[2024-01-25 19:11:20,929] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:11:20,930] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:11:20,931] [INFO] DQC Reference Directory: /var/lib/cwl/stg84725d04-de19-4fcc-ac04-99514c5cf5f7/dqc_reference
[2024-01-25 19:11:22,073] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:11:22,074] [INFO] Task started: Prodigal
[2024-01-25 19:11:22,074] [INFO] Running command: gunzip -c /var/lib/cwl/stg58a4fcab-130c-4275-ad6b-d9ea84bb2805/GCF_012976305.1_ASM1297630v1_genomic.fna.gz | prodigal -d GCF_012976305.1_ASM1297630v1_genomic.fna/cds.fna -a GCF_012976305.1_ASM1297630v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:11:25,363] [INFO] Task succeeded: Prodigal
[2024-01-25 19:11:25,364] [INFO] Task started: HMMsearch
[2024-01-25 19:11:25,364] [INFO] Running command: hmmsearch --tblout GCF_012976305.1_ASM1297630v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84725d04-de19-4fcc-ac04-99514c5cf5f7/dqc_reference/reference_markers.hmm GCF_012976305.1_ASM1297630v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:11:25,606] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:11:25,608] [INFO] Found 6/6 markers.
[2024-01-25 19:11:25,629] [INFO] Query marker FASTA was written to GCF_012976305.1_ASM1297630v1_genomic.fna/markers.fasta
[2024-01-25 19:11:25,629] [INFO] Task started: Blastn
[2024-01-25 19:11:25,630] [INFO] Running command: blastn -query GCF_012976305.1_ASM1297630v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84725d04-de19-4fcc-ac04-99514c5cf5f7/dqc_reference/reference_markers.fasta -out GCF_012976305.1_ASM1297630v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:26,212] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:26,215] [INFO] Selected 8 target genomes.
[2024-01-25 19:11:26,215] [INFO] Target genome list was writen to GCF_012976305.1_ASM1297630v1_genomic.fna/target_genomes.txt
[2024-01-25 19:11:26,224] [INFO] Task started: fastANI
[2024-01-25 19:11:26,225] [INFO] Running command: fastANI --query /var/lib/cwl/stg58a4fcab-130c-4275-ad6b-d9ea84bb2805/GCF_012976305.1_ASM1297630v1_genomic.fna.gz --refList GCF_012976305.1_ASM1297630v1_genomic.fna/target_genomes.txt --output GCF_012976305.1_ASM1297630v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:11:29,298] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:29,298] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84725d04-de19-4fcc-ac04-99514c5cf5f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:11:29,299] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84725d04-de19-4fcc-ac04-99514c5cf5f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:11:29,305] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:11:29,305] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:11:29,305] [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
Peptoniphilus gorbachii	strain=DSM 21461	GCA_016908115.1	411567	411567	type	True	84.6059	441	690	95	below_threshold
Peptoniphilus grossensis	strain=ph5	GCA_000311825.1	1465756	1465756	type	True	84.2932	459	690	95	below_threshold
Peptoniphilus senegalensis	strain=type strain: JC140	GCA_000321025.1	1465757	1465757	type	True	83.9055	419	690	95	below_threshold
Peptoniphilus timonensis	strain=JC401	GCA_000312025.1	1268254	1268254	type	True	82.488	364	690	95	below_threshold
Peptoniphilus phoceensis	strain=SIT15	GCA_001517665.2	1720298	1720298	type	True	82.4414	386	690	95	below_threshold
Peptoniphilus harei	strain=NCTC13076	GCA_900454685.1	54005	54005	suspected-type	True	81.4103	355	690	95	below_threshold
Peptoniphilus harei	strain=FDAARGOS_1136	GCA_016726485.1	54005	54005	suspected-type	True	81.3477	350	690	95	below_threshold
Peptoniphilus obesi	strain=ph1	GCA_000311865.1	1472765	1472765	type	True	79.3902	108	690	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:11:29,307] [INFO] DFAST Taxonomy check result was written to GCF_012976305.1_ASM1297630v1_genomic.fna/tc_result.tsv
[2024-01-25 19:11:29,307] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:11:29,307] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:11:29,308] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84725d04-de19-4fcc-ac04-99514c5cf5f7/dqc_reference/checkm_data
[2024-01-25 19:11:29,308] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:11:29,335] [INFO] Task started: CheckM
[2024-01-25 19:11:29,337] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012976305.1_ASM1297630v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012976305.1_ASM1297630v1_genomic.fna/checkm_input GCF_012976305.1_ASM1297630v1_genomic.fna/checkm_result
[2024-01-25 19:11:45,339] [INFO] Task succeeded: CheckM
[2024-01-25 19:11:45,339] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:11:45,356] [INFO] ===== Completeness check finished =====
[2024-01-25 19:11:45,357] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:11:45,357] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012976305.1_ASM1297630v1_genomic.fna/markers.fasta)
[2024-01-25 19:11:45,357] [INFO] Task started: Blastn
[2024-01-25 19:11:45,357] [INFO] Running command: blastn -query GCF_012976305.1_ASM1297630v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84725d04-de19-4fcc-ac04-99514c5cf5f7/dqc_reference/reference_markers_gtdb.fasta -out GCF_012976305.1_ASM1297630v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:46,101] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:46,106] [INFO] Selected 7 target genomes.
[2024-01-25 19:11:46,106] [INFO] Target genome list was writen to GCF_012976305.1_ASM1297630v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:11:46,118] [INFO] Task started: fastANI
[2024-01-25 19:11:46,118] [INFO] Running command: fastANI --query /var/lib/cwl/stg58a4fcab-130c-4275-ad6b-d9ea84bb2805/GCF_012976305.1_ASM1297630v1_genomic.fna.gz --refList GCF_012976305.1_ASM1297630v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012976305.1_ASM1297630v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:11:49,260] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:49,266] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:11:49,266] [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_012976305.1	s__Peptoniphilus_A faecalis	100.0	689	690	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	95.0	98.47	98.47	0.83	0.83	2	conclusive
GCF_016908115.1	s__Peptoniphilus_A gorbachii	84.6519	439	690	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	95.0	96.70	96.17	0.85	0.82	5	-
GCF_000311825.1	s__Peptoniphilus_A grossensis	84.2716	460	690	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	95.0	97.39	95.38	0.93	0.87	4	-
GCF_000321025.1	s__Peptoniphilus_A senegalensis	83.9374	417	690	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	95.0	98.73	97.46	0.94	0.88	3	-
GCF_000312025.1	s__Peptoniphilus_A timonensis	82.4787	365	690	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	96.7724	N/A	N/A	N/A	N/A	1	-
GCF_001517665.2	s__Peptoniphilus_A phoceensis	82.4667	383	690	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	96.7724	100.00	100.00	1.00	1.00	2	-
GCF_900454685.1	s__Peptoniphilus_A harei	81.4329	356	690	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	95.0	97.43	96.58	0.91	0.87	7	-
--------------------------------------------------------------------------------
[2024-01-25 19:11:49,268] [INFO] GTDB search result was written to GCF_012976305.1_ASM1297630v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:11:49,268] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:11:49,270] [INFO] DFAST_QC result json was written to GCF_012976305.1_ASM1297630v1_genomic.fna/dqc_result.json
[2024-01-25 19:11:49,270] [INFO] DFAST_QC completed!
[2024-01-25 19:11:49,270] [INFO] Total running time: 0h0m28s