GCF_014287795.1_ASM1428779v1_genomic.fna/checkm_result
[2024-01-24 15:03:32,132] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:32,134] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:32,170] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:32,171] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:32,171] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014287795.1_ASM1428779v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:32,171] [INFO] Task started: Blastn
[2024-01-24 15:03:32,171] [INFO] Running command: blastn -query GCF_014287795.1_ASM1428779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90310288-2584-4cf5-b0fb-7e3fdbae0e44/dqc_reference/reference_markers_gtdb.fasta -out GCF_014287795.1_ASM1428779v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:33,050] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:33,054] [INFO] Selected 14 target genomes.
[2024-01-24 15:03:33,054] [INFO] Target genome list was writen to GCF_014287795.1_ASM1428779v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:33,066] [INFO] Task started: fastANI
[2024-01-24 15:03:33,066] [INFO] Running command: fastANI --query /var/lib/cwl/stg5eacceca-a6da-4303-ada8-45da776d4c57/GCF_014287795.1_ASM1428779v1_genomic.fna.gz --refList GCF_014287795.1_ASM1428779v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014287795.1_ASM1428779v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:42,358] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:42,370] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:42,370] [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_014287795.1	s__Christensenella sp014287795	100.0	1002	1002	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Christensenellaceae;g__Christensenella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003628755.1	s__Christensenella minuta	83.8095	597	1002	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Christensenellaceae;g__Christensenella	95.0	99.90	99.68	0.97	0.85	7	-
GCF_001678845.1	s__Christensenella intestinihominis	81.2808	528	1002	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Christensenellaceae;g__Christensenella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900155415.1	s__Christensenella massiliensis	80.1	346	1002	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Christensenellaceae;g__Christensenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000981035.1	s__Christensenella hongkongensis	79.2208	244	1002	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Christensenellaceae;g__Christensenella	95.0	99.51	99.03	0.96	0.95	3	-
GCF_900087015.1	s__Christensenella timonensis	79.18	179	1002	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Christensenellaceae;g__Christensenella	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:03:42,372] [INFO] GTDB search result was written to GCF_014287795.1_ASM1428779v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:42,373] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:42,375] [INFO] DFAST_QC result json was written to GCF_014287795.1_ASM1428779v1_genomic.fna/dqc_result.json
[2024-01-24 15:03:42,375] [INFO] DFAST_QC completed!
[2024-01-24 15:03:42,375] [INFO] Total running time: 0h1m5s