[2024-01-24 15:26:37,076] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:37,078] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:37,078] [INFO] DQC Reference Directory: /var/lib/cwl/stg842de119-9ef9-4933-a720-ec357d00325d/dqc_reference
[2024-01-24 15:26:39,059] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:39,066] [INFO] Task started: Prodigal
[2024-01-24 15:26:39,066] [INFO] Running command: gunzip -c /var/lib/cwl/stg429c7e74-1cdd-4ebd-a4bc-d72116c86cf1/GCF_001020205.1_ASM102020v1_genomic.fna.gz | prodigal -d GCF_001020205.1_ASM102020v1_genomic.fna/cds.fna -a GCF_001020205.1_ASM102020v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:45,455] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:45,455] [INFO] Task started: HMMsearch
[2024-01-24 15:26:45,455] [INFO] Running command: hmmsearch --tblout GCF_001020205.1_ASM102020v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg842de119-9ef9-4933-a720-ec357d00325d/dqc_reference/reference_markers.hmm GCF_001020205.1_ASM102020v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:45,798] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:45,799] [INFO] Found 6/6 markers.
[2024-01-24 15:26:45,830] [INFO] Query marker FASTA was written to GCF_001020205.1_ASM102020v1_genomic.fna/markers.fasta
[2024-01-24 15:26:45,830] [INFO] Task started: Blastn
[2024-01-24 15:26:45,831] [INFO] Running command: blastn -query GCF_001020205.1_ASM102020v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg842de119-9ef9-4933-a720-ec357d00325d/dqc_reference/reference_markers.fasta -out GCF_001020205.1_ASM102020v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:46,816] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:46,819] [INFO] Selected 10 target genomes.
[2024-01-24 15:26:46,819] [INFO] Target genome list was writen to GCF_001020205.1_ASM102020v1_genomic.fna/target_genomes.txt
[2024-01-24 15:26:46,828] [INFO] Task started: fastANI
[2024-01-24 15:26:46,828] [INFO] Running command: fastANI --query /var/lib/cwl/stg429c7e74-1cdd-4ebd-a4bc-d72116c86cf1/GCF_001020205.1_ASM102020v1_genomic.fna.gz --refList GCF_001020205.1_ASM102020v1_genomic.fna/target_genomes.txt --output GCF_001020205.1_ASM102020v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:26:57,720] [INFO] Task succeeded: fastANI
[2024-01-24 15:26:57,720] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg842de119-9ef9-4933-a720-ec357d00325d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:26:57,721] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg842de119-9ef9-4933-a720-ec357d00325d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:26:57,730] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 15:26:57,730] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:26:57,730] [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
Clostridium sporogenes	strain=DSM 795	GCA_001020205.1	1509	1509	type	True	100.0	1379	1380	95	conclusive
Clostridium sporogenes	strain=NCIMB 10696	GCA_000973705.1	1509	1509	type	True	99.9981	1379	1380	95	conclusive
Clostridium sporogenes	strain=NCTC13020	GCA_900461305.1	1509	1509	type	True	99.9963	1377	1380	95	conclusive
Clostridium sporogenes	strain=DSM 795	GCA_000685115.1	1509	1509	type	True	99.9903	1361	1380	95	conclusive
Clostridium sporogenes	strain=ATCC 3584	GCA_002008145.1	1509	1509	type	True	99.983	1350	1380	95	conclusive
Clostridium tetanomorphum	strain=DSM 4474	GCA_017873215.1	1553	1553	type	True	77.9015	361	1380	95	below_threshold
Clostridium muellerianum	strain=P21	GCA_012926525.1	2716538	2716538	type	True	77.3096	337	1380	95	below_threshold
Clostridium acetireducens	strain=DSM 10703	GCA_001758365.1	76489	76489	type	True	77.1719	252	1380	95	below_threshold
Clostridium liquoris	strain=DSM 100320	GCA_002995785.1	1289519	1289519	type	True	76.9987	212	1380	95	below_threshold
Oceanirhabdus seepicola	strain=ZWT	GCA_023684385.1	2828781	2828781	type	True	76.0942	147	1380	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:26:57,732] [INFO] DFAST Taxonomy check result was written to GCF_001020205.1_ASM102020v1_genomic.fna/tc_result.tsv
[2024-01-24 15:26:57,733] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:26:57,733] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:26:57,733] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg842de119-9ef9-4933-a720-ec357d00325d/dqc_reference/checkm_data
[2024-01-24 15:26:57,734] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:26:57,779] [INFO] Task started: CheckM
[2024-01-24 15:26:57,779] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001020205.1_ASM102020v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001020205.1_ASM102020v1_genomic.fna/checkm_input GCF_001020205.1_ASM102020v1_genomic.fna/checkm_result
[2024-01-24 15:27:23,400] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:23,402] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:23,429] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:23,429] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:23,430] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001020205.1_ASM102020v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:23,430] [INFO] Task started: Blastn
[2024-01-24 15:27:23,430] [INFO] Running command: blastn -query GCF_001020205.1_ASM102020v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg842de119-9ef9-4933-a720-ec357d00325d/dqc_reference/reference_markers_gtdb.fasta -out GCF_001020205.1_ASM102020v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:24,241] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:24,246] [INFO] Selected 5 target genomes.
[2024-01-24 15:27:24,247] [INFO] Target genome list was writen to GCF_001020205.1_ASM102020v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:24,250] [INFO] Task started: fastANI
[2024-01-24 15:27:24,251] [INFO] Running command: fastANI --query /var/lib/cwl/stg429c7e74-1cdd-4ebd-a4bc-d72116c86cf1/GCF_001020205.1_ASM102020v1_genomic.fna.gz --refList GCF_001020205.1_ASM102020v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001020205.1_ASM102020v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:27:30,687] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:30,695] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:27:30,696] [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_001020205.1	s__Clostridium_F sporogenes	100.0	1379	1380	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	99.24	98.80	0.94	0.88	81	conclusive
GCF_001889325.1	s__Clostridium_F botulinum_A	94.3164	1165	1380	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	95.92	95.51	0.89	0.85	52	-
GCF_001276985.1	s__Clostridium_F botulinum	91.9434	1080	1380	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	97.69	95.97	0.92	0.83	213	-
GCF_001276215.1	s__Clostridium_F sp001276215	89.4793	999	1380	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	97.32	95.44	0.88	0.82	10	-
GCF_002008345.1	s__Clostridium_F tepidum	88.3304	826	1380	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	99.70	99.54	0.93	0.92	5	-
--------------------------------------------------------------------------------
[2024-01-24 15:27:30,697] [INFO] GTDB search result was written to GCF_001020205.1_ASM102020v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:27:30,698] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:27:30,701] [INFO] DFAST_QC result json was written to GCF_001020205.1_ASM102020v1_genomic.fna/dqc_result.json
[2024-01-24 15:27:30,701] [INFO] DFAST_QC completed!
[2024-01-24 15:27:30,701] [INFO] Total running time: 0h0m54s