[2024-01-24 11:26:38,852] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:38,855] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:38,855] [INFO] DQC Reference Directory: /var/lib/cwl/stgde6d6317-0951-4135-94a6-fd88ba58fdce/dqc_reference
[2024-01-24 11:26:40,198] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:40,199] [INFO] Task started: Prodigal
[2024-01-24 11:26:40,199] [INFO] Running command: gunzip -c /var/lib/cwl/stg24bc0f44-9100-4e7e-8e73-8c7243c9813d/GCF_015140235.1_ASM1514023v1_genomic.fna.gz | prodigal -d GCF_015140235.1_ASM1514023v1_genomic.fna/cds.fna -a GCF_015140235.1_ASM1514023v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:47,791] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:47,792] [INFO] Task started: HMMsearch
[2024-01-24 11:26:47,792] [INFO] Running command: hmmsearch --tblout GCF_015140235.1_ASM1514023v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde6d6317-0951-4135-94a6-fd88ba58fdce/dqc_reference/reference_markers.hmm GCF_015140235.1_ASM1514023v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:48,070] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:48,072] [INFO] Found 6/6 markers.
[2024-01-24 11:26:48,102] [INFO] Query marker FASTA was written to GCF_015140235.1_ASM1514023v1_genomic.fna/markers.fasta
[2024-01-24 11:26:48,103] [INFO] Task started: Blastn
[2024-01-24 11:26:48,103] [INFO] Running command: blastn -query GCF_015140235.1_ASM1514023v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde6d6317-0951-4135-94a6-fd88ba58fdce/dqc_reference/reference_markers.fasta -out GCF_015140235.1_ASM1514023v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:48,745] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:48,748] [INFO] Selected 18 target genomes.
[2024-01-24 11:26:48,748] [INFO] Target genome list was writen to GCF_015140235.1_ASM1514023v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:48,773] [INFO] Task started: fastANI
[2024-01-24 11:26:48,774] [INFO] Running command: fastANI --query /var/lib/cwl/stg24bc0f44-9100-4e7e-8e73-8c7243c9813d/GCF_015140235.1_ASM1514023v1_genomic.fna.gz --refList GCF_015140235.1_ASM1514023v1_genomic.fna/target_genomes.txt --output GCF_015140235.1_ASM1514023v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:57,696] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:57,697] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde6d6317-0951-4135-94a6-fd88ba58fdce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:57,697] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde6d6317-0951-4135-94a6-fd88ba58fdce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:57,703] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:57,703] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:57,703] [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
Solibaculum mannosilyticum	strain=12CBH8	GCA_015140235.1	2780922	2780922	type	True	100.0	847	847	95	conclusive
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	80.6267	56	847	95	below_threshold
Angelakisella massiliensis	strain=Marseille-P3217	GCA_900104675.1	1871018	1871018	type	True	80.2258	77	847	95	below_threshold
Fournierella massiliensis	strain=DSM 100451	GCA_004345265.1	1650663	1650663	type	True	79.298	71	847	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	79.2427	54	847	95	below_threshold
Ligaoa zhengdingensis	strain=NSJ-31	GCA_014384885.1	2763658	2763658	type	True	78.8379	68	847	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:57,708] [INFO] DFAST Taxonomy check result was written to GCF_015140235.1_ASM1514023v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:57,708] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:57,709] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:57,709] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde6d6317-0951-4135-94a6-fd88ba58fdce/dqc_reference/checkm_data
[2024-01-24 11:26:57,710] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:57,740] [INFO] Task started: CheckM
[2024-01-24 11:26:57,740] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015140235.1_ASM1514023v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015140235.1_ASM1514023v1_genomic.fna/checkm_input GCF_015140235.1_ASM1514023v1_genomic.fna/checkm_result
[2024-01-24 11:27:25,290] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:25,292] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:25,315] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:25,316] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:25,316] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015140235.1_ASM1514023v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:25,317] [INFO] Task started: Blastn
[2024-01-24 11:27:25,317] [INFO] Running command: blastn -query GCF_015140235.1_ASM1514023v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde6d6317-0951-4135-94a6-fd88ba58fdce/dqc_reference/reference_markers_gtdb.fasta -out GCF_015140235.1_ASM1514023v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:26,404] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:26,408] [INFO] Selected 23 target genomes.
[2024-01-24 11:27:26,408] [INFO] Target genome list was writen to GCF_015140235.1_ASM1514023v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:26,470] [INFO] Task started: fastANI
[2024-01-24 11:27:26,470] [INFO] Running command: fastANI --query /var/lib/cwl/stg24bc0f44-9100-4e7e-8e73-8c7243c9813d/GCF_015140235.1_ASM1514023v1_genomic.fna.gz --refList GCF_015140235.1_ASM1514023v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015140235.1_ASM1514023v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:35,444] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:35,450] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:35,450] [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_015140235.1	s__Solibaculum mannosilyticum	100.0	847	847	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Solibaculum	95.0	98.49	98.34	0.90	0.87	5	conclusive
GCA_904397895.1	s__Solibaculum sp904397895	83.3794	510	847	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Solibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104675.1	s__Angelakisella massiliensis	80.5188	77	847	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Angelakisella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018364155.1	s__JAGZMM01 sp018364155	77.4677	81	847	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__JAGZMM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904420015.1	s__JAGZMM01 sp904420015	77.0077	88	847	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__JAGZMM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904395335.1	s__Avimonas_A narfia	76.0505	59	847	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Avimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:35,452] [INFO] GTDB search result was written to GCF_015140235.1_ASM1514023v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:35,453] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:35,457] [INFO] DFAST_QC result json was written to GCF_015140235.1_ASM1514023v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:35,457] [INFO] DFAST_QC completed!
[2024-01-24 11:27:35,457] [INFO] Total running time: 0h0m57s