[2024-01-24 13:35:27,520] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:35:27,522] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:35:27,522] [INFO] DQC Reference Directory: /var/lib/cwl/stg921ec01b-1c90-4014-9779-7740357c5fe9/dqc_reference
[2024-01-24 13:35:28,722] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:35:28,723] [INFO] Task started: Prodigal
[2024-01-24 13:35:28,724] [INFO] Running command: gunzip -c /var/lib/cwl/stg1e286ae8-4e35-4ba9-bc96-ae18def3dd7b/GCF_001006285.1_ASM100628v1_genomic.fna.gz | prodigal -d GCF_001006285.1_ASM100628v1_genomic.fna/cds.fna -a GCF_001006285.1_ASM100628v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:35:33,466] [INFO] Task succeeded: Prodigal
[2024-01-24 13:35:33,467] [INFO] Task started: HMMsearch
[2024-01-24 13:35:33,467] [INFO] Running command: hmmsearch --tblout GCF_001006285.1_ASM100628v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg921ec01b-1c90-4014-9779-7740357c5fe9/dqc_reference/reference_markers.hmm GCF_001006285.1_ASM100628v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:35:33,732] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:35:33,734] [INFO] Found 6/6 markers.
[2024-01-24 13:35:33,771] [INFO] Query marker FASTA was written to GCF_001006285.1_ASM100628v1_genomic.fna/markers.fasta
[2024-01-24 13:35:33,771] [INFO] Task started: Blastn
[2024-01-24 13:35:33,771] [INFO] Running command: blastn -query GCF_001006285.1_ASM100628v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg921ec01b-1c90-4014-9779-7740357c5fe9/dqc_reference/reference_markers.fasta -out GCF_001006285.1_ASM100628v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:35:34,376] [INFO] Task succeeded: Blastn
[2024-01-24 13:35:34,380] [INFO] Selected 6 target genomes.
[2024-01-24 13:35:34,380] [INFO] Target genome list was writen to GCF_001006285.1_ASM100628v1_genomic.fna/target_genomes.txt
[2024-01-24 13:35:34,394] [INFO] Task started: fastANI
[2024-01-24 13:35:34,395] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e286ae8-4e35-4ba9-bc96-ae18def3dd7b/GCF_001006285.1_ASM100628v1_genomic.fna.gz --refList GCF_001006285.1_ASM100628v1_genomic.fna/target_genomes.txt --output GCF_001006285.1_ASM100628v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:35:39,565] [INFO] Task succeeded: fastANI
[2024-01-24 13:35:39,566] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg921ec01b-1c90-4014-9779-7740357c5fe9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:35:39,567] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg921ec01b-1c90-4014-9779-7740357c5fe9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:35:39,579] [INFO] Found 6 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:35:39,579] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:35:39,579] [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
Paraclostridium benzoelyticum	strain=JC272	GCA_001006285.1	1629550	1629550	type	True	99.9999	993	1009	95	inconclusive
Paraclostridium bifermentans	strain=ATCC 638	GCA_006802875.1	1490	1490	type	True	95.4525	882	1009	95	inconclusive
Paraclostridium dentum	strain=SKVG24	GCA_012922555.1	2662455	2662455	type	True	95.2976	871	1009	95	inconclusive
Paraclostridium bifermentans subsp. muricolitidis	strain=PAGU 1678	GCA_019650315.1	2663173	1490	type	True	95.2477	853	1009	95	inconclusive
Paraclostridium bifermentans	strain=DSM 14991	GCA_019916025.1	1490	1490	type	True	94.5954	868	1009	95	below_threshold
Paraclostridium bifermentans	strain=ATCC 638	GCA_000452245.2	1490	1490	type	True	94.554	877	1009	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:35:39,583] [INFO] DFAST Taxonomy check result was written to GCF_001006285.1_ASM100628v1_genomic.fna/tc_result.tsv
[2024-01-24 13:35:39,584] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:35:39,584] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:35:39,584] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg921ec01b-1c90-4014-9779-7740357c5fe9/dqc_reference/checkm_data
[2024-01-24 13:35:39,587] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:35:39,639] [INFO] Task started: CheckM
[2024-01-24 13:35:39,639] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001006285.1_ASM100628v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001006285.1_ASM100628v1_genomic.fna/checkm_input GCF_001006285.1_ASM100628v1_genomic.fna/checkm_result
[2024-01-24 13:36:01,070] [INFO] Task succeeded: CheckM
[2024-01-24 13:36:01,072] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:36:01,095] [INFO] ===== Completeness check finished =====
[2024-01-24 13:36:01,096] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:36:01,096] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001006285.1_ASM100628v1_genomic.fna/markers.fasta)
[2024-01-24 13:36:01,097] [INFO] Task started: Blastn
[2024-01-24 13:36:01,097] [INFO] Running command: blastn -query GCF_001006285.1_ASM100628v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg921ec01b-1c90-4014-9779-7740357c5fe9/dqc_reference/reference_markers_gtdb.fasta -out GCF_001006285.1_ASM100628v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:01,864] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:01,868] [INFO] Selected 5 target genomes.
[2024-01-24 13:36:01,868] [INFO] Target genome list was writen to GCF_001006285.1_ASM100628v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:36:01,877] [INFO] Task started: fastANI
[2024-01-24 13:36:01,878] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e286ae8-4e35-4ba9-bc96-ae18def3dd7b/GCF_001006285.1_ASM100628v1_genomic.fna.gz --refList GCF_001006285.1_ASM100628v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001006285.1_ASM100628v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:36:06,138] [INFO] Task succeeded: fastANI
[2024-01-24 13:36:06,149] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:36:06,149] [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_001006285.1	s__Paraclostridium benzoelyticum	99.9999	990	1009	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	95.4733	N/A	N/A	N/A	N/A	1	conclusive
GCF_006802875.1	s__Paraclostridium bifermentans	95.4733	881	1009	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	96.2286	97.64	96.79	0.90	0.86	14	-
GCF_000452245.2	s__Paraclostridium bifermentans_A	94.554	877	1009	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	96.2286	97.39	96.64	0.88	0.81	7	-
GCF_015668515.1	s__Paraclostridium tenue	83.561	614	1009	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	95.0	98.58	97.73	0.92	0.87	8	-
GCF_000953675.1	s__Paraclostridium sordellii	83.0154	615	1009	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	95.0	98.12	96.78	0.93	0.89	59	-
--------------------------------------------------------------------------------
[2024-01-24 13:36:06,150] [INFO] GTDB search result was written to GCF_001006285.1_ASM100628v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:36:06,151] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:36:06,153] [INFO] DFAST_QC result json was written to GCF_001006285.1_ASM100628v1_genomic.fna/dqc_result.json
[2024-01-24 13:36:06,154] [INFO] DFAST_QC completed!
[2024-01-24 13:36:06,154] [INFO] Total running time: 0h0m39s